navigate.model.microscope.Microscope

class navigate.model.microscope.Microscope(name: str, configuration: Dict[str, Any], devices_dict: dict, is_synthetic: bool = False, is_virtual: bool = False)

Bases: object

Microscope Class - Used to control the microscope.

__init__(name: str, configuration: Dict[str, Any], devices_dict: dict, is_synthetic: bool = False, is_virtual: bool = False) → None

Initialize the microscope.

Parameters:

• name (str) – Name of the microscope.

• configuration (Dict[str, Any]) – Configuration dictionary.

• devices_dict (dict) – Dictionary of devices.

• is_synthetic (bool, optional) – Is synthetic, by default False

• is_virtual (bool, optional) – Is virtual, by default False

Methods

__init__(name, configuration, devices_dict)	Initialize the microscope.
assemble_device_config_lists(device_name, ...)	Assemble device config lists.
calculate_all_waveform()	Calculate all the waveforms.
calculate_exposure_sweep_times()	Calculate the exposure and sweep times for all channels.
end_acquisition()	End the acquisition.
get_available_channels()	Get the available channels for imaging.
get_exposure_sweep_times()	Get the exposure and sweep times for all channels.
get_stage_position()	Get stage position.
load_and_start_devices(device_name, is_list, ...)	Load and start devices.
move_remote_focus([offset])	Move remote focus.
move_stage(pos_dict[, wait_until_done, ...])	Move stage to a position.
move_stage_offset([former_microscope])	Move the stage to the offset position.
prepare_acquisition()	Prepare the acquisition.
prepare_next_channel([update_daq_task_flag])	Prepare the next channel.
report_camera_settings()	Log the camera settings.
run_command(command, *args)	Run command.
set_camera_exposure_time(channel)	Set the camera exposure time.
set_camera_roi()	Set the camera ROI.
set_camera_sensor_mode()	Set the camera sensor mode.
stop_stage()	Stop stage.
terminate()	Close hardware explicitly.
turn_off_lasers()	Turn off current laser.
turn_on_laser()	Turn on the current laser.
update_data_buffer(data_buffer, number_of_frames)	Update the data buffer for the camera.
update_stage_limits([limits_flag])	Update stage limits.

Attributes

microscope_name	Name of the microscope.
output_event_queue	Output event queue.
configuration	Configuration dictionary.
data_buffer	Buffer for image data.
stages	Dictionary of stages.
stages_list	List of stages.
ask_stage_for_position	Ask stage for position.
camera	Camera object.
shutter	Shutter device.
lasers	Dictionary of lasers.
galvo	Dictionary of galvanometers.
remote_focus_device	Remote focus device.
filter_wheel	Dictionary of filter_wheels
daq	Dictionary of data acquisition devices.
info	Dictionary of microscope info.
current_channel	Current channel.
current_laser_index	Current laser index.
channels	List of all channels.
available_channels	List of available channels.
number_of_frames	Number of images.
central_focus	Central focus position.
is_synthetic	Is a synthetic microscope.
laser_wavelength	Dictionary of laser configurations.
ret_pos_dict	Dictionary of returned stage positions.
commands	Dictionary of commands
plugin_devices	Dictionary of plugin devices

assemble_device_config_lists(device_name: str, device_name_dict: dict) → tuple

Assemble device config lists.

Parameters:

• device_name (str) – Device name.

• device_name_dict (dict) – Device name dictionary.

Returns:

• device_config_list (list) – Device configuration list.

• device_name_list (list) – Device name list.

• is_list (bool) – Is list.

calculate_all_waveform() → dict

Calculate all the waveforms.

Returns:

waveform – Dictionary of all the waveforms.

Return type:

dict

calculate_exposure_sweep_times() → tuple

Calculate the exposure and sweep times for all channels.

The calculate_exposure_sweep_times function calculates and returns exposure times and sweep times for all channels in a microscope configuration. It takes the camera’s readout time as an input parameter and considers various parameters such as camera exposure time, delay percentages, and smoothing to compute these times. The function iterates through the channels, performs calculations, and returns the results as dictionaries containing exposure times and sweep times for each channel.

Returns:

• exposure_times (dict) – Dictionary of exposure times.

• sweep_times (dict) – Dictionary of sweep times.

end_acquisition() → None

End the acquisition.

This function stops the acquisition, which includes stopping the data acquisition system, closing the camera image series, closing the shutter, turning off the lasers, and moving the stage to the central focus position if it was moved during the acquisition. It also stops the stage if it is moving.

get_available_channels() → None

Get the available channels for imaging.

This function gets the available channels for imaging by identifying which channels are selected for imaging in the configuration file.

get_exposure_sweep_times() → tuple

Get the exposure and sweep times for all channels.

Returns:

• exposure_times (dict) – Dictionary of exposure times.

• sweep_times (dict) – Dictionary of sweep times.

get_stage_position() → dict

Get stage position.

Returns:

stage_position – Dictionary of stage positions.

Return type:

dict

load_and_start_devices(device_name: str, is_list: bool, device_name_list: list, device_ref_name: str, device_connection: Any, name: str, i: int, plugin_devices: dict) → None

Load and start devices.

Function uses importlib to import the device startup functions and then starts the devices. If it is a list, it will start the device at the index i. If it is a plugin, it will load the plugin device.

Parameters:

• device_name (str) – The name of the device.

• is_list (bool) – Whether the device is a list of devices.

• device_name_list (list) – The list of device names.

• device_ref_name (str) – The reference name of the device.

• device_connection (Any) – The communication instance of the device.

• name (str) – The name of the microscope.

• i (int) – Index.

• plugin_devices (dict) – Plugin Devices

move_remote_focus(offset: Optional[float] = None) → None

Move remote focus.

Parameters:

offset (Optional[float], optional) – Offset, by default None

move_stage(pos_dict: dict, wait_until_done: bool = False, update_focus: bool = True) → bool

Move stage to a position.

Parameters:

• pos_dict (dict) – Dictionary of stage positions.

• wait_until_done (bool, optional) – Wait until stage is done moving, by default False

• update_focus (bool, optional) – Update the central focus

Returns:

success – True if stage is successfully moved, False otherwise.

Return type:

bool

move_stage_offset(former_microscope: Optional[str] = None) → None

Move the stage to the offset position.

Parameters:

former_microscope (Optional[str], optional) – Name of the former microscope.

prepare_acquisition() → dict

Prepare the acquisition.

This function prepares the acquisition by identifying which channels are selected for imaging, setting the camera region of interest (ROI), setting the camera sensor mode, setting the camera binning, initializing the image series, calculating all the waveforms required for the acquisition process, and opens the shutter.

Returns:

waveform – Dictionary of all the waveforms.

Return type:

dict

prepare_next_channel(update_daq_task_flag: bool = True) → None

Prepare the next channel.

This function, prepare_next_channel, is responsible for configuring various hardware components for the next imaging channel in an experimental setup. It sequentially selects the next available channel, sets the filter wheel, camera exposure time, laser power, and other parameters based on the selected channel’s configuration. Additionally, it stops data acquisition, prepares the data acquisition system for the new channel, and adjusts the focus position as necessary, ensuring the hardware is ready for imaging the selected channel.

Parameters:

update_daq_task_flag (bool) – whether to override waveforms in the DAQ (create new tasks)

report_camera_settings() → None

Log the camera settings.

This function logs the camera settings for the current acquisition. It logs the camera parameters specified in the configuration file for the current microscope.

run_command(command: str, *args) → None

Run command.

Parameters:

• command (str) – Command.

• *args (list) – Variable input arguments.

set_camera_exposure_time(channel: dict) → None

Set the camera exposure time.

This function prepares the camera for imaging by setting the camera exposure time based on the selected channel’s configuration. It also adjusts the camera line interval if the sensor mode is set to the Light-Sheet mode.

Parameters:

channel (dict) – Dictionary of channel parameters.

set_camera_roi() → None

Set the camera ROI.

This function sets the camera region of interest (ROI) based on the camera parameters specified in the configuration file. It sets the image width, image height, and the center of the image. The camera ROI is used to define the area of the image sensor that will be used to capture images during the acquisition process.

set_camera_sensor_mode() → None

Set the camera sensor mode.

This function sets the camera sensor mode based on the camera parameters specified in the configuration file. It sets the sensor mode and the readout direction for the camera if it is in the light-sheet imaging mode.

stop_stage() → None

Stop stage.

terminate() → None

Close hardware explicitly.

Closes all devices other than plugin devices and deformable mirrors.

turn_off_lasers() → None

Turn off current laser.

turn_on_laser() → None

Turn on the current laser.

update_data_buffer(data_buffer: List[ndarray], number_of_frames: int) → None

Update the data buffer for the camera.

Parameters:

• data_buffer (List[np.ndarray]) – Data buffer for the camera.

• number_of_frames (int) – Number of frames to be acquired.

update_stage_limits(limits_flag: bool = True) → None

Update stage limits.

Parameters:

limits_flag (bool, optional) – Limits flag, by default True

ask_stage_for_position

Ask stage for position.

Type:

bool

available_channels

List of available channels.

Type:

list

camera

Camera object.

Type:

obj

central_focus

Central focus position.

Type:

float

channels

List of all channels.

Type:

list

commands

Dictionary of commands

Type:

dict

configuration

Configuration dictionary.

Type:

dict

current_channel

Current channel.

Type:

int

current_laser_index

Current laser index.

Type:

int

daq

Dictionary of data acquisition devices.

Type:

dict

data_buffer

Buffer for image data.

Type:

SharedNDArray

filter_wheel

Dictionary of filter_wheels

Type:

dict

galvo

Dictionary of galvanometers.

Type:

dict

info

Dictionary of microscope info.

Type:

dict

is_synthetic

Is a synthetic microscope.

Type:

Bool

laser_wavelength

Dictionary of laser configurations.

Type:

dict

lasers

Dictionary of lasers.

Type:

dict

microscope_name

Name of the microscope.

Type:

str

number_of_frames

Number of images.

Type:

int

output_event_queue

Output event queue.

Type:

Queue

plugin_devices

Dictionary of plugin devices

Type:

dict

remote_focus_device

Remote focus device.

Type:

Any

ret_pos_dict

Dictionary of returned stage positions.

Type:

dict

shutter

Shutter device.

Type:

Any

stages

Dictionary of stages.

Type:

dict

stages_list

List of stages.

Type:

list