======================================================================
                    R E A D M E . P R O C E S S D A T A 
                    doc: Tue May 15 18:49:00 2012
                    dlm: Fri Jul 12 12:07:38 2013
                    (c) 2012 A.M. Thurnherr
                    uE-Info: 118 71 NIL 0 0 72 75 2 8 NIL ofnI
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=Overview=

This README describes how to obtain profiles of vertical shear and
velocity from CTD/LADCP data. It assumes that all of the required
software has been installed (see [README.Install]).

The re-implemented shear method software provides two commands:

[LADCPproc]	This utility produces LADCP shear data from a raw ADCP
		data file and the corresponding CTD time series.
		Additionally, it can create profiles of acoustic
		backscatter, as well as BT-referenced velocity
		profiles near the seabed from downlooking ADCPs.

[LADCPintsh]	This utility produces profiles of horizontal velocity
		from the [LADCPproc] shear output. BT profiles (from
		[LADCPproc] or from the LDEO_IX inversion software) or
		SADCP profiles (manually constructed) can be used to
		reference the velocity profiles.

For non-standard processing, the shear output from [LADCPproc] can be
post-edited before gridding, e.g. in order to filter data collected at
very shallow depths when the ADCP may be affected by the magnetic field
of the surface vessel (see [README.PostEdit] for details).


=DATA REQUIREMENTS=

ADCP DATA: The software reads binary RDI BB ADCP files from both down-
and upward-looking ADCPs. Clock setting of the ADCP is not important.

CTD DATA: LADCP processing requires a CTD-derived time series of
pressure, temperature and salinity. Optionally, it is recommended that
an elapsed time field is supplied. A time resolution of 1Hz is
recommended. The software is capable of reading both binary and ASCII
SeaBird .cnv files with lat/lon information in the header and with the
following fields: timeS, prDM, t090C and/or t190C, sal00 and/or sal11.
Alternatively, the CTD time series can be supplied as an arbitrary
headerless ASCII CTD file with the same information, as described in
[LADCPproc.defaults].
	

=CALCULATE LADCP SHEAR PROFILE=

The following simple example shows how to create separate shear profiles
from an upward- and a downward-looking ADCP, as well as a BT-referenced
velocity profile near the seabed:

Input files:
	001DL000.000	downlooker ADCP file
	001UL000.000	uplooker ADCP file
	001.cnv		CTD file

LADCPproc -p 001DL.sh -b 001.BT 001DL000.000 001.cnv > /dev/null
	- this example creates two files, 001DL.sh (shear profiles) and
	  001.BT (bottom-track data)
	- the default output (STDOUT) from [LADCPproc] is a list of
	  valid shear samples, which is ignored (sent to /dev/null) in
	  this example
	- it is recommended that the diagnostic output (STDERR) is
	  captured in a log file; refer to the manual of your shell on
	  how to accomplish this

LADCPproc -p 001UL.sh 001UL000.000 001.cnv > /dev/null
	- this example creates one file, 001UL.sh (shear profiles)


In this simple example, processing is carried out with standard
parameters. Some of the important parameters can be modified with
[LADCPproc] options, which are listed when [LADCPproc] is ran without
input parameters. The following are the most important [LADCPproc]
options:
	-d 		generate diagnostic output (recommended)
	-r		use RDI BT data instead of echo amplitudes to find
	        	seabed and determine CTD velocity
	-o <dz>		output grid resolution (defaults to 5m)
	-p <shearprof>	generate shear profile output
	-b <btm_track>	generate BT output
	-s <setup_file>	read additional non-default processing parameters
			from <setup_file>

However, there are many more processing parameters than can be modified
with options --- a full list with comments can be found in
[LADCPproc.defaults]. To change any of the default parameter values,
create a perl-file with variable assignments (see [LADCPproc.defaults]
for syntax) and use the -s <setup_file> option in [LADCPproc].


=CALCULATE LADCP VELOCITY PROFILE=

Given the output from the above steps, different full-depth velocity
profiles can be produced as follows:

LADCPintsh 001DL.sh > 001DL.bc
	- this creates baroclinic (zero vertical mean) velocity profile
	  from the DL shear data

LADCPintsh -r 001.BT 001DL.sh > 001DL.vel
	- this creates a BT-referenced absolute velocity profile from
	  the DL shear data

LADCPintsh -r 001.BT 001UL.sh > 001UL.vel
	- this creates a BT-referenced absolute velocity profile from
	  the UL shear and the DL BT data
	- note that no -u is required in this case!

LADCPintsh -r 001.BT -u 001UL.sh 001DL.sh > 001.vel
	- this creates a BT-referenced absolute velocity profile from
	  the combined DL/UL shear data
	- note that -u is only required if both UL and DL data are used

It is also possible to use SADCP data to reference the velocity
profiles, although it is up to the user to create an input data file
in one of the supported formats. Note that it is *not* possible to use
multiple simultaneous referencing constraints with [LADCPintsh]. 

The following are common [LADCPintsh] options:
	-u		use uplooker shear (in addition to downlooker,
			which is always used)
	-r <file>	use reference-velocity data to reference baroclinic
			velocity profiles; the following file formats
			are supported 1) bottom-track output produced by
			the -b option of [LADCPproc], 2) bottom-track
			output produced by the LDEO processing software
			(.bot files). SADCP data can be used, too, but
			they have to be supplied in one of the two
			supported file formats.
	-n <samp>	set minimum number of shear samples to use
	-m <samp>	set minimum BT samples to use


=QUALITY CHECKS=

After processing, the quality of the resulting profiles must be
assessed. The following steps are recommended:

1) Compare the down- and up-cast profiles of velocity. Vertical
velocity is particularly useful in this context as problematic casts
often show a striking "X" pattern.

2) Inspect the standard deviation profiles of the binned shear and
determine (by comparison with similar data) whether the standard
deviations have the correct magnitude.

3) Calculate and compare independent solutions from the uplooker and
downlooker data. This will only validate the baroclinic velocities (i.e.
the vertical shear).

4) Compare to velocity profiles calculated with different software (e.g.
with the LDEO_IX velocity inversion code).