navigate.model.devices.camera.hamamatsu.HamamatsuOrca

class navigate.model.devices.camera.hamamatsu.HamamatsuOrca(microscope_name: str, device_connection: Any, configuration: Dict[str, Any])

Bases: HamamatsuBase

__init__(microscope_name: str, device_connection: Any, configuration: Dict[str, Any]) → None

Initialize HamamatsuOrca class.

This is for controlling the Orca Flash 4.0.

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

Methods

__init__(microscope_name, device_connection, ...)	Initialize HamamatsuOrca class.
calculate_light_sheet_exposure_time(...)	Convert normal mode exposure time to light-sheet mode exposure time.
calculate_readout_time()	Get the duration of time needed to read out an image.
close_camera()	Close HamamatsuOrca Camera
close_image_series()	Close image series.
get_line_interval()	Get HamamatsuOrca line interval.
get_new_frame()	Get frame from HamamatsuOrca camera.
get_offset_variance_maps()	Get offset and variance maps from file.
initialize_image_series([data_buffer, ...])	Initialize HamamatsuOrca image series.
report_settings()	Print Camera Settings.
set_ROI([roi_width, roi_height, center_x, ...])	Change the size of the active region on the camera.
set_binning(binning_string)	Set HamamatsuOrca binning mode.
set_exposure_time(exposure_time)	Set HamamatsuOrca exposure time.
set_line_interval(line_interval_time)	Set HamamatsuOrca line interval.
set_readout_direction(mode)	Set HamamatsuOrca readout direction.
set_sensor_mode(mode)	Set HamamatsuOrca sensor mode.

Attributes

offset	Return offset map.
serial_number	Get Camera Serial Number
variance	Return variance map.

calculate_light_sheet_exposure_time(full_chip_exposure_time, shutter_width)

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) – Updated full chip exposure time (s).

calculate_readout_time()

Get the duration of time needed to read out an image.

Returns:

readout_time – Duration of time needed to read out an image.

Return type:

float

close_camera()

Close HamamatsuOrca Camera

close_image_series()

Close image series.

Stops the acquisition and sets is_acquiring flag to False.

get_line_interval()

Get HamamatsuOrca line interval.

Returns:

line_interval_time – Line interval duration.

Return type:

float

get_new_frame()

Get frame from HamamatsuOrca camera.

Returns:

frame – Frame ids from HamamatsuOrca camera.

Return type:

numpy.ndarray

get_offset_variance_maps()

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.

initialize_image_series(data_buffer=None, number_of_frames=100)

Initialize HamamatsuOrca image series.

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.

report_settings()

Print Camera Settings.

Prints the current camera settings to the console and the log file.

set_ROI(roi_width=2048, roi_height=2048, center_x=1024, center_y=1024)

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_binning(binning_string)

Set HamamatsuOrca binning mode.

Parameters:

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

Returns:

result – True if successful, False otherwise.

Return type:

bool

set_exposure_time(exposure_time)

Set HamamatsuOrca exposure time.

Note

Units of the Hamamatsu API are in seconds.

Parameters:

exposure_time (float) – Exposure time in seconds.

set_line_interval(line_interval_time)

Set HamamatsuOrca line interval.

Parameters:

line_interval_time (float) – Line interval duration.

set_readout_direction(mode)

Set HamamatsuOrca readout direction.

Parameters:

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

set_sensor_mode(mode)

Set HamamatsuOrca sensor mode.

Parameters:

mode (str) – ‘Normal’ or ‘Light-Sheet’

camera_controller

Hardware device to connect to

Type:

object

camera_parameters

Camera parameters

Type:

dict

configuration

Configuration settings

Type:

dict

device_connection

Device connection

Type:

object

is_acquiring

Whether the camera is currently acquiring

Type:

bool

microscope_name

Name of the microscope

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

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

Returns:

offset – Offset map.

Return type:

np.ndarray

property serial_number

Get Camera Serial Number

Returns:

serial_number – Serial number for the camera.

Return type:

str

step_image_height

Minimum step size for image height.

Type:

int

step_image_width

Minimum step size for image width.

Type:

int

property variance

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