apt-setup

name	apt-setup
description	Initialize a MATLAB session for atom probe analysis. Run this at the start of every APT session to set up the toolbox, load isotope tables, and load the default color scheme.
argument-hint	[instrument]

Initialize the MATLAB session for atom probe analysis. Use the MATLAB MCP server to execute the following setup code:

setupToolbox;
load('isotopeTable_naturalAbundances.mat');
load('colorScheme_default.mat');
cfg = APTConfig.getInstance();

If the user provided an instrument name as $ARGUMENTS, also apply the instrument preset. Map common names to preset names:

• "LEAP 4000", "4000", "LEAP4000" → cfg.applyInstrumentPreset('LEAP4000XHR')
• "LEAP 5000 XR", "5000XR", "LEAP5000XR" → cfg.applyInstrumentPreset('LEAP5000XR')
• "LEAP 5000 XS", "5000XS", "LEAP5000XS" → cfg.applyInstrumentPreset('LEAP5000XS')
• "EIKOS", "eikos" → cfg.applyInstrumentPreset('EIKOS')

If no instrument is provided, ask the user which instrument their data was acquired on.

After setup, display the current configuration:

cfg.display();

Report back to the user what was initialized and the active instrument settings (detection efficiency, flight path, t0).