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