Inheritance diagram for microscope.cameras.picam.PiCamera:

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

def	get_awb_mode (self)

def	set_awb_mode (self, val)

def	set_iso_mode (self, val)

def	HW_trigger (self, channel)

def	initialize (self)

def	make_safe (self)

def	abort (self)

None	set_trigger (self, TriggerType ttype, TriggerMode tmode)

TriggerMode	trigger_mode (self)

TriggerType	trigger_type (self)

def	setLED (self, state=False)

def	set_exposure_time (self, value)

def	get_exposure_time (self)

def	get_cycle_time (self)

def	soft_trigger (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
	camera

	roi

	exposure_time

	cycle_time

	camversion

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

Definition at line 50 of file picam.py.

Constructor & Destructor Documentation

◆ init()

def 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()
 

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

Member Function Documentation

◆ abort()

def 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
 

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, and microscope.simulators.SimulatedCamera._acquiring.

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_awb_mode()

def 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
 

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

◆ get_cycle_time()

def 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()

def 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
 

References microscope.cameras.picam.PiCamera.camera.

◆ HW_trigger()

def 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])
 

References microscope.cameras.picam.PiCamera._queue, microscope.testsuite.test_device_server.DeviceServerExceptionQueue._queue, and microscope.cameras.picam.PiCamera.camera.

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

◆ initialize()

def 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()
 

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

◆ make_safe()

def 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()

def 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
 

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

◆ set_exposure_time()

def 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)
 

References microscope.cameras.picam.PiCamera.camera.

◆ set_iso_mode()

def 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]
 

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

◆ 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
 

References microscope.cameras.picam.PiCamera._trigger_type, microscope.mirror.alpao.AlpaoDeformableMirror._trigger_type, microscope.cameras.picam.PiCamera.HW_trigger(), microscope.cameras.picam.PiCamera.roi, and microscope.cameras.pvcam.PVCamera.roi.

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

◆ setLED()

def 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)
 

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

◆ soft_trigger()

def 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

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

◆ 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
 

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

◆ 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
 

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

Member Data Documentation

◆ camera

microscope.cameras.picam.PiCamera.camera

Definition at line 61 of file picam.py.

Referenced by microscope.cameras.picam.PiCamera.__init__(), microscope.cameras.picam.PiCamera.get_cycle_time(), microscope.cameras.picam.PiCamera.get_exposure_time(), microscope.cameras.picam.PiCamera.HW_trigger(), microscope.cameras.picam.PiCamera.initialize(), and microscope.cameras.picam.PiCamera.set_exposure_time().

◆ camversion

microscope.cameras.picam.PiCamera.camversion

Definition at line 155 of file picam.py.

Referenced by microscope.cameras.picam.PiCamera.get_cycle_time(), and microscope.cameras.picam.PiCamera.initialize().

◆ cycle_time

microscope.cameras.picam.PiCamera.cycle_time

Definition at line 66 of file picam.py.

Referenced by microscope.cameras.picam.PiCamera.__init__(), and microscope.cameras.pvcam.PVCamera.get_cycle_time().

◆ exposure_time

microscope.cameras.picam.PiCamera.exposure_time

Definition at line 65 of file picam.py.

Referenced by microscope.cameras.picam.PiCamera.__init__(), microscope.cameras.pvcam.PVCamera.get_exposure_time(), and microscope.cameras.pvcam.PVCamera.set_exposure_time().

◆ roi

microscope.cameras.picam.PiCamera.roi

Definition at line 63 of file picam.py.

Referenced by microscope.cameras.picam.PiCamera.__init__(), microscope.cameras.pvcam.PVCamera.initialize(), and microscope.cameras.picam.PiCamera.set_trigger().

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

F:/repos/BioImager/BioImager/PythonMicroscope/microscope/cameras/picam.py

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ 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

◆ camera

◆ camversion

◆ cycle_time

◆ exposure_time

◆ roi

◆ init()