Prioritize processing hyperspectral data from Oct 8 2018

[dlebauer]

This is a high priority for an analysis that we would like to present in February (so ... this should be the first to go through the pipeline).

From Duke Pauli:

Dr. Thorp collected spectral data with his ASD FieldSPec pro and a comparison between what the gantry and hand-held would be interesting. The data from those days are particularly interesting because we have accompanying leaf-level compositional data and because we have markers on the leaves so in the images we can get point estimates similar to where the spec readings were manually taken.

[Paheding]

@dlebauer We are currently analyzing the data (collected in the week of Oct. 8) from Gantry based downwelling sensor and the ground-based Ocean Optics sensors for the purpose of improving the current calibration framework. It would be also interesting to see a comparison between the gantry and hand-held hyperspectral data.

[dlebauer]

@Paheding and @SeanHartling could you please try to run the hyperspectral workflow on the Oct 8 VNIR data from the gantry? @max-zilla has tried and encountered some errors from NCO that he has been unable to debug. The errors that Max got are here: hyperspectral_errors.txt, and says "Debug this":

hyperspectral_workflow.sh: ERROR Failed to translate raw data. Debug this:
ncks -O  --hdr_pad=10000 --no_tmp_fl --trr_wxy=939,1600,22045 --trr typ_in=NC_USHORT --trr typ_out=NC_USHORT --trr ntl_in=bil --trr ntl_out=bsq --trr_in=/home/extractor/sites/ua-mac/raw_data/VNIR/2018-10-08/2018-10-08__13-02-12-387/c053899d-f643-45f9-9fdd-1fa0f6a9bff5_raw /home/extractor/hyperspectral_dummy.nc /tmp/terraref_tmp_trn.nc.pid408.fl00.tmp

[Paheding]

@dlebauer It seems some values are missing since it states, "No value for $TERM and no -T specified
tput", we will look deep into it.