NHP_Matlab_Utilities

Note: this repo must be added as a submodule named +utils for most of the functions to work together properly. Matlab package containing miscellaneous utility functions such as file-transfer shortcuts or random math functions.

Install

You should be in the repository folder that is the parent repo of this submodule, which should be added as a MATLAB package (i.e. with the leading + in the name of the submodule folder). For example, add it to your workspace repository as:

git submodule add git@github.com:Neuro-Mechatronics-Interfaces/NHP_MATLAB_Utilities.git +utils

This will add the folder with the correct package name. Adding +utils to the end of the git submodule add command is critical for making sure the functions work together properly.

Contents

Filtering Functions

• add_sd_threshold - Adds yline threshold to plot using pre-stimulus data.
• apply_emg_filters - Apply filtering to EMG signal in data struct x.
• get_default_filtering_pars - Return default filtering parameters struct.
• get_filtering_label_string - Returns string to indicate what filtering was done.
• ordered_emg_filters - Apply filtering to EMG signal in data struct x according to a specific order of operations.

Math

• interpsmooth - This function interpolates and smoothes a curve onto data points.
• NEO - Returns the nonlinear energy operator (NEO) for signal X.
• SNEO - Returns the smoothed nonlinear energy operator (SNEO) for signal X.

Parsers

• tmsi_folder_2_datetime - Convert TMSi folder timestring to datetime.
• tmsi_header_2_datetime - Convert TMSi header start_time field to datetime.
• parse_artifact_sync - Outputs a vector of trigger events that match up with logic parsed from a threshold set under the assumption that the input is a vector with large stimulus-related artifacts in it.
• parse_date_args - Parse date input arguments.
• parse_bit_sync - Outputs a vector of trigger events that match up with the bit value from sync_bit. Accepts either a struct or vector.
• parse_parameters - Parses input parameters given a default struct.
• parse_polybench_data_manager_notes - Parse notes taken in Polybench Data Manager.
• parse_uevt_trials - Parse table from io.load_uevt, identifying trial metadata.
• parse_xml - Convert XML file to a MATLAB structure.
• parse_xy_grid_vec - Parses xy grid to encapsulate values in x and values in y.
• parameters - Return parameters struct, which sets default values for things like epoch durations etc.

Handling NML Data Structures

• apply_debounce - Debounce vector of sample times so that each is separated by at least min_sample_interval samples.
• export_emg_for_muedit - export_emg_for_muedit(data, fsamp, nChan, ngrid, gridname, muscle) Exports matfile for MUedit app.
• generate_output_container_folder - Generate output folder (windows-like) path-string.
• get_block_name - Return the string info corresponding to a given block.
• get_subj_query - Return the subject-info args for most "load" and "plot" queries, given the subject query struct.
• print_timing_info - Prints total time for a given function to run.
• print_windows_folder_link - Print or return string to link to windows folder(s).
• transfer_plexon_files - Transfer files from local location to remote data share.
• patch_2_struct - Convenience function to convert patch handle to struct.

Typesetting and Formatting Text

• showModelInfo - Print model info and optionally make figure for covariances.
• contents_report_2_markdown - Convert Contents.m MATLAB index file into formatted Contents for README.md.
• fixCase - Fixes the input string so first character in string is capitalized and rest are lower-case.
• get_tmsi_stim_data - Return stim data specifically for TMSi blocks.
• print_model_info - Prints sfit object model coefficients in Command Window, or to a text file ID (if specified).
• pattern_name_to_metadata - Helper function to convert pattern files to metadata struct.
• save_figure - Exports figure in desired file formats, creating output folder if needed.