Bash workflow for processing HyTools BRDF and topographic corrections with subsequent trait estimation for ABoVE data from the AVIRIS-NG sensor.

1. HyTools_CHTC.sub - Initial processing script for submitting jobs to the UW-CHTC cluster.

   Controls distribution of jobs using parameters from list /Tables/ABOVE_joblistfull.txt

2. HyTools_CHTC.sh - Bash shell script for processing job on single node (also local machine).

   Runs specific job on each node using lines pulled from url locations and BRDF grouped according to file /Tables/ABOVE_Lines.txt. This file allows for the specification of different locations for both the OBS_ORT file and image binary and .hdr files (as has been the case with existing AVIRIS-NG repos).

Processing steps within HyTools_CHTC.sh are as follows:

1. Set environmental variables (specified from HyTools_CHTC.sub).
2. Import and set Python environment (available here). Add this file to "/Zips".
3. Import and organize files necessary for processing.
4. Make folders and populate lists with necessary information from /Tables/ABOVE_Lines.txt file.
5. Correct OBS_ORT rotation by creating newly corrected OBS_ORT file.
6. Carry out topographic and grouped FlexBRDF correction.
7. Apply trait models to produce trait maps (base: NEON 2016-2018 models).
8. TAR and GZ all output files.
9. Cleanup temporary files.