navigate.model.devices.camera.base.CameraBase

class navigate.model.devices.camera.base.CameraBase(microscope_name: str, device_connection: Any, configuration: dict[str, Any], *args: Optional[Any], **kwargs: Optional[Any])

Bases: ABC

Abstract base class for cameras.

This class provides the interface and common functionality for controlling cameras with navigate.

__init__(microscope_name: str, device_connection: Any, configuration: dict[str, Any], *args: Optional[Any], **kwargs: Optional[Any]) → None

Initialize CameraBase class.

Parameters:

• microscope_name (str) – Name of microscope in configuration

• device_connection (Any) – Hardware device to connect to

• configuration (Dict[str, Any]) – Global configuration of the microscope

Raises:

NameError – If microscope name is not in configuration

Methods

__init__(microscope_name, device_connection, ...)	Initialize CameraBase class.
calculate_light_sheet_exposure_time(...)	Convert normal mode exposure time to light-sheet mode exposure time.
close_camera()	Close camera.
close_image_series()	Close image series.
get_line_interval()	Return stored camera line interval.
get_new_frame()	Get a new frame from the camera.
get_offset_variance_maps()	Get offset and variance maps from file.
initialize_image_series([data_buffer, ...])	Initialize image series and attach the given data_buffer, which serves as the destination for incoming images.
set_ROI([roi_width, roi_height, center_x, ...])	Change the size of the active region on the camera.
set_ROI_and_binning([roi_width, roi_height, ...])	Change the size of the active region on the camera and set the binning mode.
set_binning([binning])	Set the camera binning mode.
set_exposure_time(exposure_time)	Set the camera exposure time.
set_line_interval(line_interval_time)	Set the camera line interval time.
set_readout_direction(mode)	Set HamamatsuOrca readout direction.
set_sensor_mode(mode)	Set camera sensor mode.
set_trigger_mode([trigger_source])	Set the camera trigger source to external or internal free run mode.

Attributes

offset	Return offset map.
variance	Return variance map.
microscope_name	Name of microscope in configuration
configuration	Global configuration of the microscope
camera_controller	Hardware device to connect to
camera_parameters	Camera parameters
is_acquiring	Whether the camera is currently acquiring
min_image_width	Minimum image width
min_image_height	Minimum image height
step_image_width	Minimum step size for image width.
step_image_height	Minimum step size for image height.
x_pixels	Number of pixels in the x direction
y_pixels	Number of pixels in the y direction
minimum_exposure_time	minimum exposure time

abstract calculate_light_sheet_exposure_time(full_chip_exposure_time: float, shutter_width: int) → tuple[float, float, float]

Convert normal mode exposure time to light-sheet mode exposure time. Calculate the parameters for an acquisition

Parameters:

• full_chip_exposure_time (float) – Normal mode exposure time in seconds.

• shutter_width (int) – Width of light-sheet rolling shutter.

Returns:

• exposure_time (float) – Light-sheet mode exposure time (s).

• camera_line_interval (float) – HamamatsuOrca line interval duration (s).

• full_chip_exposure time (float) – Full chip exposure time (s).

close_camera() → None

Close camera.

abstract close_image_series() → None

Close image series.

This abstract method must be implemented by all subclasses.

get_line_interval() → Optional[float]

Return stored camera line interval.

Returns:

line_interval – line interval duration (s).

Return type:

float

abstract get_new_frame() → list[int]

Get a new frame from the camera.

This abstract method must be implemented by all subclasses.

Returns:

frame_ids – New frame ids from the camera.

Return type:

list[int]

get_offset_variance_maps() → Any

Get offset and variance maps from file.

Returns:

• offset (np.ndarray) – Offset map.

• variance (np.ndarray) – Variance map.

Raises:

FileNotFoundError – If offset or variance map is not found.

abstract initialize_image_series(data_buffer: Optional[list] = None, number_of_frames: int = 100) → None

Initialize image series and attach the given data_buffer, which serves as the destination for incoming images.

This abstract method must be implemented by all subclasses.

Parameters:

• data_buffer – List of SharedNDArrays of shape=(self.img_height, self.img_width) and dtype=”uint16” Default is None.

• number_of_frames (int) – Number of frames. Default is 100.

abstract set_ROI(roi_width: int = 2048, roi_height: int = 2048, center_x: int = 1024, center_y: int = 1024) → bool

Change the size of the active region on the camera.

Parameters:

• roi_width (int) – Width of active camera region.

• roi_height (int) – Height of active camera region.

• center_x (int) – X position of the center of view

• center_y (int) – Y position of the center of view

Returns:

result – True if successful, False otherwise.

Return type:

bool

set_ROI_and_binning(roi_width: int = 2048, roi_height: int = 2048, center_x: int = 1024, center_y: int = 1024, binning: str = '1x1') → bool

Change the size of the active region on the camera and set the binning mode.

Parameters:

• roi_width (int) – Width of active camera region.

• roi_height (int) – Height of active camera region.

• center_x (int) – X position of the center of view

• center_y (int) – Y position of the center of view

• binning (str) – Desired binning properties (e.g., ‘1x1’, ‘2x2’, ‘4x4’, ‘8x8’, ‘16x16’, ‘1x2’, ‘2x4’)

Returns:

result – True if successful, False otherwise.

Return type:

bool

abstract set_binning(binning: str = '1x1') → bool

Set the camera binning mode.

Parameters:

binning (str) – Desired binning properties (e.g., ‘1x1’, ‘2x2’, ‘4x4’, ‘1x2’, ‘2x4’)

Returns:

result – True if successful, False otherwise.

Return type:

bool

abstract set_exposure_time(exposure_time: float) → bool

Set the camera exposure time.

abstract set_line_interval(line_interval_time: float) → bool

Set the camera line interval time.

This abstract method must be implemented by all subclasses.

Returns:

result – True if successful, False otherwise.

Return type:

bool

abstract set_readout_direction(mode: str) → None

Set HamamatsuOrca readout direction.

Parameters:

mode (str) – ‘Top-to-Bottom’, ‘Bottom-to-Top’, ‘bytrigger’, or ‘diverge’.

abstract set_sensor_mode(mode: str) → None

Set camera sensor mode.

Parameters:

mode (str) – Sensor mode. Options are ‘Normal’ or ‘Light-Sheet’.

abstract set_trigger_mode(trigger_source: str = 'External') → None

Set the camera trigger source to external or internal free run mode.

This abstract method must be implemented by all subclasses.

Parameters:

trigger_source (str) – Trigger source. Options are ‘External’ or ‘Internal’.

camera_controller

Hardware device to connect to

Type:

object

camera_parameters

Camera parameters

Type:

dict

configuration

Global configuration of the microscope

Type:

dict

is_acquiring

Whether the camera is currently acquiring

Type:

bool

microscope_name

Name of microscope in configuration

Type:

str

min_image_height

Minimum image height

Type:

int

min_image_width

Minimum image width

Type:

int

minimum_exposure_time

minimum exposure time

Type:

float

property offset: Any

Return offset map. If not present, load from file.

Returns:

offset – Offset map.

Return type:

np.ndarray

step_image_height

Minimum step size for image height.

Type:

int

step_image_width

Minimum step size for image width.

Type:

int

property variance: Any

Return variance map. If not present, load from file.

Returns:

variance – Variance map.

Return type:

np.ndarray

x_pixels

Number of pixels in the x direction

Type:

int

y_pixels

Number of pixels in the y direction

Type:

int