3.1.5.11. Loading files generated by getmat

  1. You will probably want the matlab program load_getmat.m

  2. Identify the location of the files generated by getmat. For example, a modern UHDAS installation writes files in contour/allbins_*.mat You can see the live processing directory and access the allbins*.mat files by looking at the shared data directory and following the example in the next step. (see this link for information about network shares)

  3. If the location of the getmat output is uhdas_data/km1001c/proc/os38nb/contour then load the files with matlab as follows:

data = load_getmat('uhdas_data/km1001c/proc/os38nb/contour/allbins_');

% DO apply the editing mask:
u = data.u .* data.nanmask;
v = data.v .* data.nanmask;

  1. Variable names are documented with “help load_getmat”, shown below.

Fieldnames in "load_getmat" output:

    fieldnames   size         meaning:
     dday       1 x nprofs   zero-based decimal day (end of profile)
     time       6 x nprofs   year,month,day,hour,minute,second (end of profile)
  iblkprf       2 x nprofs   database block and profile number
      lon       1 x nprofs   longitude (from smoothed navigation; end of profile)
      lat       1 x nprofs   latitude  (from smoothed navigation; end of profile)
  heading       1 x nprofs   average primary heading (usually gyro)
  tr_temp       1 x nprofs   average temperature
  last_temp     1 x nprofs   last temperature
  last_good_bin 1 x nprofs   last good bin (-1 is bad profile)
      amp   nbins x nprofs   signal return amplitude or rssi (averaged)
     amp1   nbins x nprofs   signal return amplitude or rssi (beam 1)
     amp2   nbins x nprofs   signal return amplitude or rssi (beam 2)
     amp3   nbins x nprofs   signal return amplitude or rssi (beam 3)
     amp4   nbins x nprofs   signal return amplitude or rssi (beam 4)
    swcor   nbins x nprofs   spectral width (nb150) or correlation (os or wh)
    umeas   nbins x nprofs   measured  velocity (positive east, m/s)
    umeas_bt  1   x nprofs   measured  velocity (positive east, m/s) from bottom track
    uship     1   x nprofs   ship      velocity (positive east, m/s)
        u   nbins x nprofs   ocean     velocity (positive east, m/s)
    umean     1   x nprofs   ref layer velocity (positive east, m/s)
    vmeas   nbins x nprofs   measured  velocity (positive north, m/s)
    vmeas_bt  1   x nprofs   measured  velocity (positive north, m/s) from bottom track
    vship     1   x nprofs   ship      velocity (positive north, m/s)
        v   nbins x nprofs   ocean     velocity (positive north, m/s)
    vmean     1   x nprofs   ref layer velocity (positive north, m/s)
        w   nbins x nprofs   vertical  velocity (up   , m/s)
    wmean       1 x nprofs   mean vertical velocity for each profile
        e   nbins x nprofs   error velocity (m/s)
    depth   nbins x nprofs   center depth for each bin and profile, positive down
       pg   nbins x nprofs   percent good
    pflag   nbins x nprofs   0 is unflagged, otherwise there is a code.  see www docs
  nanmask   nbins x nprofs   suitable for dot-multiply with velocity

  ---- all diagnostics: only if called with (......'all')
                (some might not be present in any case)

     mps        1 x nprofs   ship speed, m/s
    fmeas   nbins x nprofs   measured velocity (positive ship's fwd direction, m/s)
    pmeas   nbins x nprofs   measured velocity (positive ship's port direction, m/s)
     fvel   nbins x nprofs   ocean velocity (positive ship's fwd direction, m/s)
     pvel   nbins x nprofs   ocean velocity (positive ship's port direction, m/s)
  head_misalign 1 x nprofs   heading correction (best_head = heading - head_misalign)
  scale_factor  1 x nprofs   scale factor applied to watertrack data

  -------------------------------------------------------------------
  data =  load_getmat(prefix)
  input:
          prefix is the whole path up to the common base of the files
                 or, use path as well as prefix

  eg
          cd cruisedir
          data = load_getmat('allbins_');
  eg
          data = load_getmat(fullfile(cruisedir, 'allbins_'));

  The field "nanmask" holds the editing flags and is designed to turn bad
  velocity data into NaNs.    Use as follows

  u = data.u .* data.nanmask;
  v = data.v .* data.nanmask;

  ---------------

  depending on the version of "getmat", some of these fields may not be available

  NOTE: (1) decimal day starts with zero, i.e. Jan 1 noon is 0.5 (not 1.5)
        (2) The following values are from the END of the ensemble
                 decimal day, time
                 longitude
                 latitude
        (3) To get additional diagnostic fields, call with
                 load_getmat('allbins_', 'all');