NOAA PSD CAPRICORN matlab codes README

Analysis codes are grouped into several categories as separate
directories.  Each directory should be self-sufficient in terms
of the subroutines required to run the main scripts.  A current
version of Matlab including the Signal Processing Toolbox is the
base requirement.

NOTE: OUTPUT FILES DO NOT HAVE HEADERS.  CONSULT THE MATLAB
CODE FOR OUTPUT FORMATS.

check_ship_data: a variety of scripts written during the cruise
to read ship data files and examine specific variables.

flux: scripts normally used for QA/QC of NOAA and ship met data
on a daily basis during the cruise.  Products: plots of raw met
and navigation parameters (Raw_Images) and 1-minute averages of 
raw data in ascii format (Processed_Raw files).  1-min average
data files are produced as a convenient format for preliminary
analysis but are 'as is' and not screened in any way for bad values.
Bulk fluxes and averages are also computed at 5 and 30 min 
timescales.  These are also considered 'preliminary'.  Turbulent
fluxes are not computed in these scripts.

motcorr_flux: scripts to compute motion-corrected winds, 
turbulent fluxes, spectra and cospectra on 10-min intervals.
All met and nav data are also averaged to 10-min.  Products:
1) 'da' file of 10-min met, nav and flux results. 2) 'cr' file
of 10-min results from the LICOR sensor.  3) 'sp' file of
10-min spectra and cospectra.  4) 'motion_decorr' files of 
10Hz ship motion.  5) 'uvwStream_decorr' files of motion corrected
10Hz 3D wind data rotated into the streamline (mean V & W are zero).
Data are 'as is' and not screened in any way for bad values or
missing segments.  Plots produced: 1) WindPlots_decorr: plots of
raw and motion corrected 10Hz wind variables.  2) SpectraPlots_decorr:
plots of variance spectra and cospectra for winds, sonic temperature
and specific humidity.  3) Daily_decorr: summary plots of various
variables for each day.

da_red_analysis:  scripts that read the 10-min result files 
produced by the motcorr_flux run and process filtered final
results for the entire cruise.  Adjustments and corrections are
applied to bulk met data as needed, filters are applied to screen
bad turbulent flux values, and final bulk fluxes are computed from
the best available raw bulk parameters.  A variety of summary and
diagnostic plots are produced (da_red_plots).  Final results are
saved in 10-min and 1-hr format as ascii text files (whole cruise):
	CAPRICORN_2016_flux_10_v4_decorr.txt
	CAPRICORN_2016_flux_hr_v4_decorr.txt

Riegl_Hs_fixed:  scripts to compute motion corrected wave height and
wave spectra from the raw Riegl fixed point LIDAR data files.
Wave processing is slow due to the interpolation and gap-filling.
10Hz ship motion files (motion_decorr) from the motcorr_flux
run are required.  Saves 10-min summary wave statistics and spectra
for the entire cruise as ascii text files:
	CAPRICORN_2016_WaveSpectra.txt
	CAPRICORN_2016_WaveStats.txt
Plots of significant wave height (Hs), variance spectra, peroid (Tp),
raw wave height time series and missing data are saved in the directory
'riegl_wave_plots'.