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R E A D M E . P O S T E D I T
doc: Wed Jun 13 20:30:10 2012
dlm: Thu Jun 14 18:22:13 2012
(c) 2012 A.M. Thurnherr
uE-Info: 95 50 NIL 0 0 72 3 2 8 NIL ofnI
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=Summary=
This README explains how to post-edit the shear output from b[LADCPproc]
before feeding it to [LADCPintsh], e.g. for removing data collected when
the ADCP was very shallow and possibly affected by the ship's magnetic
field.
=Nitty-Gritty=
The default output from [LADCPproc] is a so-called time-depth-series
(.tds) file with one record per valid shear sample. Each record
contains the following fields:
ens ensemble number the shear sample is from
elapsed elapsed time in seconds of the present ensemble
CTD_depth depth of CTD at the time the ensemble was recorded
downcast a boolean flag set to 1 (nan) for down(up)cast records
depth "nominal" depth of shear sample (center depth in gridded profile)
u_z vertical shear of zonal velocity
v_z vertical shear of meridional velocity
w_z vertical shear of vertical velocity
This is the "general" output of [LADCPproc]. For standard processing,
the shear is bin-averaged in depth space. While this can easily be
accomplished, e.g. with a Matlab script, for convenience the binned
output can be requested with the -p option of [LADCPproc]. The binned
output cannot be post-edited!
The .tds data can be post-edited. Matlab users can import these files
with [loadANTS.m] (see [README.Output]), edit the structures, bin the
shear in depth space, and export the new structures as ANTS files with
[struct2ANTS.m]. For example, to remove all data collected with the
ADCP shallower than 5m, simply delete the records for which CTD_depth
<= 5. Or, you can bin your shear data with different statistics (e.g.
median), instead of the arithmetic mean used by [LADCPproc] -p.
Inconveniently, [LADCPintsh] at present requires its shear input to be
in the format generated by the -p option of [LADCPproc], with the
following fields (Matlab version):
depth center depth of bin
dc_elapsed mean elapsed time of downcast shear samples in present bin
dc_nsamp number of downcast shear samples in bin
dc_u_z bin-averaged downcast vertical shear of zonal velocity
dc_u_z_sig corresponding standard deviation
dc_v_z same for meridional velocity
dc_v_z_sig
dc_w_z same for vertical velocity
dc_w_z_sig
uc_elapsed mean elapsed time of upcast shear samples in present bin
uc_nsamp number of upcast shear samples in bin
uc_u_z bin-averaged upcast vertical shear of zonal velocity
uc_u_z_sig corresponding standard deviation
uc_v_z same for meridional velocity
uc_v_z_sig
uc_w_z same for vertical velocity
uc_w_z_sig
elapsed mean elapsed time of mean dn/upcast shear samples in present bin
nsamp number of mean dn/upcast shear samples in bin
u_z bin-averaged mean dn/upcast vertical shear of zonal velocity
u_z_sig corresponding standard deviation
v_z same for meridional velocity
v_z_sig
w_z same for vertical velocity
w_z_sig
Sv bin-averaged acoustic volume scattering coefficient
Sv.nsamp number of samples in bin
Note that the .tds file does not contain acoustic backscatter
information, i.e. the Sv field should be set to nan and the Sv.nsamp to
zero.
After binning the shear data, Matlab users can create a structure with
the fields listed above. Metadata (scalars in the .tds import
structure) should be copied verbatim from the .tds import structure.
Each of the listed fields is a vector and they must all have the same
length. (Since the down- and upcasts do not usually cover exactly the
same depth range, padding is almost always required.) The resulting
structure can then be exported with [struct2ANTS.m]; the 'dependencies'
argument should be set to the filename(s) of the .tds file(s) from
which the binned shear profile was constructed.
The only option for non-Matlab users is to create an ASCII file with
the required columns (nan values are permitted) in the order listed
above and prepend this with the header from the corresponding
[LADCPproc] output file produced by the -p option.