navigate.model.devices.stages.synthetic.SyntheticStage

class navigate.model.devices.stages.synthetic.SyntheticStage(microscope_name: str, device_connection: Optional[Any], configuration: Dict[str, Any], device_id: int = 0)

Bases: StageBase

Synthetically generated stage for testing purposes.

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

Initialize the stage.

Parameters:

• microscope_name (str) – Name of the microscope.

• device_connection (str) – Connection string for the device.

• configuration (dict) – Configuration dictionary for the device.

• device_id (int) – Device ID for the device.

Methods

__init__(microscope_name, device_connection, ...)	Initialize the stage.
close()	Close the stage.
get_abs_position(axis, axis_abs)	Ensure the requested position is within axis bounds and return it.
get_axis_position(axis)	Get the current position of the stage along a single axis.
get_position_dict()	Return a dictionary with the saved stage positions.
get_speed(axis)	Get the speed of the stage.
load_sample()	Load a sample.
move_absolute(move_dictionary[, wait_until_done])	Move stage along a single axis.
move_axis_absolute(axis, abs_pos[, ...])	Implement movement logic along a single axis.
report_position()	Report the current position of the stage.
scanr(start_position_mm, end_position_mm, ...)	Scan the stage using the constant velocity mode along a single axis.
set_speed(velocity_dict)	Set the speed of the stage.
start_scan(axis)	Start a scan along a single axis.
stop()	Stop all stage movement abruptly.
stop_scan()	Stop a scan.
unload_sample()	Unload a sample.
update_waveform(waveform_dict)
verify_abs_position(move_dictionary[, is_strict])	Ensure the requested moving positions are within axes bounds

Attributes

default_speed	The default speed of the stage in mm/s.
axes_mapping	Dictionary mapping software axes to hardware axes.

close()

Close the stage.

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 the current position of the stage along a single axis.

Parameters:

axis (str) – An axis. For example, ‘x’, ‘y’, ‘z’, ‘f’, ‘theta’.

Returns:

The current position of the stage along the specified axis.

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 the speed of the stage.

Parameters:

axis (str) – An axis. For example, ‘x’, ‘y’, ‘z’, ‘f’, ‘theta’.

Returns:

The speed of the stage along the specified axis.

Return type:

float

load_sample()

Load a sample.

Warning

Not implemented.

move_absolute(move_dictionary, wait_until_done=False)

Move stage along a single axis.

Parameters:

• move_dictionary (dict) – A dictionary of values required for movement. Includes ‘x_abs’, etc. for one or more axes. Expects 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)

Implement movement logic along a single axis.

Parameters:

• axis (str) – An axis. For example, ‘x’, ‘y’, ‘z’, ‘f’, ‘theta’.

• 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()

Report the current position of the stage.

Returns:

position_dict – Dictionary containing the current position of the stage.

Return type:

dict

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

Scan the stage using the constant velocity mode along a single axis.

Parameters:

• start_position_mm (float) – Starting position of the scan in mm.

• end_position_mm (float) – Ending position of the scan in mm.

• enc_divide (int) – Encoder divide value.

• axis (str) – An axis. For example, ‘x’, ‘y’, ‘z’, ‘f’, ‘theta’.

set_speed(velocity_dict)

Set the speed of the stage.

Parameters:

velocity_dict (dict) – Dictionary containing the speed of the stage along each axis.

start_scan(axis)

Start a scan along a single axis.

Parameters:

axis (str) – An axis. For example, ‘x’, ‘y’, ‘z’, ‘f’, ‘theta’.

stop()

Stop all stage movement abruptly.

stop_scan()

Stop a scan.

unload_sample()

Unload a sample.

Warning

Not implemented.

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

axes

List of stage axes available.

Type:

list

axes_mapping

Dictionary mapping software axes to hardware axes.

Type:

dict

default_speed

The default speed of the stage in mm/s.

Type:

float

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