/******************************************************************************

  FILE:  adcpsect.cnt

  This control file is used with the adcpsect program
  to extract ADCP data for specified sections along a cruise track
  from a CODAS database, perform the desired calculations,
  and write the result to text and Matlab files.
  The sections are specified as time ranges.

  This particular version is used to extract an ASCII file
  with the data listed below.

  INPUT:  CODAS database
  OUTPUT: 1. text file (.sub file) with following columns:
	     a. time (in decimal days)
             b. longitude (in decimal degrees)
             c. latitude  (in decimal degrees)
	     d. mean transducer temperature (in degrees C)
	     e. mean ship U (in m/s)
	     f. variance of ship U
	     g. mean ship V (in m/s)
	     h. variance of ship V
             one or more pairs of: (one for each layer in the depth grid)
             i. absolute zonal velocity for a given layer (in m/s)
             j. absolute meridional velocity (in m/s)
             .
             .
             .
          2. text file of statistics--mean (.sta file)
          3. Matlab files
             a. _uv.mat contains array "uv" with two columns for each ensemble,
                first u and then v.  The row corresponds to the depth grid.
             b. _xy.mat contains array "xyt" with a column for each ensemble,
                and three rows: longitude, latitude, decimal day;
                and vectors "z" and "zc" with the depth grid and the grid
                interval centers, respectively.
-------------------------------------------------------------------------------
  CONTROL FILE STRUCTURE:

  dbname:       < CODAS database name >
  output:       < output filename >
  step_size:    < number of profiles to advance >
  ndepth:       < number of depth bins to read and process >
  time_ranges:  < combined or separate >
  year_base=    < base year for decimal days >

  option_list:
    [ verbose ]                       { prints debugging and auxiliary output }
    [ underway?    < no | yes limit= <3> > ]                   { limit in m/s }
    [ pg_min=      <30> ]
    [ AGC_margin=  <10> ]

    [ skew_limit:
        agc_limit=  <100>
        max_velocity_difference= <0.8> ]                                { m/s }

    [ reference:       { choose only one of the following: }
        < reference_bins <5> to <20> |
          none |
          final_ship_ref |
          nav_position |
          nav_velocity |
          bottom_track |
          dir_position > ]

    [ navigation:      { output in .nav text file }
                       { choose one or more of the ff. then 'end' }
        [reference_bins <5> to <20>] {bin range; first bin is 1}
        [final_ship_ref]
        [nav_position]
        [nav_velocity]
        [bottom_track]
        [dir_position]
        end ]

    [ rotate:  < ship_coordinates | n > ]
        { where <n> is the angle in degrees, old x-axis to new x-axis }

    [ ctd:
        dbname:  < CODAS CTD database name > ]

    [ regrid:
        < integrate | interpolate | centered_average | average |
          per_grid_interval >
        < depth | svan | pot_svan | sigma_theta | sigma_t >
          { one of the last 4 only if the ctd: option has been selected }
        < grid      number= <50> origin= <16> increment= <8> |
          grid_list number= < 5> boundaries: <20> <40> <60> <80> <100> > ]

    [ contour:         { output in .con text file }
        < latitude | longitude | time >
        < middle | mean >
        minimum_npts= <10>
        units=        <0.01> ]

    [ vector:          { output in .vec text file }
        minimum_npts= <10> ]

    [ transport:       { output in .trn text file and _tr.mat Matlab Mat-file }
        minimum_npts= <10>
        units=        <1.e6>                                  { for Sverdrups }
        direction=    < all | left | right | along > ]

    [ sequential_cor:  { output in .cor text file }
        bin_range: <3> to <40> ]  { starting from 1, inclusive }

    [ ascii:           { output in .sub text file } 
        [ minimum_percent= <0.50> ] { %ensembles in time range with good data }
	end ]                       { less than this, mean U/V is set to 99999 }

    [ statistics:      { output in .sta text file }
        [ mean ]
        [ variance ]
        [ extrema ]
        [ norm_extrema ]
        [ indices ]
        [ all ]
        units= <0.01>
        end ]

    [ flag_mask:
        < bit-mask > { bit-mask is any one or more of those defined in
        .              adcpflag.h; these cumulatively indicate which
        .              criteria to consider in flagging profile bins
        .              as bad prior to calculations.  Use this option
        end ]          if you want flagging other than the default ALL_BITS }

    end

  { list of YMDHMS time pairs: }
  < yy/mm/dd hh:mm:ss > to < yy/mm/dd hh:mm:ss >
  .
  .
  .
-----------------------------------------------------------------------------*/

  dbname:                  ../adcpdb/ademo
  output:                  ademo  /* must be <= 5 chars. for DOS */
  step_size:               1
  ndepth:                  58
  time_ranges:             separate
  year_base=               1993
  option_list:
    pg_min=                30
    reference:             final_ship_ref
    regrid:                average
                           depth
      grid_list number=    10
        boundaries:        /* 20 */ 21  25  75 125 /* The 1st boundary must */
                           175 225 275   /* start at or below the */
                           325 375 425   /* shallowest depth bin  */
    ascii:
      minimum_percent=     .2
      end
    flag_mask:             ALL_BITS
      end
    end

/*  Grid boundaries for:
     dbname: ../adcpdb/ademo     output: ademoall.llg     year_base: 1993     step_size: 1    
     latitude      origin: -0.050000     increment: 0.100000    
     longitude      origin: -0.050000     increment: 0.100000
*/
/* 
 Time range: 93/04/09  00:02:00 to 93/04/10  23:58:00 */
93/04/09  00:02:32  /*  13.014   -91.788,     98.00176 (begin time range) */to
93/04/09  11:27:32  /*  13.050   -91.762,     98.47745;  685 min */
93/04/09  11:32:32  /*  13.061   -91.757,     98.48093 */to
93/04/09  11:37:32  /*  13.073   -91.753,     98.48440;    5 min */
93/04/09  11:42:33  /*  13.085   -91.748,     98.48788 */to
93/04/09  15:22:32  /*  13.150   -91.717,     98.64065;  220 min */
93/04/09  15:27:32  /*  13.162   -91.713,     98.64412 */to
93/04/09  19:02:32  /*  13.246   -91.677,     98.79343;  215 min */
93/04/09  19:07:32  /*  13.258   -91.675,     98.79690 */to
93/04/10  00:22:32  /*  13.344   -91.659,     99.01565;  315 min */
93/04/10  00:27:32  /*  13.357   -91.654,     99.01912 */to
93/04/10  00:27:32  /*  13.357   -91.654,     99.01912;    0 min */
93/04/10  00:32:32  /*  13.369   -91.649,     99.02259 */to
93/04/10  04:19:51  /*  13.442   -91.617,     99.18045;  227 min */
93/04/10  04:24:52  /*  13.453   -91.612,     99.18394 */to
93/04/10  07:46:01  /*  13.522   -91.560,     99.32362;  201 min */
93/04/10  07:51:02  /*  13.514   -91.549,     99.32711 */to
93/04/10  08:26:01  /*  13.455   -91.472,     99.35140;   35 min */
93/04/10  08:31:02  /*  13.447   -91.461,     99.35488 */to
93/04/10  08:36:00  /*  13.438   -91.451,     99.35833;    5 min */
93/04/10  08:41:01  /*  13.429   -91.440,     99.36182 */to
93/04/10  09:21:03  /*  13.359   -91.353,     99.38962;   40 min */
93/04/10  09:26:01  /*  13.350   -91.342,     99.39307 */to
93/04/10  09:26:01  /*  13.350   -91.342,     99.39307;    0 min */
93/04/10  09:31:01  /*  13.342   -91.331,     99.39654 */to
93/04/10  10:06:05  /*  13.279   -91.254,     99.42089;   35 min */
93/04/10  10:11:01  /*  13.270   -91.243,     99.42432 */to
93/04/10  10:21:01  /*  13.253   -91.221,     99.43126;   10 min */
93/04/10  10:26:02  /*  13.244   -91.210,     99.43475 */to
93/04/10  10:51:00  /*  13.201   -91.156,     99.45208;   25 min */
93/04/10  10:56:02  /*  13.193   -91.145,     99.45558 */to
93/04/10  11:21:01  /*  13.151   -91.090,     99.47293;   25 min */
93/04/10  11:26:03  /*  13.142   -91.079,     99.47642 */to
93/04/10  11:36:01  /*  13.126   -91.057,     99.48334;   10 min */
93/04/10  11:41:00  /*  13.118   -91.046,     99.48681 */to
93/04/10  12:21:02  /*  13.051   -90.958,     99.51461;   40 min */
93/04/10  12:26:00  /*  13.043   -90.947,     99.51806 */to
93/04/10  13:11:01  /*  12.968   -90.852,     99.54932;   45 min */
93/04/10  13:16:01  /*  12.959   -90.842,     99.55279 */to
93/04/10  13:21:01  /*  12.951   -90.832,     99.55626;    5 min */
93/04/10  13:26:03  /*  12.942   -90.821,     99.55976 */to
93/04/10  13:56:00  /*  12.892   -90.760,     99.58056;   30 min */
93/04/10  14:01:00  /*  12.883   -90.750,     99.58403 */to
93/04/10  14:16:01  /*  12.857   -90.719,     99.59446;   15 min */
93/04/10  14:21:00  /*  12.849   -90.709,     99.59792 */to
93/04/10  14:46:01  /*  12.808   -90.658,     99.61529;   25 min */
93/04/10  14:51:02  /*  12.799   -90.647,     99.61877 */to
93/04/10  15:16:00  /*  12.758   -90.596,     99.63611;   25 min */
93/04/10  15:21:01  /*  12.750   -90.586,     99.63959 */to
93/04/10  15:36:01  /*  12.726   -90.555,     99.65001;   15 min */
93/04/10  15:41:00  /*  12.718   -90.545,     99.65347 */to
93/04/10  16:21:00  /*  12.654   -90.463,     99.68125;   40 min */
93/04/10  16:26:01  /*  12.645   -90.453,     99.68473 */to
93/04/10  16:26:01  /*  12.645   -90.453,     99.68473;    0 min */
93/04/10  16:31:02  /*  12.637   -90.443,     99.68822 */to
93/04/10  17:15:59  /*  12.566   -90.353,     99.71943;   45 min */
93/04/10  17:21:01  /*  12.558   -90.343,     99.72293 */to
93/04/10  17:26:02  /*  12.550   -90.332,     99.72641;    5 min */
93/04/10  17:31:00  /*  12.540   -90.319,     99.72986 */to
93/04/10  17:51:02  /*  12.501   -90.261,     99.74377;   20 min */
93/04/10  17:56:00  /*  12.491   -90.246,     99.74722 */to
93/04/10  18:16:01  /*  12.454   -90.184,     99.76112;   20 min */
93/04/10  18:21:00  /*  12.445   -90.168,     99.76458 */to
93/04/10  18:26:01  /*  12.436   -90.152,     99.76807;    5 min */
93/04/10  18:31:02  /*  12.427   -90.135,     99.77155 */to
93/04/10  18:56:02  /*  12.382   -90.053,     99.78891;   25 min */
93/04/10  19:01:00  /*  12.371   -90.038,     99.79236 */to
93/04/10  19:06:02  /*  12.361   -90.023,     99.79586;    5 min */
93/04/10  19:11:03  /*  12.350   -90.007,     99.79934 */to
93/04/10  19:26:01  /*  12.318   -89.963,     99.80973;   15 min */
93/04/10  19:31:01  /*  12.307   -89.948,     99.81321 */to
93/04/10  19:56:00  /*  12.252   -89.874,     99.83056;   25 min */
93/04/10  20:01:01  /*  12.241   -89.859,     99.83404 */to
93/04/10  20:01:01  /*  12.241   -89.859,     99.83404;    0 min */
93/04/10  20:06:01  /*  12.230   -89.844,     99.83751 */to
93/04/10  20:37:11  /*  12.158   -89.755,     99.85916;   31 min */
93/04/10  20:42:12  /*  12.147   -89.740,     99.86264 */to
93/04/10  21:12:11  /*  12.075   -89.656,     99.88346;   30 min */
93/04/10  21:17:09  /*  12.064   -89.641,     99.88691 */to
93/04/10  21:22:11  /*  12.053   -89.626,     99.89041;    5 min */
93/04/10  21:27:12  /*  12.042   -89.611,     99.89389 */to
93/04/10  21:47:11  /*  11.996   -89.552,     99.90777;   20 min */
93/04/10  21:52:11  /*  11.985   -89.538,     99.91124 */to
93/04/10  22:02:12  /*  11.961   -89.509,     99.91819;   10 min */
93/04/10  22:07:11  /*  11.949   -89.494,     99.92166 */to
93/04/10  22:22:12  /*  11.914   -89.452,     99.93208;   15 min */
93/04/10  22:27:11  /*  11.902   -89.438,     99.93554 */to
93/04/10  22:47:12  /*  11.853   -89.381,     99.94944;   20 min */
93/04/10  22:52:12  /*  11.840   -89.367,     99.95292 */to
93/04/10  22:57:11  /*  11.828   -89.353,     99.95638;    5 min */
93/04/10  23:02:11  /*  11.815   -89.339,     99.95985 */to
93/04/10  23:27:11  /*  11.753   -89.269,     99.97721;   25 min */
93/04/10  23:32:11  /*  11.740   -89.255,     99.98068 */to
93/04/10  23:32:11  /*  11.740   -89.255,     99.98068;    0 min */
93/04/10  23:37:12  /*  11.727   -89.242,     99.98417 */to
93/04/10  23:57:12  /*  11.681   -89.184,     99.99806;   20 min (end time range) */