README.md

+io

Matlab package for input/output conventional consistency.

Install

Once this has been added as a submodule to a given repository, you can then run io.setup to install other required repos:
(From the command window)

io.setup;

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 repository as:

git submodule add git@github.com:Neuro-Mechatronics-Interfaces/matlab_package__io.git +io

This will add the folder with the correct package name.

Contents

• Classes
• Primary Functions
• Exporters
• General Utility
• GUIs
• Impedance-Handling
• Intan-Specific
• LSL-Specific
• Message-Capture
• Microdrive-Specific
• Stimulation-Experiment-Specific
• ROS2-Specific
• TMSi-Specific
• Wrist-Task-Specific
• Installer (may be deprecated)

Classes

• JSON - Class to access contents of JSON file.
• TimeoutEventData - Issued as part of a timer callback event.

Primary Functions

• load_data - API access-point for loading TMSi or Intan HD-EMG data.
• load_tmsi - API access-point for load_tmsi_mat or load_tmsi_raw.
• load_spikes - Load spikes that have been exported via batch pipeline.

Exporters

• configure - Write and return configuration JSON object for a given session.
• write_wrist_xy_2_sto - Write data from wrist task into .sto format for OpenSim.

General Utility

• load_muscle_map - Loads JSON muscle map object.
• load_sync - Loads processed sync data.
• new - Open new m-file with both documented and dynamical headers.
• parse_about - Parse about.yaml in notes of raw_data for a given tank.
• quick_selector_gui - Blocking function to manually select key experiment parameters (for constructor).

GUIs

• quick_selector_gui - Blocking function to manually select key experiment parameters (for constructor).

Impedance-Handling

• load_impedance - Load impedance if it's been parsed in generated_data.
• load_nanoz - Loads electrode impedances table struct for NanoZ measurements.
• process_raw_impedances - Process impedances from "raw" format.

Intan-Specific

• convert_intan_data_2_tmsi_format - Convert Intan data to TMSi format.
• load_intan - Reader entry point for INTAN data files.
• read_Intan_RHD2000_file - Reads Intan RHD data format files into MATLAB.

LSL-Specific

• load_xdf - Import an XDF file.

Message-Capture

• load_uevt - Load .uevt file (which contains wrist task behavior events).
• pcap2matlab - Imports network protocol analyzer capabilties into MATLAB.
• read_events - Reads in "events-export.csv" file for a given session.

Microdrive-Specific

• load_trec_depth - Loads timetable with TREC drive depth information.

Stimulation-Experiment-Specific

• load_block_hd_emg - Loads processed data block.
• load_block_simulation - Loads simulated field data associated with a given experimental block.
• load_percept_data - Load percept yaml data for a given subject collected using perceptMapper variant for N3 analyses.

ROS2-Specific

• load_rosbag - Loads data saved in raw_data in .mat format after parsing from .db3 bag files.

TMSi-Specific

• convert_intan_data_2_tmsi_format - Convert Intan data to TMSi format.
• load_align_saga_data - Loads data from 2 TMSi-SAGA and aligns samples.
• load_tmsi - API access-point for load_tmsi_mat or load_tmsi_raw.
• load_tmsi_channel - Loads TMSi channel if it has been parsed.
• load_tmsi_mat - Loads "raw" data block that was saved via TMSiServer MATLAB API.
• load_tmsi_potentiometers - Loads ISO AUX-1 and ISO AUX-2 (potentiometers).
• load_tmsi_raw - Loads raw data block.
• load_tmsi_triggers - Loads TMSi sync triggers if they have been parsed.
• parse_polybench_data_manager_notes - Parse notes taken in Polybench Data Manager.

Wrist-Task-Specific

• load_aligned_target_data - Loads target-aligned data.
• load_combined - Load spikes that have been clustered across all trials and combined with cluster index indicator, as exported via batch pipeline.
• load_cursor - Loads timetable with TREC drive depth information.
• load_task - Load task state machine.
• load_uevt - Load .uevt file (which contains wrist task behavior events).
• load_wrist_event_table_trial - Load a wrist center-out task trial from event table.
• load_wrist_task_parameters - Import logging parameters for a given subject.
• load_wrist_task_parsed_logs - Load parsed position/logs/header data.
• load_wrist_task_training_summary - Reads table of training history.
• load_wrist_task_raw_logs - Import data from a text file.
• load_wrist_task_trial_data - Import data from a trial .txt file.
• load_wrist_task_trial_logs - Import data from trial .logs file.
• parse_cursor - Import data from a text file.
• parse_wrist_task_position_parameters - Returns parameters table associated with Position timetable.
• parse_wrist_task_trials - Return Trial timetable from Logs timetable.
• parse_wrist_task_txt_header - Parse header of TrialData.txt file.
• save_parsed_wrist_task_logs - Save parsed behavioral logging to generated_data on server.
• save_wrist_task_trial_data - Saves trial data to generated data location on server.
• uevt_2_behavior_data - Convert .uevt files to basic behavior data tables.

Installer

• batch_import_modules - Use repos struct to init a bunch of git submodules.
• batch_import_repos - Use repos struct to clone bunch of git repos.
• read_repos_list - Get list of all repos in .repos file.
• setup - Can run this to automatically get dependencies of +io package via git.