navigate.model.devices.stage.ni.NIStage

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

Bases: StageBase, NIDevice

Galvo Stage Class (only supports one axis)

Generic analog controlled stage. Could be used to control piezoelectric devices, galvos, etc. Currently set up to handle National Instruments data acquisition cards.

Retrieves the volts per micron from the configuration file and uses that to determine the correct voltage to send to the stage.

__init__(microscope_name: str, device_connection: Any, configuration: Dict[str, Any], device_id: int = 0) → None

Initialize the Galvo Stage.

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 of the stage

Methods

`__init__`(microscope_name, device_connection, ...)	Initialize the Galvo Stage.
`close`()	Close the Galvo stage.
`get_abs_position`(axis, axis_abs)	Ensure the requested position is within axis bounds and return it.
`get_position_dict`()	Return a dictionary with the saved stage positions.
`move_absolute`(move_dictionary[, wait_until_done])	Move Absolute Method.
`move_axis_absolute`(axis, abs_pos[, ...])	Implement movement logic along a single axis.
`report_position`()	Reports the position for all axes, and create position dictionary.
`stop`()	Stop all stage movement abruptly.
`switch_mode`([mode, exposure_times, sweep_times])	Switch Galvo stage working mode.
`update_waveform`(waveform_dict)	Update the waveform for the stage.
`verify_abs_position`(move_dictionary[, is_strict])	Ensure the requested moving positions are within axes bounds

Attributes

`volts_per_micron`	volts per micron scaling factor.
`axes_channels`	channel number for each axis
`galvo_max_voltage`	maximum voltage for each axis
`galvo_min_voltage`	minimum voltage for each axis
`distance_threshold`	Distance threshold for wait until delay
`stage_settle_duration`	Stage settle duration in milliseconds.
`axes_mapping`	Mapping of software axes to hardware axes.
`daq`	Hardware device to connect to.
`microscope_name`	Name of the microscope.
`configuration`	Global configuration of the microscope.
`trigger_source`	Trigger source for the DAQ.
`camera_delay`	Percent of the camera delay.
`sample_rate`	Sample rate of the DAQ.
`exposure_times`	Dictionary of exposure times for each channel.
`sweep_times`	Dictionary of sweep times for each channel.
`waveform_dict`	Dictionary of waveforms for each channel.
`ao_task`	DAQ ao task

close() → None: Close the Galvo 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_position_dict()

Return a dictionary with the saved stage positions.

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

move_absolute(move_dictionary, wait_until_done=True)

Move Absolute Method.

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 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, and create position dictionary.

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

stop(): Stop all stage movement abruptly.

switch_mode(mode='normal', exposure_times=None, sweep_times=None)

Switch Galvo stage working mode.

Parameters:

mode (str) – Name of the stage working mode Current supported modes are: confocal-projection, normal
exposure_times (dict) – Dictionary of exposure times for each channel
sweep_times (dict) – Dictionary of sweep times for each channel

update_waveform(waveform_dict)

Update the waveform for the stage.

Parameters:: waveform_dict (dict) – Dictionary of waveforms for each channel
Returns:: result – success or failed
Return type:: bool

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

ao_task

DAQ ao task

Type:: object

axes

List of stage axes available.

Type:: list

axes_channels

channel number for each axis

Type:: int

axes_mapping

Mapping of software axes to hardware axes.

Type:: dict

camera_delay

Percent of the camera delay.

Type:: float

configuration

Global configuration of the microscope.

Type:: multiprocessing.managers.DictProxy

daq

Hardware device to connect to.

Type:: object

device_connection

Device connection object.

Type:: Any

distance_threshold

Distance threshold for wait until delay

Type:: float

exposure_times

Dictionary of exposure times for each channel.

Type:: dict

galvo_max_voltage

maximum voltage for each axis

Type:: float

galvo_min_voltage

minimum voltage for each axis

Type:: float

microscope_name

Name of the microscope.

Type:: str

sample_rate

Sample rate of the DAQ.

Type:: float

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

stage_settle_duration

Stage settle duration in milliseconds.

Type:: float

sweep_times

Dictionary of sweep times for each channel.

Type:: dict

trigger_source

Trigger source for the DAQ.

Type:: str

volts_per_micron

volts per micron scaling factor.

Type:: float

waveform_dict

Dictionary of waveforms for each channel.

Type:: dict