NeuroAnalyzer Preferences

Preferences control how NeuroAnalyzer behaves: which messages are shown, whether progress bars are displayed and whether channels marked as bad are used in analyses. They are stored with Preferences.jl, so they persist between Julia sessions.

Available preferences

Preference	Default	Function	Effect
verbose	true	set_verbose()	show NeuroAnalyzer info and warning messages
progress_bar	true	set_progress_bar()	show progress bars in long-running functions
exclude_bads	false	set_exclude_bads()	skip channels marked as bad when channels are selected
colors	true	set_colors()	print messages in color

Each function takes true or false. The new value takes effect immediately and is saved, so it is also used in the next sessions.

Viewing the current settings

info() shows the current preferences together with the NeuroAnalyzer and Julia versions, the plugins and resources paths, the number of threads and the versions of the installed packages:

info()

The preferences are also listed when NeuroAnalyzer is loaded.

Changing preferences

One at a time:

set_verbose(false)       # hide info and warning messages
set_progress_bar(false)  # hide progress bars
set_exclude_bads(true)   # skip bad channels
set_colors(false)        # plain (uncolored) messages

All at once (all four keyword arguments are required):

set_prefs(verbose = true,
          progress_bar = true,
          exclude_bads = false,
          colors = true)

Notes

verbose

With verbose = false, messages printed by NeuroAnalyzer functions ([ Info: …, [ Warning: …) are hidden. Errors are always shown, and so are messages printed by Julia or by other packages (e.g. the messages shown when NeuroAnalyzer is loaded).

Tip: Warnings often explain why a result may be unexpected (e.g. a filter cutoff adjusted to the Nyquist frequency); turn verbose off only for well-tested scripts.

progress_bar

Progress bars are shown by functions that process many channels, epochs or frequencies (e.g. filtering, ICA, spectrograms, ITPC, bootstrapping). Turn them off when the output is written to a log file, where each update of the bar adds a line.

exclude_bads

Channels are marked as bad in obj.header.recording[:bad_channel], e.g. by channel_reject!() or manually. With exclude_bads = true, these channels are left out whenever channels are selected with the ch argument (e.g. ch = "eeg"), so they do not enter analyses or plots. With exclude_bads = false (default), bad channels are only marked and are used like any other channel.

To leave out channels in a single call regardless of this preference, list the channels to use in ch.

colors

Colored messages are easier to read in a terminal; turn colors off if the terminal or log viewer shows escape codes (e.g. [36m) instead of colors.

Where preferences are stored

Preferences are saved in the LocalPreferences.toml file next to the Project.toml of the active Julia environment, e.g. ~/.julia/environments/v1.12/LocalPreferences.toml for the default environment:

[NeuroAnalyzer]
verbose = true
progress_bar = false
exclude_bads = false
colors = true

Each project environment has its own preferences, so different projects can use different settings. Deleting the [NeuroAnalyzer] section restores the defaults.