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BioImager
4.9.0
A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.
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Public Member Functions | |
| __init__ (self, index=0, **kwargs) | |
| get_id (self) | |
| abort (self) | |
| initialize (self) | |
| set_readout_mode (self, index) | |
| set_exposure_time (self, value) | |
| get_exposure_time (self) | |
| get_cycle_time (self) | |
| 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.FloatingDeviceMixin | |
Public Member Functions inherited from microscope.abc.Camera | |
| 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 | |
| handle = None | |
| tuple | shape = (None, None) |
| tuple | roi = (None, None, None, None) |
| binning = microscope.Binning(1, 1) | |
| float | exposure_time = 0.001 |
| float | cycle_time = self.exposure_time |
| set_exposure_time | |
| dict | roi = self._params[PARAM_READOUT_PORT].values |
Public Attributes inherited from microscope.abc.Camera | |
| 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 | open_cameras = [] |
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) | |
Protected Member Functions | |
| _region (self) | |
| _fetch_data (self) | |
| _do_enable (self) | |
| _do_disable (self) | |
| None | _do_shutdown (self) |
| _get_sensor_shape (self) | |
| _get_binning (self) | |
| _set_binning (self, binning) | |
| _get_roi (self) | |
| _set_roi (self, roi) | |
| None | _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 | |
| _pv_name = None | |
| _trigger = TRIG_STROBED | |
| _buffer = None | |
| dict | _params = {} |
| int | _circ_buffer_length = 10 |
| bool | _using_callback = True |
| _eof_callback = CALLBACK(cb) | |
| bool | _acquiring = True |
| dict | _cbs |
| list | _readout_modes = [] |
| list | _readout_mode_parameters = [] |
| _readout_mode = index | |
Protected Attributes inherited from microscope.abc.FloatingDeviceMixin | |
| _index = index | |
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 = {} |
Implements the CameraDevice interface for the pvcam library.
| microscope.cameras.pvcam.PVCamera.__init__ | ( | self, | |
| index = 0, | |||
| ** | kwargs ) |
Reimplemented from microscope.abc.FloatingDeviceMixin.
Definition at line 1413 of file pvcam.py.
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Disable the hardware for a short period of inactivity.
Reimplemented from microscope.abc.Device.
Definition at line 1613 of file pvcam.py.
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Enable the camera hardware and make ready to respond to triggers. Return True if successful, False if not.
Reimplemented from microscope.abc.Device.
Definition at line 1480 of file pvcam.py.
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Disable the hardware for a prolonged period of inactivity.
Reimplemented from microscope.abc.Device.
Definition at line 1618 of file pvcam.py.
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Actual trigger of the device. Classes implementing this interface should implement this method instead of `trigger`.
Reimplemented from microscope.abc.TriggerTargetMixin.
Definition at line 1893 of file pvcam.py.
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Fetch data - for use in fetch_loop.
Reimplemented from microscope.abc.DataDevice.
Definition at line 1475 of file pvcam.py.
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Return the current binning (horizontal, vertical).
Reimplemented from microscope.abc.Camera.
Definition at line 1635 of file pvcam.py.
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Return the current ROI (left, top, width, height).
Reimplemented from microscope.abc.Camera.
Definition at line 1645 of file pvcam.py.
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Return the sensor shape (width, height).
Reimplemented from microscope.abc.Camera.
Definition at line 1631 of file pvcam.py.
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Return a rgn_type for current roi and binning settings.
Definition at line 1462 of file pvcam.py.
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Set binning to (h, v).
Reimplemented from microscope.abc.Camera.
Definition at line 1640 of file pvcam.py.
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Set the ROI to (left, tip, width, height).
Reimplemented from microscope.abc.Camera.
Definition at line 1650 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.abort | ( | self | ) |
Abort acquisition. This should put the camera into a state in which settings can be modified.
Reimplemented from microscope.abc.DataDevice.
Definition at line 1664 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.get_cycle_time | ( | self | ) |
Return the cycle time. Just return self.cycle_time, which is updated with the real value during _do_enable.
Reimplemented from microscope.abc.Camera.
Definition at line 1839 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.get_exposure_time | ( | self | ) |
Return the current exposure time. Just return self.exposure_time, which is updated with the real value during _do_enable.
Reimplemented from microscope.abc.Camera.
Definition at line 1832 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.get_id | ( | self | ) |
Get hardware's unique identifier.
Reimplemented from microscope.abc.FloatingDeviceMixin.
Definition at line 1660 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.initialize | ( | self | ) |
Initialise the camera.
Reimplemented from microscope.abc.Device.
Definition at line 1676 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.set_exposure_time | ( | self, | |
| value ) |
Set the exposure time to value.
Reimplemented from microscope.abc.Camera.
Definition at line 1828 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.set_readout_mode | ( | self, | |
| index ) |
Set the readout mode and transform.
Reimplemented from microscope.abc.Camera.
Definition at line 1812 of file pvcam.py.
| None microscope.cameras.pvcam.PVCamera.set_trigger | ( | self, | |
| microscope.TriggerType | ttype, | ||
| microscope.TriggerMode | tmode ) |
Set device for a specific trigger.
Reimplemented from microscope.abc.TriggerTargetMixin.
Definition at line 1883 of file pvcam.py.
| microscope.cameras.pvcam.PVCamera.soft_trigger | ( | self | ) |
Expose software triggering to a client. Deprecated, use trigger(). Trigger an exposure in TRIG_SOFT mode. Log some debugging stats in other trigger modes.
Definition at line 1847 of file pvcam.py.
| microscope.TriggerMode microscope.cameras.pvcam.PVCamera.trigger_mode | ( | self | ) |
Reimplemented from microscope.abc.TriggerTargetMixin.
Definition at line 1876 of file pvcam.py.
| microscope.TriggerType microscope.cameras.pvcam.PVCamera.trigger_type | ( | self | ) |
Reimplemented from microscope.abc.TriggerTargetMixin.
Definition at line 1880 of file pvcam.py.
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| microscope.cameras.pvcam.PVCamera.binning = microscope.Binning(1, 1) |
| float microscope.cameras.pvcam.PVCamera.cycle_time = self.exposure_time |
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| tuple microscope.cameras.pvcam.PVCamera.roi = (None, None, None, None) |
| dict microscope.cameras.pvcam.PVCamera.roi = self._params[PARAM_READOUT_PORT].values |
| tuple microscope.cameras.pvcam.PVCamera.shape = (None, None) |