navigate.model.devices.stage.asi.MFC2000Stage

class navigate.model.devices.stage.asi.MFC2000Stage(microscope_name: str, device_connection: Any, configuration: Dict[str, Any], device_id: int = 0)

Bases: ASIStage

Applied Scientific Instrumentation (ASI) Stage Class

ASI Documentation: https://asiimaging.com/docs/products/serial_commands

ASI Quick Start Guide: https://asiimaging.com/docs/command_quick_start

Note

ASI firmware requires all distances to be in a 10th of a micron.

__init__(microscope_name: str, device_connection: Any, configuration: Dict[str, Any], device_id: int = 0)

Initialize the ASI Stage connection.

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
device_id (int) – Device ID for the stage, default to 0

Methods

`__init__`(microscope_name, device_connection, ...)	Initialize the ASI Stage connection.
`close`()	Close the stage.
`connect`(port[, baudrate, timeout])	Connect to the ASI Stage
`disconnect`()	Disconnect from serial device.
`get_abs_position`(axis, axis_abs)	Ensure the requested position is within axis bounds and return it.
`get_axis_position`(axis)	Get position of specific axis
`get_position_dict`()	Return a dictionary with the saved stage positions.
`get_speed`(axis)	Get scan velocity of the axis.
`move_absolute`(move_dictionary[, wait_until_done])	Move Absolute Method.
`move_axis_absolute`(axis, abs_pos[, ...])	Move stage along a single axis.
`report_position`()	Reports the position for all axes in microns, and create position dictionary.
`scanr`(start_position_mm, end_position_mm, ...)	Set scan range
`scanv`(start_position_mm, end_position_mm, ...)	Set scan range
`set_speed`([velocity_dict, percent])	Set scan velocity.
`start_scan`(axis)	Start scan state machine
`stop`()	Stop all stage movement abruptly.
`stop_scan`()	Stop scan
`verify_abs_position`(move_dictionary[, is_strict])	Ensure the requested moving positions are within axes bounds
`verify_move`(move_dictionary)	Don't submit a move command for axes that aren't moving.
`wait_until_complete`(axis)

Attributes

close(): Close the stage.

classmethod connect(port, baudrate=115200, timeout=0.25)

Connect to the ASI Stage

Parameters:

port (str) – Communication port for ASI Tiger Controller - e.g., COM1
baudrate (int) – Baud rate for ASI Tiger Controller - e.g., 9600
timeout (float) – Timeout value.

Returns:

asi_stage – Successfully initialized stage object.

Return type:

object

disconnect(): Disconnect from serial device.

get_abs_position(axis, axis_abs)

Ensure the requested position is within axis bounds and return it.

Parameters:

axis (str) – An axis: x, y, z, f, theta
axis_abs (float) – Absolute position value

Returns:

Position to move the stage to for this axis.

Return type:

float

get_axis_position(axis)

Get position of specific axis

Parameters:: axis (str) – Axis to get position of
Returns:: position
Return type:: float

get_position_dict()

Return a dictionary with the saved stage positions.

Returns:: Dictionary of stage positions.
Return type:: dict

get_speed(axis)

Get scan velocity of the axis.

Parameters:: axis (str) – axis name, such as ‘x’, ‘y’, ‘z’
Returns:: velocity – Velocity
Return type:: float

move_absolute(move_dictionary, wait_until_done=False)

Move Absolute Method.

XYZ Values should remain in microns for the ASI API Theta Values are not accepted.

Parameters:

move_dictionary (dict) – A dictionary of values required for movement. Includes ‘x_abs’, etc. for one or more axes. Expect values in micrometers, except for theta, which is in degrees.
wait_until_done (bool) – Block until stage has moved to its new spot.

Returns:

success – Was the move successful?

Return type:

bool

move_axis_absolute(axis, abs_pos, wait_until_done=False)

Move stage along a single axis.

Move absolute command for ASI is MOVE [Axis]=[units 1/10 microns]

Parameters:

axis (str) – An axis prefix in move_dictionary. For example, axis=’x’ corresponds to ‘x_abs’, ‘x_min’, etc.
abs_pos (float) – Absolute position value
wait_until_done (bool) – Block until stage has moved to its new spot.

Returns:

Was the move successful?

Return type:

bool

report_position()

Reports the position for all axes in microns, and create position dictionary.

Returns:: Dictionary of positions for each axis in microns.
Return type:: dict

scanr(start_position_mm, end_position_mm, enc_divide, axis='z')

Set scan range

Parameters:

start_position_mm (float) – scan start position
end_position_mm (float) – scan end position
enc_divide (float) – Step size desired.
axis (str) – fast axis name

Returns:

success – Was the setting successful?

Return type:

bool

scanv(start_position_mm, end_position_mm, number_of_lines, overshoot, axis='z')

Set scan range

Parameters:

start_position_mm (float) – scan start position
end_position_mm (float) – scan end position
number_of_lines (int) – number of steps.
overshoot (float) – overshoot_time ms
axis (str) – fast axis name

Returns:

success – Was the setting successful?

Return type:

bool

set_speed(velocity_dict=None, percent=None)

Set scan velocity.

Parameters:

velocity_dict (dict) – velocity for specific axis {‘x’: float, ‘y’: float, ‘z’: float}
percent (float) – Percent of maximum speed

Returns:

success – Was the setting successful?

Return type:

bool

start_scan(axis)

Start scan state machine

Parameters:: axis (str) – fast axis name, such as ‘x’, ‘y’, and ‘z’
Returns:: success – Was it successful?
Return type:: bool

stop(): Stop all stage movement abruptly.

stop_scan(): Stop scan

verify_abs_position(move_dictionary, is_strict=False)

Ensure the requested moving positions are within axes bounds

Parameters:

move_dictionary (dict) – A dictionary of values required for movement. Includes ‘x_abs’, ‘y_abs’, etc. for one or more axes. Expect values in micrometers, except for theta, which is in degrees.
is_strict (bool, optional) – If True, return an empty dict if any axis is out of bounds.

Returns:

a verified moving dict {axis: abs_position}

Return type:

dict

verify_move(move_dictionary)

Don’t submit a move command for axes that aren’t moving. The Tiger controller wait time for each axis is additive.

Parameters:: move_dictionary (dict) – A dictionary of values required for movement. Includes ‘x_abs’, etc. for one or more axes. Expect values in micrometers, except for theta, which is in degrees.
Returns:: res_dict – A dictionary of values required for movement. Includes ‘x_abs’, etc. for one or more axes. Expect values in micrometers, except for theta, which is in degrees.
Return type:: dict

axes

List of stage axes available.

Type:: list

axes_mapping: Initial setting for all positions self.x_pos, self.y_pos etc are the true axis positions, no matter whether the stages are zeroed or not. All units are in microns.

device_connection

Device connection object.

Type:: Any

stage_feedback

Feedback alignment value for the stage. Default is None.

Type:: int

stage_limits

Whether the stage has limits enabled or not. Default is True.

Type:: bool