1. What is the Goodman High Throughput Spectrograph?.

This is thoroughly documented in SOAR web site and links within.

1. How does the pipeline select the reference lamp?.

The lamps are selected comparing two keywords. OBJECT and WAVMODE

2. How should I organize the data?.

More than organized your data should be cleaned of undesired files. There are some general assumptions in the implementation of the pipeline’s data organization system that might get confused by files that are not supposed to be there.

1. What is slit trim?.

Is a process to trim the 2D spectroscopic images to the slit illuminated area only. It works by fitting a box function to the dispersion-axis-collapsed spatial profile.

The box function is Box1D . The reason for doing it is because the non-illuminated area causes all sorts of problems in later steps, such as: existence of nan in master flats.