Measurement#

class pyscan.measurement.run_info.RunInfo#

Object that contains information of how to run the experiment.

Attributes:

scan<#>: ps.PropertyScan, ps.RepeatScan, ps.FunctionScan, ps.FunctionScan: Instance of ps.AbstractScan to a scan object representing one independent experimental variable. The scan property or function will be scanned during the experiment, with scan0 being the innermost scan loop.
measuredlist: List that contains the names of collected data, defined by the measure_function return.
measure_functionfunc: User-defined function that controls how to measure data. It should accept a ps.Experiment object as its only parameter, and returns an ItemAttribute object containing the measured data. The names of the measured data, each being an attribute of the return object, will appear as keys of the experiment after it is run.
initial_pausefloat: Pause before first setting instruments in seconds, defaults to 0.1.
_pyscan_versionstr: Current version of pyscan to be saved as metadata.
(Properties)
scanslist: Returns array of all scans
dimstuple: Returns tuple containing the length of each scan, in order from scan0 to scan3, and excludes scans of size 1
average_dimstuple: Returns tuple containing the length of each scan, excluding scans of size 1 and the averaged scan
ndimint: Returns number of scans
has_average_scanbool: Returns a boolean of whether or not an average scan is present.
indiciestuple: Returns tuple of the current scan iteration indicies,
average_indiciestuple: Returns tuple of the current scan iteration indicies, excluding scans of size 1 and averaged scan.
average_indexint: Returns the index of the scan to be averaged.

Methods

check()
check_sequential_scans()
check_property_scan()
check_repeat_scan()
check_average_scan()
check_continuous_scan()

property average_dims#: Returns tuple containing the length of each scan, excluding scans of size 1 and the averaged scan

property average_index#: Returns the index of the scan to be averaged. Used by pyscan.AverageExperiment.

property average_indicies#: Returns tuple of the current scan iteration indicies, excluding scans of size 1 and averaged scan. Used by .AverageExperiment.

check()#

Checks to see if runinfo is properly formatted. Called by Experiment object’s run() methods.

Automatically sets self.average_index to the correct scan index (i.e., the scan which contains an instance of .AverageScan) to average over.

check_average_scan()#: Checks to see if there is an average scan present and sets self.average_index to the correct index.

check_property_scans()#: Checks to see if there are any errors with PropertyScans

check_repeat_scan()#: Checks to see if there a repeat scan present and if there are more the one repeat scans

property continuous_index#: Returns the index of the scan to be averaged. Used by pyscan.AverageExperiment.

property dims#: Returns tuple containing the length of each scan, in order from scan0 to scan3, and excludes scans of size 1

property has_average_scan#: Returns a boolean of whether or not an average scan is present.

property has_continuous_scan#: Returns a boolean of whether or not an continuous scan is present.

property indicies#: Returns tuple of the current scan iteration indicies,

property n_average_dim#: Returns number of scans that are neither size-1 nor average scans

property ndim#: Returns number of scans

property scans#: Returns array of all scans

Scans#

class pyscan.measurement.scans.AbstractScan(dictionary=None)#

Abstract class for different scan types. Inherits from .ItemAttribute.

Methods

`check_same_length`()	A function to be implemented by inheriting Scan classes.
`iterate`(index, devices)	A function to be implemented by inheriting Scan classes.

check_same_length()#: A function to be implemented by inheriting Scan classes.

iterate(index, devices)#: A function to be implemented by inheriting Scan classes.

class pyscan.measurement.scans.AverageScan(n_average, dt=0)#

Class for averaging inner loops.

Parameters:

n_averageint: Number of times to average data from inner loops
dtfloat: Wait time in seconds before each measurement. Used by Experiment classes, defaults to 0.

Methods

`check_same_length`()	Not used
`iterate`(expt, i, d)	Place holder, does nothing
`iterator`()	The following iterates over n

check_same_length()#: Not used

iterate(expt, i, d)#: Place holder, does nothing

iterator()#: The following iterates over n

class pyscan.measurement.scans.ContinuousScan(n_max=None, dt=0)#

Class for performing a continuous scan, which runs indefinitely or until a specified maximum number of iterations. Inherits from pyscan.measurement.scans.AbstractScan.

Parameters:

dtfloat, optional: Wait time in seconds after each iteration. Used by experiment classes, defaults to 0.
n_maxint, optional: Maximum number of iterations to run. If not specified, the scan will run indefinitely.

Methods

`iterate`(expt, i, d)	A function to be implemented by inheriting Scan classes.
`iterator`()	The following iterates over n_max if n_max is specified, otherwise it iterates indefinitely.

iterate(expt, i, d)#: A function to be implemented by inheriting Scan classes.

iterator()#: The following iterates over n_max if n_max is specified, otherwise it iterates indefinitely.

class pyscan.measurement.scans.FunctionScan(function, values, dt=0)#

Class for iterating a function with input values inside an experimental loop. Inherits from pyscan.measurement.scans.AbstractScan.

Parameters:

functionfunc: Function to be applied during each iteration. Must take a single argument representing one item in the values array. The function’s return value is not used.
valueslist: An array of values to run the function on.
dt: float: Wait time in seconds after running function once, and before the runinfo.measure_function is called. Used by experiment classes, defaults to 0.

Methods

`check_same_length`()	A function to be implemented by inheriting Scan classes.
`iterate`(expt, i, d)	Executes function(self.values[index]).
`iterator`()	The following iterates over n

check_same_length()#: A function to be implemented by inheriting Scan classes.

iterate(expt, i, d)#

Executes function(self.values[index]). Used by a Experiment class’s run() function.

Parameters:

index: The index of the values array to run the function on. The FunctionScan’s values at the given index will be the function input.
devices:: Not used

iterator()#: The following iterates over n

class pyscan.measurement.scans.PropertyScan(input_dict, prop, dt=0)#

Class for iterating a property of an intruments inside an experimental loop. Inherits from pyscan.measurement.scans.AbstractScan.

Parameters:

input_dictdict{string:array}: key:value pairs of device name strings and arrays of values representing the new prop values you want to set for each device.
propstr: String that indicates the property of the device(s) to be changed
dtfloat: Wait time in seconds after changing a single property value, and before the measure_function is called. Used by experiment classes, defaults to 0.

Methods

`check_same_length`()	Check that the input_dict has values that are arrays of the same length.
`iterate`(expt, i, d)	Changes prop of the listed devices to the value of PropertyScan's input_dict at the given index.
`iterator`()	The following iterates over n

check_same_length()#: Check that the input_dict has values that are arrays of the same length.

iterate(expt, i, d)#

Changes prop of the listed devices to the value of PropertyScan’s input_dict at the given index.

Parameters:

index – The index of the data array
devices (ItemAttribute) – ItemAttribute instance of experimental devices

iterator()#: The following iterates over n

class pyscan.measurement.scans.RepeatScan(nrepeat, dt=0)#

Class for repeating inner loops.

Parameters:

n_repeatint: Number of times to repeat inner loops.
dtfloat: Wait time in seconds after repeat. Used by experiment classes, defaults to 0.

Methods

`check_same_length`()	Not used
`iterate`(expt, i, d)	Iterates repeat loop.
`iterator`()	The following iterates over n

check_same_length()#: Not used

iterate(expt, i, d)#: Iterates repeat loop.

iterator()#: The following iterates over n

Experiments#

class pyscan.measurement.experiment.Experiment(runinfo, devices, data_dir=None)#

Experiment class that takes data after each scan0 iteration.

Parameters:

runinfops.RunInfo instance: Contains all information about the experiment
devicesItemAttribute instance: ItemAttribute instance containing all experiment devices
data_dirstr, optional: The path to save the data, defaults to ‘./backup’

Attributes:

runinfops.RunInfo: Contains all information about the experiment
devicesItemAttribute: ItemAttribute instance containing all experiment devices

Methods

# Setup methods
setup_data_dir(data_dir)
check_runinfo()
save_metadata(metadata_name)
# Data methods
preallocate(data)
reallocate(data)
rolling_average(data)
save_point(data)
# Running experiment methods
start_thread()
stop()
run()

check_runinfo()#: Function that is run at the beginning of experiment to ensure runinfo is property formatted.

preallocate(data)#

Preallocate save data based on the first value of the measurement function

Parameters:

dataItemAttribute: ItemAttribute instance containing data from self.runinfo.measure_function

reallocate(data)#

Reallocates memory for continuous experiments save files and measurement attribute arrays.

Parameters:

dataItemAttribute: ItemAttribute instance containing data from self.runinfo.measure_function

rolling_average(data)#

Does a rolling average of newly measured data

Parameters:

data: ItemAttribute instance of newly measured data point

save_metadata(metadata_name)#

Formats and saves metadata to the hdf5 file

Parameters:

metadata_namestr: Name of the metadata to be saved, ex. “runinfo”, “devices”

save_point(data)#: Saves single point of data for current scan indicies. Does not return anything.

setup_data_dir(data_dir)#

Creates save directory if it does not exist

Parameters:

data_dirstr, optional: Path to save the data, defaults to ‘./backup’

start_thread()#: Starts experiment as a background thread, this works in conjunction with live plot

stop()#: Stops the experiment after the next data point is take ensuring that the data is saved properly. Sets the associated runinfo.complete setting to ‘stopped’ and runinfo.running to False.

pyscan.measurement.load_experiment.find_measured_datasets(runinfo, all_datasets)#

HDF5 files contain two types of datasets. Measured datasets are data from the measure_function, and while running a list of measured datasets is included in runinfo.measured. Pyscan generated datasets are created when the experiment runs. This function identifies the generated dataset from each scan.

Returns:: List of datasets generated by pyscan.

pyscan.measurement.load_experiment.load_experiment(file_name)#

Function to load experimental data created by pyscan

Parameters:

file_namestr: Path to file that is to be loaded