API Documentation¶

API reference for the module.

Table of Contents¶

File I/O ¶

Functions for file I/O.

NWB & Custom file I/O ¶

`save_nwbfile`(nwbfile, file_name[, folder])	Save out an NWB file.
`load_nwbfile`(file_name[, folder, return_io])	Load an NWB file.
`save_config`(cdict, file_name[, folder])	Save out a config file.
`load_config`(file_name[, folder])	Load an individual config file.
`load_configs`(files[, folder])	Load all configs together.
`save_object`(custom_object, file_name[, folder])	Save a custom object.
`load_object`(file_name[, folder])	Load a custom object.

General file I/O ¶

`save_txt`(text, file_name[, folder])	Save out text to a txt file.
`load_txt`(file_name[, folder])	Load text from a txt file.
`save_json`(data, file_name[, folder])	Save out a dictionary of data to a JSON file.
`load_json`(file_name[, folder])	Load from a JSON file.
`save_jsonlines`(data, file_name[, folder])	Save out data to a JSONlines file.
`load_jsonlines`(file_name[, folder])	Load from a JSON lines file.
`load_matfile`(file_name[, folder, version])	Load a .mat file.
`load_jsons_to_df`(files[, folder])	Load a collection of JSON files into a dataframe.
`open_h5file`(file_name[, folder, mode, ext])	Context manager to open a HDF5 file.
`save_to_h5file`(data, file_name[, folder, ext])	Save data to a HDF5 file.
`load_from_h5file`(fields, file_name[, ...])	Load one or more specified field(s) from a HDF5 file.

Utilities ¶

`get_files`(folder[, select, ignore, ...])	Get a list of files from a specified folder.
`get_subfolders`(folder[, select, ignore])	Get a list of sub-folders from a given folder.
`make_session_name`(subject, experiment, session)	Create a standardized session name.
`make_file_list`(experiment, files[, ext])	Make a list of subject files.

Validate Functions ¶

validate_nwb(file_name[, folder, ...])

Validate a NWB file.

NSP ¶

Functionality related to NSP (Neural Signal Processors).

I/O ¶

load_blackrock(file_name, folder[, ...])

Load a set of Blackrock files.

Checks ¶

check_blackrock_file_info(reader)

Check some basic information and metadata from a set of Blackrock files.

Objects ¶

Custom objects.

Electrodes ¶

Electrodes([subject, fs])

Object for collecting / managing electrode information.

TaskBase ¶

TaskBase()

Base object for collecting task information.

Paths ¶

Path management.

Paths Object ¶

Paths(project_path[, subject, experiment, ...])

Paths object for a session of single-unit data.

Directory Creators ¶

`make_folder`(path)	Make a folder, if it does not already exist.
`create_project_directory`(base_path, project)	Create the folder structure for a project.
`create_subject_directory`(project_path, subject)	Create the folder structure for a subject.
`create_session_directory`(project_path, ...)	Create the folder structure for a session of data.

Plots ¶

Plotting functions and utilities.

Timestamps ¶

`plot_alignment`(sync1, sync2[, n_pulses, ax])	Plot the alignment between synchronization pulses.
`plot_peaks`(data, peak_inds, peak_heights[, ax])	Plot detected peaks on a time series.

Timestamps ¶

Functions and helpers for managing timestamps and temporal alignment.

Alignment ¶

`fit_sync_alignment`(sync_behav, sync_neural)	Fit a model to align synchronization pulses from different recording systems.
`predict_times`(times, intercept, coef)	Predict times alignment from model coefficients.
`predict_times_model`(times, model)	Predict times alignment from a model object.
`match_pulses`(sync_behav, sync_neural, n_pulses)	Match pulses to each other based on ISIs.

Peaks ¶

detect_peaks(data, fs, height[, distance, ...])

Process peaks from a time series.

Update ¶

`offset_time`(times, offset)	Apply an offset to timestamps.
`change_time_units`(times, value[, operation])	Change the units of timestamps.
`change_sampling_rate`(times, fs_from, fs_to)	Change the effective sampling rate for a set of times values.

Utils ¶

`convert_samples_to_time`(n_samples, fs[, output])	Convert a number of samples to corresponding time length.
`create_timestamps_from_samples`(samples, fs)	Create a set of timestamps for a set of samples.

Sorting ¶

Spike sorting related functionality.

I/O ¶

`load_spike_data_file`(channel, folder, polarity)	Load a spike detection output file from Combinato - files with the form data_chan_XX.h5.
`load_sorting_data_file`(channel, folder, ...)	Load a combinato sorting output file - files with the file name sort_cat.h5.
`save_units`(units, folder)	Save out units information.
`load_units`(folder)	Load a set of units files from a folder.

Processing ¶

`collect_all_sorting`(spike_data, sort_data)	Collect together all the organized spike sorting information for a channel of data.
`process_combinato_data`(channel, ...[, ...])	Helper function to run the process of going from combinato -> extracted units files.

Utilities ¶

`get_group_labels`(class_labels, groups)	Get the group label for each spike (based on spike class + group mapping).
`get_sorting_kept_labels`(groups)	Get the valid clas / group information from the combinato organized groups info array.
`extract_clusters`(data)	Extract individual clusters from a channel of data.

Utils ¶

Utilities & helper functions.

Check Functions ¶

`is_empty`(var)	Check if a variable is empty, across possible types.
`is_type`(var, var_type)	Check is a variable is of the given type(s).
`check_str_contents`(str_to_check, contents)	Check whether a given string has specified contents.
`clean_strings`(lst)	Helper function to clean a list of string values for adding to NWB.

Convert Functions ¶

`convert_str_to_bool`(string)	Convert a string to a boolean.
`convert_strlist_to_bool`(lst)	Convert a list of strings to a list of boolean.
`convert_type`(variable, dtype)	Convert type of a given variable.
`convert_to_array`(data, dtype)	Convert to an array of specified data type.
`convert_time_to_date`(timestamp[, tz])	Convert a time value to a datetime date.

Extract Functions ¶

`get_event_time`(event_times, start, end)	Select a (single) event based on time range, returning NaN if not found.
`get_trial_value`(trials, data, trial[, dtype])	Extract a value for a specified trial.

Log Functions ¶

print_status(verbose, message[, level])

Print a status update.

Run Functions ¶

catch_error(proceed, name, path[, verbose, ...])

Catch a raised error, with the option to save an error log and proceed.

Tool Functions ¶

`incrementer`([start, end])	Generator that returns an incrementing index value.
`get_current_date`([tz])	Get the current datetime.