navigate.model.model.Model

class navigate.model.model.Model(args: Namespace, configuration: Optional[Dict[str, Any]] = None, event_queue: Optional[Queue] = None)

Bases: object

Navigate Model Class

Model for Model-View-Controller Software Architecture.

__init__(args: Namespace, configuration: Optional[Dict[str, Any]] = None, event_queue: Optional[Queue] = None) → None

Initialize the Model.

Parameters:

• args (argparse.Namespace) – Command line arguments.

• configuration (Optional[Dict[str, Any]]) – Configuration dictionary. Defaults to None.

• event_queue (multiprocessing.Queue) – Event queue. Receives events from the controller.

Methods

__init__(args[, configuration, event_queue])	Initialize the Model.
change_resolution(resolution_value)	Switch resolution mode of the microscope.
create_pipe(pipe_name)	Create a data pipe.
destroy_virtual_microscope(microscope_name)	Destroy a virtual microscope.
end_acquisition()	End the acquisition.
get_active_microscope()	Get the active microscope.
get_camera_line_interval_and_exposure_time(...)	Get camera line interval time, light sheet exposure, and full chip exposure times.
get_data_buffer([img_width, img_height])	Get the data buffer.
get_feature_list(idx)	Get feature list str by index
get_microscope_info()	Return Microscopes device information.
get_offset_variance_maps()	Get the offset variance maps.
get_stage_position()	Get the position of the stage.
launch_virtual_microscope(microscope_name, ...)	Launch a virtual microscope.
load_feature_list_from_file(filename, features)	Append feature list from the file
load_feature_list_from_str(feature_list_str)	Append feature list from feature_list_str
load_feature_records()	Load installed feature lists from system folder
load_images([filenames])	Load/Unload images to the Synthetic Camera
mark_saving_flags(frame_ids)	Mark saving flags for the ImageWriter
move_stage(pos_dict[, wait_until_done])	Moves the stages.
pause_data_thread()	Pause the data thread.
prepare_acquisition([turn_off_flags])	Prepare the acquisition.
release_pipe(pipe_name)	Close a data pipe.
reset_feature_list()	Reset live mode feature list.
resume_data_thread()	Resume the data thread.
run_acquisition()	Run acquisition along with a feature list one time.
run_command(command, *args, **kwargs)	Receives commands from the controller.
run_data_process([num_of_frames, data_func])	Run the data process.
run_live_acquisition()	Stream live image to the GUI.
simplified_data_process(microscope, ...[, ...])	Run the data process.
snap_image()	Acquire an image after updating the waveforms.
stop_stage()	Stop the stages.
terminate()	Terminate the model.
update_data_buffer([img_width, img_height])	Update the Data Buffer
update_ilastik_setting([...])	Update the ilastik setting.
update_mirror([coef, flatten])	Update the mirror.

Attributes

logger	Logger object.
configuration	Configuration dictionary.
plugin_acquisition_modes	Dictionary of plugin acquisition modes
virtual_microscopes	Dictionary of virtual microscopes.
microscopes	Dictionary of physical microscopes.
active_microscope	Name of the active microscope.
active_microscope_name	Name of the active microscope.
imaging_mode	Imaging mode.
image_count	Number of images acquired.
acquisition_count	Number of acquisitions.
total_acquisition_count	Total number of acquisitions.
total_image_count	Total number of images.
current_exposure_time	Current exposure time in milliseconds
pre_exposure_time	Pre-exposure time in milliseconds
camera_wait_iterations	Number of timeouts before aborting acquisition.
start_time	Time before acquisition.
data_buffer	Data buffer for image frames.
img_width	Number of active pixels in the x-dimension.
img_height	Number of active pixels in the y-dimension.
binning	Binning mode.
data_buffer_positions	stage positions.
data_buffer_saving_flags	saving flags for a frame
is_acquiring	Is the model acquiring?
f_position	Current focus position.
max_entropy	Autofocus maximum entropy.
focus_pos	Autofocus maximum entropy position.
signal_thread	Signal thread.
data_thread	Data thread.
show_img_pipe	Show image pipe.
plot_pipe	Plot pipe.
event_queue	Waveform queue.
frame_id	Frame ID.
injected_flag	Inject a feature list?
is_live	Is the model live?
is_save	Is the model saving the data?
stop_acquisition	Stop signal and data threads?
stop_send_signal	Stop signal thread?
pause_data_event	Pause data event.
pause_data_ready_lock	Pause data ready lock.
ask_to_pause_data_thread	Submit a request to pause the data thread?
number_of_frames	Number of frames in the data buffer.
image_writer	Image writer.
addon_feature	add on feature in customized mode
feature_list	List of features.

change_resolution(resolution_value: str) → None

Switch resolution mode of the microscope.

Parameters:

resolution_value (str) – Resolution mode.

create_pipe(pipe_name: str) → Pipe

Create a data pipe.

Creates a pair of connection objects connected by a pipe which by default is duplex (two-way)

Parameters:

pipe_name (str) – Name of pipe to create.

Returns:

The writable end of the newly created duplex pipe.

Return type:

multiprocessing.Pipe

destroy_virtual_microscope(microscope_name: str) → None

Destroy a virtual microscope.

Parameters:

microscope_name (str) – Name of microscope.

end_acquisition() → None

End the acquisition.

Sets the current channel to 0, clears the signal and data containers, disconnects buffer in live mode and closes the shutters.

get_active_microscope() → Microscope

Get the active microscope.

Returns:

microscope – Active microscope.

Return type:

Microscope

get_camera_line_interval_and_exposure_time(exposure_time: float, number_of_pixel: int) → Tuple[float, float, float]

Get camera line interval time, light sheet exposure, and full chip exposure times.

Parameters:

• exposure_time (float) – camera global exposure time

• number_of_pixel (int) – number of pixel in light sheet mode

Returns:

camera_times –

• camera_exposure_timefloat

  camera exposure time (s)

• camera_line_intervalfloat

  camera line interval (s)

• full_chip_exposure_timefloat

  Updated full chip exposure time (s).

Return type:

Tuple[float, float, float]

get_data_buffer(img_width: int = 512, img_height: int = 512) → List[SharedNDArray]

Get the data buffer.

If the number of active pixels in x and y changes, updates the data buffer and returns newly sized buffer.

Parameters:

• img_height (int) – Number of active pixels in the x-dimension.

• img_width (int) – Number of active pixels in the y-dimension.

Returns:

data_buffer – Shared memory object.

Return type:

List[SharedNDArray]

get_feature_list(idx: int) → str

Get feature list str by index

Parameters:

idx (int) – index of the feature list

Returns:

feature_list_str –

• Any empty string if the feature is not found

• The name of the feature if it is found

Return type:

str

get_microscope_info() → Dict[str, Any]

Return Microscopes device information.

Returns:

microscope_info – Microscope device information.

Return type:

Dict[str, Any]

get_offset_variance_maps() → Tuple[ndarray, ndarray]

Get the offset variance maps.

Returns:

offset_variance_maps – Offset variance maps.

Return type:

Tuple[np.ndarray, np.ndarray]

get_stage_position() → Dict[str, Any]

Get the position of the stage.

Returns:

ret_pos_dict – Dictionary of stage positions.

Return type:

dict

launch_virtual_microscope(microscope_name: str, microscope_config: Dict[str, Any]) → List[SharedNDArray]

Launch a virtual microscope.

Parameters:

• microscope_name (str) – Name of microscope.

• microscope_config (dict) – Configuration of microscope.

Returns:

data_buffer – List of data buffer.

Return type:

list

load_feature_list_from_file(filename: str, features: list[str]) → None

Append feature list from the file

Parameters:

• filename (str) – filename of the feature list.

• features (list[str]) – list of feature names to load from the file.

load_feature_list_from_str(feature_list_str: str) → None

Append feature list from feature_list_str

Parameters:

feature_list_str (str) – the str of a feature list

load_feature_records() → None

Load installed feature lists from system folder

Note

System folder can be found at ‘…./.navigate/feature_lists’

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

Load/Unload images to the Synthetic Camera

Parameters:

filenames (Optional[list[str]]) – The list of filenames to load.

mark_saving_flags(frame_ids: list)

Mark saving flags for the ImageWriter

Parameters:

frame_ids (list) – a list of frame ids

move_stage(pos_dict: Dict[str, Any], wait_until_done=False) → bool

Moves the stages.

Updates the stage dictionary, moves to the desired position, and reports the position.

Parameters:

• pos_dict (Dict[str, Any]) – Dictionary of stage positions.

• wait_until_done (bool) – Checks “on target state” after command and waits until done.

Returns:

success – Was the move successful?

Return type:

bool

pause_data_thread() → None

Pause the data thread.

Function is called when user pauses the acquisition.

Returns:

Execution pauses until resume_data_thread() is called.

Return type:

None

prepare_acquisition(turn_off_flags: bool = True) → bool

Prepare the acquisition.

This function is called when the user starts the acquisition, sets flags, calculates all the waveforms, sets the Camera Sensor Mode, initializes the data buffer and starts the cameras, and opens Shutters.

Parameters:

turn_off_flags (bool) – Turn off the flags.

Returns:

Was the preparation successful?

Return type:

bool

release_pipe(pipe_name: str) → None

Close a data pipe.

Parameters:

pipe_name (str) – Name of pipe to close.

Returns:

Always returns None.

Return type:

None

reset_feature_list() → None

Reset live mode feature list.

resume_data_thread() → None

Resume the data thread.

Function is called when the user resumes the acquisition.

Returns:

Execution continues after pause.

Return type:

None

run_acquisition() → None

Run acquisition along with a feature list one time.

Returns:

Completes after acquisition pass ends.

Return type:

None

run_command(command: str, *args: List[Union[str, int]], **kwargs: Dict[str, Any]) → None

Receives commands from the controller.

Parameters:

• command (str) – Type of command to run.

• *args (List[Union[str, int]]) – List of arguments to pass to the command.

• **kwargs (Dict[str, Any]) – Dictionary of keyword arguments to pass to the command.

Returns:

This method always returns None.

Return type:

None

run_data_process(num_of_frames: Optional[int] = 0, data_func: Optional[callable] = None) → None

Run the data process.

This function is the structure of the data thread.

So long as the acquisition is not stopped, it will keep acquiring frames. If it expects a frame, but does not receive one, it will wait for a certain number of iterations before aborting the acquisition. If it receives a frame, it will count it, send it to the controller for display, and run the data_func function on the acquired data. If the data_func is not provided, it will simply display the image. If the number of frames to acquire is specified, it will stop acquiring frames when the specified number is reached.

Parameters:

• num_of_frames (Optional[int]) – Number of frames to acquire. Default is 0.

• data_func (Optional[callable]) – Function to run on the acquired data. Default is None.

Returns:

Terminates when acquisition ends or errors occur.

Return type:

None

run_live_acquisition() → None

Stream live image to the GUI.

Recalculates the waveforms for each image, thereby allowing people to adjust acquisition parameters in real-time.

Returns:

Terminates when live acquisition is stopped.

Return type:

None

simplified_data_process(microscope: Microscope, show_img_pipe: Pipe, data_func: Optional[callable] = None) → None

Run the data process.

Parameters:

• microscope (Microscope) – Instance of the Microscope object.

• show_img_pipe (multiprocessing.Pipe) – The pipe for delivering images to the Controller.

• data_func (callable) – Function to run on the acquired data.

Returns:

Terminates when acquisition stops.

Return type:

None

snap_image() → None

Acquire an image after updating the waveforms.

Can be used in acquisitions where changing waveforms are required, but there is additional overhead due to the need to write the waveforms into the buffers of the DAQ cards.

Returns:

Completes after the image is captured and buffered.

Return type:

None

stop_stage() → None

Stop the stages.

terminate() → None

Terminate the model.

update_data_buffer(img_width: int = 512, img_height: int = 512) → None

Update the Data Buffer

Parameters:

• img_width (int) – Number of active pixels in the x-dimension.

• img_height (int) – Number of active pixels in the y-dimension.

Returns:

Completes after the data buffer is resized and reinitialized.

Return type:

None

update_ilastik_setting(display_segmentation: Optional[bool] = False, mark_position: Optional[bool] = True, target_labels: Optional[list[int]] = [1]) → None

Update the ilastik setting.

Parameters:

• display_segmentation (Optional[bool]) – Display segmentation. Default is False.

• mark_position (Optional[bool]) – Mark position. Default is True.

• target_labels (Optional[list[int]]) – Target labels. Default is [1].

update_mirror(coef: list = [], flatten: bool = False) → None

Update the mirror.

Parameters:

• coef (list) – The list of coefficients. Default is [].

• flatten (bool) – Flatten the mirror? Default is False.

acquisition_count

Number of acquisitions.

Type:

int

active_microscope

Name of the active microscope.

Type:

str

active_microscope_name

Name of the active microscope.

Type:

str

addon_feature

add on feature in customized mode

Type:

list

ask_to_pause_data_thread

Submit a request to pause the data thread?

Type:

bool

binning

Binning mode.

Type:

str

camera_wait_iterations

Number of timeouts before aborting acquisition.

Type:

int

configuration

Configuration dictionary.

Type:

dict

current_exposure_time

Current exposure time in milliseconds

Type:

float

data_buffer

Data buffer for image frames.

Type:

List[SharedNDArray]

data_buffer_positions

stage positions.

Type:

array

data_buffer_saving_flags

saving flags for a frame

Type:

array

data_thread

Data thread.

Type:

threading.Thread

event_queue

Waveform queue.

Type:

multiprocessing.Queue

f_position

Current focus position.

Type:

float

feature_list

List of features.

Type:

list

focus_pos

Autofocus maximum entropy position.

Type:

float

frame_id

Frame ID.

Type:

int

image_count

Number of images acquired.

Type:

int

image_writer

Image writer.

Type:

ImageWriter

imaging_mode

Imaging mode.

Type:

str

img_height

Number of active pixels in the y-dimension.

Type:

int

img_width

Number of active pixels in the x-dimension.

Type:

int

injected_flag

Inject a feature list?

Type:

bool

is_acquiring

Is the model acquiring?

Type:

bool

is_live

Is the model live?

Type:

bool

is_save

Is the model saving the data?

Type:

bool

logger

Logger object.

Type:

object

max_entropy

Autofocus maximum entropy.

Type:

float

microscopes

Dictionary of physical microscopes.

Type:

dict

number_of_frames

Number of frames in the data buffer.

Type:

int

pause_data_event

Pause data event.

Type:

event

pause_data_ready_lock

Pause data ready lock.

Type:

threading.Lock

plot_pipe

Plot pipe.

Type:

multiprocessing.connection.Connection

plugin_acquisition_modes

Dictionary of plugin acquisition modes

Type:

dict

pre_exposure_time

Pre-exposure time in milliseconds

Type:

float

show_img_pipe

Show image pipe.

Type:

multiprocessing.connection.Connection

signal_thread

Signal thread.

Type:

threading.Thread

start_time

Time before acquisition.

Type:

float

stop_acquisition

Stop signal and data threads?

Type:

bool

stop_send_signal

Stop signal thread?

Type:

bool

total_acquisition_count

Total number of acquisitions.

Type:

int

total_image_count

Total number of images.

Type:

int

virtual_microscopes

Dictionary of virtual microscopes.

Type:

dict