Command line

This page lists the commands installed with the package. Each opens the GUI window.

alignment-gui

Opens the GUI on data on your own disk.

alignment-gui [-y YAML]

-y, --yaml

Path to a session YAML (see Session YAML). The session is loaded when the window opens. Without it the window opens empty, and a data folder or session YAML is chosen from the data source button (...).

alignment-gui-ibl

Opens the GUI on IBL data from the Alyx database, through ONE. Requires the ibl extra (see Optional dependencies); without it the command exits with a message saying how to install it.

alignment-gui-ibl [-p PID | -c CSV]

Without options, the subject, session and probe are chosen from dropdowns in the window.

-p, --pid

A probe insertion id. The dropdowns are set to that insertion and its data is loaded when the window opens.

-c, --csv

A CSV file listing sessions recorded with two channel maps on the same probe: the dense map, read through ONE, and the quarter map, read from the local disk. Both are shown side by side as two configurations. Cannot be used together with --pid.

In this mode uploading an alignment also asks for a quality assessment of the alignment and the recording (see Plugins).

Logging

Every command logs what it is loading to the terminal, at INFO level.