5.6. Configuring Pipeline Behaviour

It is also possible to configure some internal pipeline behaviour via ConfigManager. It can be done either via the command-line interface (CLI) or the application programming interface (API).

To use via the CLI, one would do:

<CONFIG-KEY>=<CONFIG-VAL> junifer run ...

and via the API like so:

from junifer.utils import config

# Add config
config.set(key="<config-key>", val=<config-val>)

# do feature extraction
...

# Remove config
config.delete("<config-key>")

5.6.1. Available Configurations

CLI Key	API Key	Value	Description
JUNIFER_DATA_LOCATION	data.location	str	Alternative location for junifer-data
JUNIFER_DATAGRABBER_SKIPIDCHECK	datagrabber.skipidcheck	bool	Skip DataLad-based DataGrabber’s ID check
JUNIFER_DATAGRABBER_SKIPDIRTYCHECK	datagrabber.skipdirtycheck	bool	Skip Git “dirty” check for a DataLad dataset clone of a DataGrabber
JUNIFER_PREPROCESSING_DUMP_LOCATION	preprocessing.dump.location	str	Dump location of pre-processed data for debugging purposes
JUNIFER_PREPROCESSING_DUMP_GRANULARITY	preprocessing.dump.granularity	“full” or “final”	Dump all pre-processing steps or just the final pre-processed data
JUNIFER_PREPROCESSING_WARPING_CHUNKSIZE	preprocessing.warping.chunksize	int	Number of volumes of 4D data to warp at once with SpaceWarper (default 100). The memory used by ANTs and FSL grows with the number of volumes, so smaller chunks use less memory
JUNIFER_MARKERS_SPHERES_CHUNKSIZE	markers.spheres.chunksize	int	Number of volumes of 4D data to read at once to extract the signals of spheres (e.g., SphereAggregation) (default 100). Only the signals of the voxels of the spheres are kept, so the whole data is never in memory, and smaller chunks use less memory