Inheritance diagram for microscope.cameras.picam.PiCamera:

Public Member Functions
	__init__ (self, args, *kwargs)

	get_awb_mode (self)

	set_awb_mode (self, val)

	set_iso_mode (self, val)

	HW_trigger (self, channel)

	initialize (self)

	make_safe (self)

	abort (self)

None	set_trigger (self, TriggerType ttype, TriggerMode tmode)

TriggerMode	trigger_mode (self)

TriggerType	trigger_type (self)

	setLED (self, state=False)

	set_exposure_time (self, value)

	get_exposure_time (self)

	get_cycle_time (self)

	soft_trigger (self)

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
	camera = None

	roi = ROI(None, None, None, None)

float	exposure_time = 0.001

float	cycle_time = self.exposure_time

	trigger_mode

str	camversion = self.camera.revision

tuple	camversion = (2592, 1944)

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
	_fetch_data (self)

	_do_disable (self)

	_do_shutdown (self)

	_do_enable (self)

	_get_roi (self)

	_set_binning (self, h_bin, v_bin)

	_get_binning (self)

	_set_roi (self, left, top, width, height)

	_get_sensor_shape (self)

	_do_trigger (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

float	_exposure_time = 0.1

bool	_triggered = False

	_trigger_type = TriggerType.SOFTWARE

	_queue = queue.Queue()

	_awb_modes = picamera.PiCamera.AWB_MODES

list	_iso_modes = [0, 100, 200, 320, 400, 500, 640, 800]

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

Definition at line 50 of file picam.py.

Constructor & Destructor Documentation

◆ init()

microscope.cameras.picam.PiCamera.__init__	(		self,
		*	buffer_length,
		**	kwargs )

Derived.__init__ must call this at some point.

Reimplemented from microscope.abc.Camera.

Definition at line 51 of file picam.py.

    def __init__(self, *args, **kwargs):
        super(PiCamera, self).__init__(**kwargs)
        # example parameter to allow setting.
        #        self.add_setting('_error_percent', 'int',
        #                         lambda: self._error_percent,
        #                         self._set_error_percent,
        #                         lambda: (0, 100))
        self._acquiring = False
        self._exposure_time = 0.1
        self._triggered = False
        self.camera = None
        # Region of interest.
        self.roi = ROI(None, None, None, None)
        # Cycle time
        self.exposure_time = 0.001  # in seconds
        self.cycle_time = self.exposure_time
        # initialise in soft trigger mode
        self._trigger_type = TriggerType.SOFTWARE
        # setup hardware triggerline
        GPIO.setmode(GPIO.BCM)
        # GPIO trigger line is an input
        GPIO.setup(GPIO_Trigger, GPIO.IN)
        # GPIO control over camera LED is an output
        GPIO.setup(GPIO_CAMLED, GPIO.OUT)
        # add trigger to settings
        trg_source_names = [x.name for x in TrgSourceMap]
        # set up queue to store images as they are acquired
        self._queue = queue.Queue()
        self._awb_modes = picamera.PiCamera.AWB_MODES
        self._iso_modes = [0, 100, 200, 320, 400, 500, 640, 800]
 
        def _trigger_source_setter(index: int) -> None:
            trigger_type = TrgSourceMap[trg_source_names[index]].value
            self.set_trigger(trigger_type, self.trigger_mode)
 
        self.add_setting(
            "trig source",
            "enum",
            lambda: TrgSourceMap(self._trigger_type).name,
            _trigger_source_setter,
            trg_source_names,
        )
        self.add_setting(
            "AWB",
            "enum",
            lambda: self._awb_modes[self.get_awb_mode()],
            lambda awb: self.set_awb_mode(awb),
            values=(list(self._awb_modes.keys())),
        )
 
        self.add_setting(
            "ISO",
            "enum",
            lambda: self._iso_modes.index(self.camera.iso),
            lambda iso: self.set_iso_mode(iso),
            values=(self._iso_modes),
        )
 
        # self.add_setting(
        #     "pixel size",
        #     "float",
        #     lambda: self._pixel_size,
        #     lambda pxsz: setattr(self, "_pixel_size", pxsz),
        #     # technically should be: (nextafter(0.0, inf), nextafter(inf, 0.0))
        #     values=(0.0, float("inf")),
        # )
        self.initialize()
 

Member Function Documentation

◆ _do_disable()

microscope.cameras.picam.PiCamera._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 168 of file picam.py.

    def _do_disable(self):
        self.abort()
 

◆ _do_enable()

microscope.cameras.picam.PiCamera._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 175 of file picam.py.

    def _do_enable(self):
        _logger.info("Preparing for acquisition.")
        if self._acquiring:
            self.abort()
        # actually start camera
        if not self.camera:
            self.initialize()
        self._acquiring = True
        _logger.info("Acquisition enabled.")
        return True
 

◆ _do_shutdown()

microscope.cameras.picam.PiCamera._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 171 of file picam.py.

    def _do_shutdown(self):
        self._do_disable()
        self.camera.close()
 

◆ _do_trigger()

microscope.cameras.picam.PiCamera._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 260 of file picam.py.

    def _do_trigger(self):
        self.soft_trigger()
 

◆ _fetch_data()

microscope.cameras.picam.PiCamera._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 136 of file picam.py.

    def _fetch_data(self):
        if self._queue.qsize() is not 0:
            data = self._queue.get()
            _logger.info("Sending image")
            return data
        else:
            return None
 

◆ _get_binning()

microscope.cameras.picam.PiCamera._get_binning ( self )

protected

Return the current binning.

Reimplemented from microscope.abc.Camera.

Definition at line 227 of file picam.py.

    def _get_binning(self):
        return Binning(1, 1)
 

◆ _get_roi()

microscope.cameras.picam.PiCamera._get_roi ( self )

protected

Return the current ROI (left, top, width, height).

Reimplemented from microscope.abc.Camera.

Definition at line 220 of file picam.py.

    def _get_roi(self):
        """Return the current ROI (left, top, width, height)."""
        return self.roi
 

◆ _get_sensor_shape()

microscope.cameras.picam.PiCamera._get_sensor_shape ( self )

protected

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

Reimplemented from microscope.abc.Camera.

Definition at line 252 of file picam.py.

    def _get_sensor_shape(self):
        if self.camversion == "ov5647":  # picam version 1
            self.camera.resolution = (2592, 1944)
        # faqll back to defualt if not set above.
        res = self.camera.resolution
        self._set_roi(0, 0, res[0], res[1])
        return res
 

◆ _set_binning()

microscope.cameras.picam.PiCamera._set_binning	(	self,
		binning,
		v_bin )

protected

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

Reimplemented from microscope.abc.Camera.

Definition at line 224 of file picam.py.

    def _set_binning(self, h_bin, v_bin):
        return True
 

◆ _set_roi()

microscope.cameras.picam.PiCamera._set_roi	(	self,
		left,
		top,
		width,
		height )

protected

Set the ROI to (left, tip, width, height).

Reimplemented from microscope.abc.Camera.

Definition at line 231 of file picam.py.

    def _set_roi(self, left, top, width, height):
        """Set the ROI to (left, tip, width, height)."""
        self.roi = ROI(left, top, width, height)
 

◆ abort()

microscope.cameras.picam.PiCamera.abort ( self )

Stop acquisition as soon as possible.

Reimplemented from microscope.abc.DataDevice.

Definition at line 186 of file picam.py.

    def abort(self):
        _logger.info("Disabling acquisition.")
        if self._acquiring:
            self._acquiring = False
 

◆ get_awb_mode()

microscope.cameras.picam.PiCamera.get_awb_mode ( self )

Definition at line 119 of file picam.py.

    def get_awb_mode(self):
        return self.camera.awb_mode
 

◆ get_cycle_time()

microscope.cameras.picam.PiCamera.get_cycle_time ( self )

Return the cycle time in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 247 of file picam.py.

    def get_cycle_time(self):
        # fudge to make it work initially
        # exposure times are in us, so multiple by 1E-6 to get seconds.
        return self.camera.exposure_speed * 1.0e-6 + 0.1
 

◆ get_exposure_time()

microscope.cameras.picam.PiCamera.get_exposure_time ( self )

Return the current exposure time in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 243 of file picam.py.

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

◆ HW_trigger()

microscope.cameras.picam.PiCamera.HW_trigger	(		self,
			channel )

Function called by GPIO interupt, needs to trigger image capture

Definition at line 130 of file picam.py.

    def HW_trigger(self, channel):
        """Function called by GPIO interupt, needs to trigger image capture"""
        with picamera.array.PiYUVArray(self.camera) as output:
            self.camera.capture(output, format="yuv", use_video_port=False)
            self._queue.put(output.array[:, :, 0])
 

◆ initialize()

microscope.cameras.picam.PiCamera.initialize ( self )

Initialise the Pi Camera camera.
Open the connection, connect properties and populate settings dict.

Reimplemented from microscope.abc.Device.

Definition at line 144 of file picam.py.

    def initialize(self):
        """Initialise the Pi Camera camera.
        Open the connection, connect properties and populate settings dict.
        """
        if not self.camera:
            try:
                # initialise camera in still image mode.
                self.camera = picamera.PiCamera(sensor_mode=2)
            except:
                raise Exception("Problem opening camera.")
        _logger.info("Initializing camera.")
        self.camversion = self.camera.revision
        _logger.info("cam version " + self.camversion)
 
        # create img buffer to hold images.
        # disable camera LED by default
        self.setLED(False)
        self.set_awb_mode(0)  # set auto white balance to off
        self._get_sensor_shape()
 

◆ make_safe()

microscope.cameras.picam.PiCamera.make_safe ( self )

Definition at line 164 of file picam.py.

    def make_safe(self):
        if self._acquiring:
            self.abort()
 

◆ set_awb_mode()

microscope.cameras.picam.PiCamera.set_awb_mode	(		self,
			val )

Definition at line 122 of file picam.py.

    def set_awb_mode(self, val):
        for key, value in self._awb_modes.items():
            if value == val:
                self.camera.awb_mode = key
 

◆ set_exposure_time()

microscope.cameras.picam.PiCamera.set_exposure_time	(		self,
			value )

Set the exposure time on the device in seconds.

Reimplemented from microscope.abc.Camera.

Definition at line 239 of file picam.py.

    def set_exposure_time(self, value):
        # exposure times are set in us.
        self.camera.shutter_speed = int(value * 1.0e6)
 

◆ set_iso_mode()

microscope.cameras.picam.PiCamera.set_iso_mode	(		self,
			val )

Definition at line 127 of file picam.py.

    def set_iso_mode(self, val):
        self.camera.iso = self._iso_modes[val]
 

◆ set_trigger()

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

Set device for a specific trigger.

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 191 of file picam.py.

    ) -> None:
        if ttype == self._trigger_type:
            return
        elif ttype == TriggerType.SOFTWARE:
            GPIO.remove_event_detect(GPIO_Trigger)
            self._trigger_type = TriggerType.SOFTWARE
        elif ttype == TriggerType.RISING_EDGE:
            GPIO.add_event_detect(
                GPIO_Trigger,
                GPIO.RISING,
                callback=self.HW_trigger,
                bouncetime=10,
            )
            self._trigger_type = TriggerType.RISING_EDGE
 

◆ setLED()

microscope.cameras.picam.PiCamera.setLED	(		self,
			state = False )

Definition at line 236 of file picam.py.

    def setLED(self, state=False):
        GPIO.output(GPIO_CAMLED, state)
 

◆ soft_trigger()

microscope.cameras.picam.PiCamera.soft_trigger ( self )

Definition at line 263 of file picam.py.

    def soft_trigger(self):
        _logger.info(
            "Trigger received; self._acquiring is %s." % self._acquiring
        )
        if self._acquiring:
            with picamera.array.PiYUVArray(self.camera) as output:
                self.camera.capture(output, format="yuv", use_video_port=False)
                self._queue.put(output.array[:, :, 0])
 
 
# ongoing implemetation notes
 
# should be able to use rotation and hflip to set specific output image
# rotations
 
# roi's can be set with the zoom function, default is (0,0,1,1) meaning all the data.
 
# Need to setup a buffer for harware triggered data aquisition so we can
# call the acquisition and then download the data at our leasure

◆ trigger_mode()

TriggerMode microscope.cameras.picam.PiCamera.trigger_mode ( self )

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 209 of file picam.py.

    def trigger_mode(self) -> TriggerMode:
        #        if self._trigger_type==devices.TRIGGER_BEFORE:
        return TriggerMode.ONCE
 

◆ trigger_type()

TriggerType microscope.cameras.picam.PiCamera.trigger_type ( self )

Reimplemented from microscope.abc.TriggerTargetMixin.

Definition at line 217 of file picam.py.

    def trigger_type(self) -> TriggerType:
        return self._trigger_type
 

Member Data Documentation

◆ _acquiring

bool microscope.cameras.picam.PiCamera._acquiring = False

protected

Definition at line 58 of file picam.py.

◆ _awb_modes

microscope.cameras.picam.PiCamera._awb_modes = picamera.PiCamera.AWB_MODES

protected

Definition at line 79 of file picam.py.

◆ _exposure_time

float microscope.cameras.picam.PiCamera._exposure_time = 0.1

protected

Definition at line 59 of file picam.py.

◆ _iso_modes

list microscope.cameras.picam.PiCamera._iso_modes = [0, 100, 200, 320, 400, 500, 640, 800]

protected

Definition at line 80 of file picam.py.

◆ _queue

microscope.cameras.picam.PiCamera._queue = queue.Queue()

protected

Definition at line 78 of file picam.py.

◆ _trigger_type

microscope.cameras.picam.PiCamera._trigger_type = TriggerType.SOFTWARE

protected

Definition at line 68 of file picam.py.

◆ _triggered

bool microscope.cameras.picam.PiCamera._triggered = False

protected

Definition at line 60 of file picam.py.

◆ camera

microscope.cameras.picam.PiCamera.camera = None

Definition at line 61 of file picam.py.

◆ camversion [1/2]

str microscope.cameras.picam.PiCamera.camversion = self.camera.revision

Definition at line 155 of file picam.py.

◆ camversion [2/2]

tuple microscope.cameras.picam.PiCamera.camversion = (2592, 1944)

Definition at line 253 of file picam.py.

◆ cycle_time

float microscope.cameras.picam.PiCamera.cycle_time = self.exposure_time

Definition at line 66 of file picam.py.

◆ exposure_time

float microscope.cameras.picam.PiCamera.exposure_time = 0.001

Definition at line 65 of file picam.py.

◆ roi

microscope.cameras.picam.PiCamera.roi = ROI(None, None, None, None)

Definition at line 63 of file picam.py.

◆ trigger_mode

microscope.cameras.picam.PiCamera.trigger_mode

Definition at line 84 of file picam.py.

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

BioImager/PythonMicroscope/microscope/cameras/picam.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_awb_mode()

◆ get_cycle_time()

◆ get_exposure_time()

◆ HW_trigger()

◆ initialize()

◆ make_safe()

◆ set_awb_mode()

◆ set_exposure_time()

◆ set_iso_mode()

◆ set_trigger()

◆ setLED()

◆ soft_trigger()

◆ trigger_mode()

◆ trigger_type()

Member Data Documentation

◆ _acquiring

◆ _awb_modes

◆ _exposure_time

◆ _iso_modes

◆ _queue

◆ _trigger_type

◆ _triggered

◆ camera

◆ camversion [1/2]

◆ camversion [2/2]

◆ cycle_time

◆ exposure_time

◆ roi

◆ trigger_mode

◆ init()