routines

Routines

A set of common, useful stage operations implemented using common calls from abstracted motors and auxiliary devices. In theory, setups utilizing different hardware should be able to use the same routines without any modification.

Using this module, you can

• define routines that take advantage of abstracted objects like a "stage" or a "data acquisition unit".
• reuse routines even with different hardware, given they implement the interfaces defined in autogator.hardware

It is easy to write your own routines that will work regardless of the hardware available. This makes them reusable between different setups. Routines are written to be functional, rather than object oriented. They usually accept as parameters preconfigured classes with a known API, such as a Stage, a Laser, or a DataAcquisitionUnitBase. The routine doesn't do any configuration on such objects; they should be passed in preconfigured.

auto_calibration_callback(stage, daq, circuit, controller)

Moves to the specified circuit and optimizes alignment.

Parameters:

Name	Type	Description	Default
stage	Stage	The stage to move.	required
daq	DataAcquisitionUnitBase	The DAQ to use for data acquisition.	required
circuit	Circuit	The circuit being moved to for calibration.	required
controller	KeyboardControl	The controller to use for control input.	required

auto_scan(stage, daq, stage_x=None, stage_y=None, gds_x=None, gds_y=None, stage_center=None, gds_center=None, span=0.06, step_size=0.005, step_size_x=None, step_size_y=None, plot=False, settle=0.2)

Performs a box scan of given dimensions and then refines the scan around the peak.

The stage always moves to the max position upon completion of this function.

You must specify one of the following sets of parameters: * stage_x and stage_y * gds_x and gds_y * stage_center and span * gds_center and span * span (with center not specified, centers assumes current location)

Additionally, you must specify one of the following parameter sets: * step_size * step_size_x and step_size_y

Parameters:

Name	Type	Description	Default
stage	Stage	The stage object that provides access to the hardware.	required
daq	DataAcquisitionUnitBase	The preconfigured data acquisition unit to use for taking measurements. This function repeatedly calls the func:DataAcquisitionUnitBase.measure method to acquire scan data.	required
stage_x	Tuple[float, float]	The x-coordinate span of the stage to scan, in motor units, from smallest value to largest.	None
stage_y	Tuple[float, float]	The y-coordinate span of the stage to scan, in motor units, from smallest value to largest.	None
gds_x	Tuple[float, float]	The x-coordinate span of the GDS to scan, from smallest value to largest.	None
gds_y	Tuple[float, float]	The y-coordinate span of the GDS to scan, from smallest value to largest.	None
stage_center	Tuple[float, float]	The (x, y) center of the scan, in motor units.	None
gds_center	Tuple[float, float]	The (x, y) center of the scan, in GDS coordinates.	None
span	float	The width of the scan. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If neither is defined, then this is in motor units. The span is from the center ± span/2.	0.06
step_size	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If set, step_size is equal for both x and y axes.	0.005
step_size_x	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. Use this parameter to set a different step size for the x-axis.	None
step_size_y	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. Use this parameter to set a different step size for the y-axis.	None
plot	bool	Whether to plot the scan data (default False).	False
settle	float	Amount of time in seconds the motors will pause in between move commands to allow for settling time (lets vibration/residual motion die out) and improve data reliability (default 0.2).	0.2

Returns:

Type	Description
Tuple[float, float]	The position of the highest reading in the motor coordinate system.

basic_scan(stage, daq, stage_x=None, stage_y=None, gds_x=None, gds_y=None, stage_center=None, gds_center=None, span=None, span_x=None, span_y=None, step_size=None, step_size_x=None, step_size_y=None, plot=False, settle=0.2)

Performs a box scan of given dimensions and goes to position of highest readings returned.

You must specify one of the following sets of parameters: * stage_x and stage_y * gds_x and gds_y * stage_center and span * gds_center and span * span (with center not specified, center assumes current location) * span_x and span_y (with center not specified, center assumes current location)

Additionally, you must specify one of the following parameter sets: * step_size * step_size_x and step_size_y

Parameters:

Name	Type	Description	Default
stage	Stage	The stage object that provides access to the hardware.	required
daq	DataAcquisitionUnitBase	The preconfigured data acquisition unit to use for taking measurements. This function repeatedly calls the func:DataAcquisitionUnitBase.measure method to acquire scan data.	required
stage_x	Tuple[float, float]	The x-coordinate span of the stage to scan, in motor units, from smallest value to largest.	None
stage_y	Tuple[float, float]	The y-coordinate span of the stage to scan, in motor units, from smallest value to largest.	None
gds_x	Tuple[float, float]	The x-coordinate span of the GDS to scan, from smallest value to largest.	None
gds_y	Tuple[float, float]	The y-coordinate span of the GDS to scan, from smallest value to largest.	None
stage_center	Tuple[float, float]	The (x, y) center of the scan, in motor units.	None
gds_center	Tuple[float, float]	The (x, y) center of the scan, in GDS coordinates.	None
span	float	The width of the scan. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If neither is defined, then this is in motor units. The span is from the center ± span/2.	None
span_x	float	The width of the scan in the x-direction. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If neither is defined, then this is in motor units. The span is from the center ± span_x/2.	None
span_y	float	The width of the scan in the y-direction. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If neither is defined, then this is in motor units. The span is from the center ± span_y/2.	None
step_size	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. If set, step_size is equal for both x and y axes.	None
step_size_x	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. Use this parameter to set a different step size for the x-axis.	None
step_size_y	float	Jog step size motors will use when iterating through the box. Units are derived from context; if stage_center is defined, this is in motor units. If gds_center is defined, this is in GDS coordinates. Use this parameter to set a different step size for the y-axis.	None
plot	bool	If a windowed plot is generated displaying data returned from scan. If True, matplotlib will be used to generate and open the plot (default False).	False
settle	float	Amount of time in seconds the motors will pause in between move commands to allow for settling time (lets vibration/residual motion die out) and improve data reliability (default 0.2).	0.2

Returns:

Type	Description
Tuple[float, Tuple[float, float]]	The value of the data acquisition unit at the position of the highest reading, and the position of that reading in the coordinate system defined by the context.

calibrate(stage, daq, circuits, callback, controller=None)

Calculates the calibration for converting from hardware coordinates to GDS coordinates.

Parameters:

Name	Type	Description	Default
stage	Stage	The stage device to use for calibration.	required
daq	DataAcquisitionUnitBase	The configured data acquisition unit (or class that inherits from class:DataAcquisitionUnitBase) to use for calibration.	required
circuits	List[autogator.circuits.Circuit]	The three calibration circuits.	required
callback	Callable	A callback function used to optimize at each point. Could be an automatic scan or a function that interacts with the user. It should block until the stage has settled on a point, but it does not need to return anything; the settled point location will be obtained from the Stage object. It should accept the following parameters, in the corresponding order: - stage: The stage object to use for calibration. - daq: The data acquisition unit to use for calibration. - circuit: The circuit currently being referenced for calibration. - controller: The controller to use for control input.	required

Returns:

Type	Description
ndarray	The affine transformation matrix that converts from hardware coordinates to GDS coordinates.

line_scan(stage, daq, axis, start, step_size=0.0005, settle=0.2, iterations=15, plot=False)

Performs a line scan of the specified axis.

You should only employ a linear scan if you're already picking up light, as it is intended to take very small steps and will therefore be very slow. Additionally, it will automatically terminate the scan if it goes iterations steps without finding a new maximum. This is intended to stop scanning if you're starting to leave the area of interest.

Parameters:

Name	Type	Description	Default
stage	Stage	The stage to move.	required
daq	DataAcquisitionUnitBase	The data acquisition unit to use.	required
axis	str	The axis to move. Must be one of 'x', 'y', or 'z'.	required
start	float	The starting position of the scan.	required
step_size	float	The step size of the scan (default 0.0005 microns).	0.0005
settle	float	The time to wait after each move in seconds before taking a reading (default 0.2).	0.2
iterations	int	The number of moves to take without finding a new maximum before terminating the scan (default 15).	15
plot	bool	Whether to plot the data (default False).	False

Returns:

Type	Description
float	The location of the maximum in the motor's units.