lyse.Sequence

class lyse.Sequence(h5_path, run_paths, no_write=False)

Bases: lyse.Run

__init__(h5_path, run_paths, no_write=False)

Generic results storage that is not associated with a specific Run.

This is typically used to save results from a multi-shot analysis to an independent h5 file.

Parameters

• h5_path (str) – Path to h5 file to save to. If file does not exist, will try to create it assuming no_write=False. If file exists, opens a handle to it.

• run_paths (list or pandas.DataFrame) – List of runs to associate with the sequence. If a dataframe is supplied, will introspect the runs from the 'filepath' data.

• no_write (bool, optional) – If True, opens file in read-only mode.

Raises

PermissionError – If trying to create a file in read-only mode.

Methods

__init__(h5_path, run_paths[, no_write])	Generic results storage that is not associated with a specific Run.
get_all_image_labels()	Return all existing images labels in the h5 file.
get_attrs(group)	Returns all attributes of the specified group as a dictionary.
get_globals([group])	Get globals from the shot.
get_globals_expansion()	Get the expansion type of each global.
get_globals_raw([group])	Get the raw global values from the shot.
get_image(*args)	Not implemented!
get_image_attributes(orientation)	Return the attributes of a saved orientation image group.
get_images(orientation, label, *images)	Get multiple saved images from orientation and label.
get_images_dict(orientation, label, *images)	Get multiple saved images from orientation and label.
get_result(group, name)	Retrieve result from prior calculation.
get_result_array(*args)	Get the specified result array from each run in the sequence.
get_result_arrays(*args)	Not implemented!
get_results(group, *names)	Return multiple results from the same group.
get_trace(*args)	Get the named trace from each run in the sequence.
get_traces(*args)	Not implemented!
get_units([group])	Get the units of globals.
get_wait(name)	Returns the wait paramteres: label, timeout, duration, and time out status.
get_waits()	Returns the parameters of all waits in the experiment.
globals_diff(other_run[, group])	Take a diff between this run and another run.
globals_groups()	Get names of all the globals groups.
open(mode)	Context manager to open the Run's h5 file for successive reads/writes.
save_result(name, value[, group, overwrite])	Save a result to the hdf5 file.
save_result_array(name, data[, group, ...])	Save an array of data to the hdf5 h5 file.
save_result_arrays(*args, **kwargs)	Save multiple result arrays.
save_results(*args, **kwargs)	Save multiple results to the hdf5 file.
save_results_dict(results_dict[, uncertainties])	Save results dictionary.
set_group(groupname)	Set the default hdf5 file group for saving results.
trace_names()	Return a list of all saved data traces in Run.

Attributes

group	The group in the hdf5 file in which results are saved by default.
h5_file	opened h5py file handle for the shot
h5_path	The value provided for h5_path during instantiation.
no_write	The value provided for no_write during instantiation.

get_image(*args)

Not implemented!

Attention

Not implemented, but could be.

get_result_array(*args)

Get the specified result array from each run in the sequence.

Parameters

*args (str) – Passed directly to get_result_array. Should be group and name to result to obtain.

Returns

Dictionary of path:result pairs for each run.

Return type

dict

get_result_arrays(*args)

Not implemented!

Attention

Not implemented, but could be.

get_trace(*args)

Get the named trace from each run in the sequence.

Parameters

*args (str) – Name of trace. Passed directly to get_trace.

Returns

Dictonary of path:trace pairs for each run.

Return type

dict

get_traces(*args)

Not implemented!

Attention

Not implemented, but could be.