ravepipeline (version 0.0.1)

raveio-option: Set/Get 'RAVE' option

Description

Persist settings on local configuration file

Usage

raveio_setopt(key, value, .save = TRUE)
raveio_resetopt(all = FALSE)
raveio_getopt(key, default = NA, temp = TRUE)
raveio_confpath(cfile = "settings.yaml")

Value

raveio_setopt returns modified value; raveio_resetopt returns current settings as a list; raveio_confpath returns absolute path for the settings file; raveio_getopt returns the settings value to the given key, or default if not found.

Arguments

key

character, option name

value

character or logical of length 1, option value

.save

whether to save to local drive, internally used to temporary change option. Not recommended to use it directly.

all

whether to reset all non-default keys

default

is key not found, return default value

temp

when saving, whether the key-value pair should be considered temporary, a temporary settings will be ignored when saving; when getting options, setting temp to false will reveal the actual settings.

cfile

file name in configuration path

Side-Effects

The following options will alter other packages and might cause changes in behaviors:

'disable_fork_clusters'

This option will change the options 'dipsaus.no.fork' and 'dipsaus.cluster.backup', which handles the parallel computing

'threeBrain_template_subject'

This option will set and persist option 'threeBrain.template_subject', which changes the default group-level template brain.

Details

raveio_setopt stores key-value pair in local path. The values are persistent and shared across multiple sessions. There are some read-only keys such as "session_string". Trying to set those keys will result in error.

The following keys are reserved by 'RAVE':

data_dir

Directory path, where processed data are stored; default is at home directory, folder ~/rave_data/data_dir

raw_data_dir

Directory path, where raw data files are stored, mainly the original signal files and imaging files; default is at home directory, folder ~/rave_data/raw_dir

max_worker

Maximum number of CPU cores to use; default is one less than the total number of CPU cores

mni_template_root

Directory path, where 'MNI' templates are stored

raveio_getopt returns value corresponding to the keys. If key is missing, the whole option will be returned.

If set all=TRUE, raveio_resetopt resets all keys including non-standard ones. However "session_string" will never reset.

See Also

R_user_dir

Examples

# get one RAVE option
ncore <- raveio_getopt("max_worker")
print(ncore)

# get all options
raveio_getopt()

# set option
raveio_setopt("disable_fork_clusters", FALSE)