Cheat Sheet

Open mkpy.mkh5 .h5 file for read/write

mkh5()

establish a read/write connection to the .h5 database file for subsequent operations

Load .crw/.log into a mkpy .h5 file

create_mkdata()

start a new data group with .crw, .log and .yhdr extended header YAML data, e.g., single subject, single session EEG recordings.

append_mkdata()

append .crw, .log to an existing data group, e.g., to add separate calibration pulse .crw/.log files or combine split-session recordings.

Align EEG recordings with other experimental variables

YAML header files: .yhdr

Extend the recorded EEG header with arbitrary data (JSON key: value), e.g., individual subject, session, attributes.

Event codemap files: .xlsx, .ytbl, .txt

Tag recorded event codes with arbitrary variables based on event code sequence patterns, e.g., single trial item attributes.

codemap cheat sheet
YAML header data extractors: .yhdx

extract key:value from the HDF5 dblock headers as column:values in the event data table

get_event_table()

look up and tag single-trial event codes and event code sequences with imported experimental variables in a data table format.

set_epochs()

write the single-trial tagged EEG epoch lookup table to the mkh5 file

Exporting EEG and event data for analysis

export_event_table()

write out tabular event data in tab-separated text (.txt) or feather binary data interchange format (.fthr).

export_epochs_table()

write out tabular epochs data in tab-separated text (.txt) or feather binary data interchange format (.fthr).

export_epochs() write out single trial EEG

data epochs defined by the epochs data table as 1-D vectors of compound data types in HDF5 (.h5) or with pandas.DataFrame writers to HDF5 (.pdh5), feather (.fthr) binary data interchange formats or as tab-separated text (.txt)

Data inspection and visualization

pygarv()

EEG data and artifact dashboard

pygarv_all_views

pygarv dashboard

plotcals()

butterfly plot the single trial cal pulses that will be used to scale .crw A/D values to microvolts given the parameters

plot_cals

plot_cals

headinfo()

report contents of datablock headers in the .h5 database, optionally filtered by regular expression pattern match

info()

report contents of datablock headers and snippets of data for all of the datablocks, c.f., HDF5 utility h5ls -rds

calibrate_mkdata()

scale .crw A/D digtized EEG to microvolts