navigate.model.devices.camera.synthetic.SyntheticCamera

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

Bases: CameraBase

SyntheticCamera camera class.

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

Initialize SyntheticCamera 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

Methods

__init__(microscope_name, device_connection, ...)	Initialize SyntheticCamera class.
calculate_light_sheet_exposure_time(...)	Convert normal mode exposure time to light-sheet mode exposure time.
calculate_readout_time()	Calculate duration of time needed to read out an image.
close_camera()	Close SyntheticCamera Camera
close_image_series()	Close image series.
generate_new_frame()	Generate a synthetic image.
get_line_interval()	Return stored camera line interval.
get_new_frame()	Get frame from SyntheticCamera camera.
get_offset_variance_maps()	Get offset and variance maps from file.
initialize_image_series([data_buffer, ...])	Initialize SyntheticCamera image series.
load_images([filenames, ds])	Pre-populate the buffer with images.
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 SyntheticCamera binning mode.
set_exposure_time(exposure_time)	Set SyntheticCamera exposure time.
set_line_interval(line_interval_time)	Set SyntheticCamera line interval.
set_readout_direction(mode)	Set HamamatsuOrca readout direction.
set_sensor_mode(mode)	Set SyntheticCamera sensor mode.

Attributes

offset	Return offset map.
variance	Return variance map.
microscope_name	Name of the microscope
device_connection	Device connection
configuration	Configuration settings
is_acquiring	Whether the camera is currently acquiring
current_frame_idx	current image id
data_buffer	data buffer
num_of_frame	number of frames
pre_frame_idx	previous image id
random_image	whether to use random image
serial_number	serial number
camera_exposure_time	exposure time
x_binning	x binning
y_binning	y binning
x_pixels	width
y_pixels	height
center_x	center x
center_y	center y
img_id	current image id
current_tif_id	current tif id
tif_images	list of tif images

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) – Full chip exposure time (s).

static calculate_readout_time() → float

Calculate duration of time needed to read out an image.

Calculates the readout time and maximum frame rate according to the camera configuration settings.

Returns:

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

Return type:

float

close_camera() → None

Close SyntheticCamera Camera

close_image_series() → None

Close image series.

Stops the acquisition and sets is_acquiring flag to False.

generate_new_frame() → None

Generate a synthetic image.

get_line_interval() → float

Return stored camera line interval.

Returns:

line_interval – line interval duration (s).

Return type:

float

get_new_frame() → List[int]

Get frame from SyntheticCamera camera.

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: Optional[List[SharedNDArray]] = None, number_of_frames: int = 100)

Initialize SyntheticCamera image series.

Parameters:

• data_buffer (Optional[List[SharedNDArray]]) – The shared data buffer. Default is None.

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

load_images(filenames: Optional[str] = None, ds=None) → None

Pre-populate the buffer with images. Can either come from TIFF files or Numpy stacks.

report_settings() → None

Print Camera Settings.

set_ROI(roi_width: int = 2048, roi_height: int = 2048, center_x: int = 1024, center_y: int = 1024) → None

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

set_binning(binning_string: str) → None

Set SyntheticCamera binning mode.

Parameters:

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

set_exposure_time(exposure_time: float) → None

Set SyntheticCamera exposure time.

All of our units are in milliseconds. Function converts to seconds.

Parameters:

exposure_time (float) – Exposure time in seconds.

set_line_interval(line_interval_time: float) → None

Set SyntheticCamera line interval.

Parameters:

line_interval_time (float) – Line interval duration.

set_readout_direction(mode) → None

Set HamamatsuOrca readout direction.

Parameters:

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

set_sensor_mode(mode: str) → None

Set SyntheticCamera sensor mode.

Parameters:

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

camera_controller

Hardware device to connect to

Type:

object

camera_exposure_time

exposure time

Type:

float

camera_parameters

Camera parameters

Type:

dict

center_x

center x

Type:

int

center_y

center y

Type:

int

configuration

Configuration settings

Type:

Dict[str, Any]

current_frame_idx

current image id

Type:

int

current_tif_id

current tif id

Type:

int

data_buffer

data buffer

Type:

object

device_connection

Device connection

Type:

Any

img_id

current image id

Type:

int

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

num_of_frame

number of frames

Type:

int

property offset

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

Returns:

offset – Offset map.

Return type:

np.ndarray

pre_frame_idx

previous image id

Type:

int

random_image

whether to use random image

Type:

bool

serial_number

serial number

Type:

int

step_image_height

Minimum step size for image height.

Type:

int

step_image_width

Minimum step size for image width.

Type:

int

tif_images

list of tif images

Type:

list

property variance

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

Returns:

variance – Variance map.

Return type:

np.ndarray

x_binning

x binning

Type:

int

x_pixels

width

Type:

int

y_binning

y binning

Type:

int

y_pixels

height

Type:

int