#                    dlm: Tue Mar 29 07:28:54 2016

#                    uE-Info: 371 0 NIL 0 0 72 2 2 4 NIL ofnI

#   ! plots:

#       - avoid over-plotting axis labels

#       - allow for different nsamp magnitudes

#       - add "dc" "uc" labels

#       - add software version

#       - add seabed to eps.VKE profile

#       - add seabed to LADCP_w_postproc .wprof output

#   ! use instrument tilt in sidelobe editing

#   ! change w_tt output to w_t output; change -a to use w_t or remove -a? 

#   - worry about water-depth differences (disabled warning) 

#   - make upcast-flag valid for yoyo casts

#   - make diagnostic output 3-beam field work for Earth coordinates

#   ? remove water-depth from BT code, which is not really used and a bit of an outlier

#     because mean and stddev are used instead of median/mad

#   Dec 17, 2010: - created from [mergeCTD+LADCP]

#   Dec 18, 2010: - made to work

#   Dec 19, 2010: - improved considerably

#   Dec 20, 2010: - onward

#                 - BUG: depth-binning was off by 1 bin?!

#                 - added binning correction for instrument tilt

#   Dec 21, 2010: - added -h (seafloor depth)

#   Dec 22, 2010: - BUG: had not applied soundspeed-correction to w

#                 - debugged opt_d

#   Dec 23, 2010: - continued implementation of soundspeed corrections

#   Dec 24, 2010: - added winch_w, wave_w

#                 - removed beampair velocities from code

#   Dec 25, 2010: - adapted for surface-wave correction in terms of acceleration (CTD_w_t)

#                 - removed elapsed_mismatch

#                 - removed winch_w, wave_w

#   Dec 26, 2010: - made -p output layout independent of -x to avoid Makefile problems

#   Dec 30, 2010: - cleaned up some

#                 - folded-in backscatter calculation from shear method

#                 - folded-in BT calculation from shear method

#   Dec 31, 2010: - added weighted mean w profile to output

#   Jan  2, 2010: - BUG: BT_w.mad could bomb with division by 0

#                 - BUG: division by zero if no valid data

#   Jan  5, 2010: - adapted to allow for gaps in CTD time series

#   Feb 16, 2011: - cosmetics

#   Jun 22, 2011: - cosmetics

#   Jun 23, 2011: - disabled error on large rms reflr w

#                 - added -l

#                 - removed CTD headers from output

#   Jun 26, 2011: - added -u

#                 - changed package correction from acceleration to velocity, because of

#                   Stan's Antarctic data set where accelerations are zero but package effects are

#                   there

#   Jul  2, 2011: - increased tilt default to 15 degrees

#   Jul  3, 2011: - replaced old package-velocity correction -x code by new beamvel correction

#                 - removed -p

#                 - replaced -d by residual (diagnostics) output

#   Jul  4, 2011: - saved a snapshot in [Jul_04_2011]

#                 - removed output of binned profile (but not calculation code, which is required for residual)

#                 - BUG: firstGoodEns or lastGoodEns could end up in a reflr_w gap when valid LADCP data begin

#                        or end with CTD in water

#                 - moved rarely used option -s to -k

#                 - added -s)kip <ens> option

#                 - had to very very slightly relax an assertion (by 1e-10 seconds...)

#   Aug  3, 2011: - added -z)ap to truncate range, based on Stan's 2009 data set (017-019 most clearly)

#                   obs that final 2 velocities are outliers; could be due to color bar, should check with

#                   residuals

#   Sep 22, 2011: - removed (commented out) CTD acceleration

#                 - added basename to Parameter File Matching

#   Sep 23, 2011: - cosmetics (lots)

#                 - added -d)

#   Oct  6, 2011: - removed old commented-out code (CTD acceleration & old -x)

#                 - renamed time-series field names

#                 - added uncorrected reflr w to time-series output

#   Oct 10, 2011: - BUG: LADCP_w in .tds output had not been soundspeed corrected

#                 - removed -x

#                 - added "false-positives" editing filter

#   Oct 11, 2011: - adapted to the new parameter file, removing a few options

#   Oct 12, 2011: - added surface-layer editing

#                 - made %min/max_depth/elapsed more accurate

#   Oct 13, 2011: - fiddled

#   Oct 14, 2011: - renamed .prof fields from .N to .nsamp

#                 - added %output_basename

#                 - removed all ">" from open to allow use in pipelines

#                 - made <run-label> argument optional

#                 - replaced stdout output by $w_out

#                 - renamed _out to out_; output_basename to out_basename

#   Oct 15, 2011: - added editWOutliers()

#                 - added step to remove single-ping noise

#   Oct 16, 2011: - BUG: ensemble and bin numbers in output files were off by 1

#   Oct 17, 2011: - added default run label

#                 - added out_BR

#                 - BUG: closed STDOUT caused problems with tee in plotting scripts

#                 - added %run_label

#                 - added PostProcess.sh

#   Oct 18, 2011: - BUG: %{min,max}_ens used ensemble indices, rather than numbers

#                 - disabled false-positives editing (removes too much good data on 2011_IWISE)

#   Oct 19, 2011: - BUG: time-series output included ensembles without valid w

#                 - increased post-process sleep time to 30s

#                 - added corr, Sv and echo_amplitude as new fields to w output

#   Oct 20, 2011: - added editFarBins()

#                 - added downcast flag to time-series output

#                 - added ensemble number to LADCP-time-series output

#   Oct 21, 2011: - BUG: Sv code was not enabled for uplooker data

#   Oct 24, 2011: - added code to copy %lat/%lon from CTD data

#                 - added %ADCP_freuquency, %ADCP_blanking_distance

#                 - %LADCP_bin_length => %ADCP_bin_length

#   Oct 26, 2011: - added $first_guess_timelag

#   Oct 27, 2011: - added w12, w34, ww (pitch/roll-weighted average) to full output

#                 - removed ww because it apparently does not improve the solutions

#                 - moved editTilt() to after time-series calculation to allow

#                   time matching to work even with strict tilt limit

#                 - added correctAttitude()

#   May 22, 2012: - adapted to ANTS V5

#   Oct 15, 2012: - added $edit_data_hook

#                 - HG COMMIT

#                 - separated dc/uc time lagging

#                 - removed support for TLhist

#   Oct 16, 2012: - added support for dc/uc only solutions

#   Oct 17, 2012: - renamed $edit_data_hook to $post_merge_hook

#                 - HG COMMIT

#   Feb 13, 2013: - BUG: CTD_neg_press_offset did not work for CTD time series with -ve starting depth

#   Mar 23, 2013: - cosmetics

#                 - HG COMMIT

#   Apr 22, 2013: - removed opt_? variable aliases

#   May  8, 2013: - replaced default run label (default to profiles) to make more readable directory structure

#   May 14, 2013: - opt_m => w_max_lim

#                 - BUG: time-series output had two messed-up fields

#   May 15, 2013: - added w12 and w34 (2-beam solutions) to profile output

#   May 16, 2013: - added CTD_w_tt to time-series & all-sample outputs

#                 - -a => -d (CTD depth offset)

#                 - implemented pressure-sensor acceleration correction (-a)

#                 - added re-gridding of full profile after ping-coherent error removal

#   Jun  5, 2013: - renamed $discard_velocities_from_beam to $bad_beam

#                 - BUG: $bad_beam did not discard BT_VELOCITY data

#   Jun  6, 2013: - BUG: error message had -a instead of -d

#   Sep  5, 2013: - BUG: w12/w34 do not work for earth-coordinate data, of course

#   Apr 17, 2014: - BUG: edit_tilt was never called when all recorded bins are valid

#   Apr 21, 2014: - updated comments

#   May 19, 2014: - began adding support for PPI filtering

#   May 20, 2014: - changed volume_scattering_coeff to Sv in output

#                 - added editPPI()

#   Jul  6, 2014: - BUG: nan water depth had been interpreted as known

#                 - BUG: sVelProf[] was not allowed to have any gaps

#   Jul  9, 2014: - BUG: Jul 6 bug fixes had been applied to older

#                        version

#                 - BUG: code meant to ensure gap-free svel profiles did not work correctly

#   Jul 12, 2014: - finally made output files executable

#   Apr  5, 2015: - added check for required software

#                 - BUG: removed dc/uc mean w fields from .prof again

#   Apr  7, 2015: - made LADCP_w callable from installation directory

#                 - BUG: -v default was wrong in usage message

#                 - replaced 'ens' in output files by 'ensemble'

#   Apr 16, 2015: - turned output specifies into lists (re-design of

#                   plotting sub-system)

#                 - removed 30s sleep from PostProcess.sh call

#                 - disabled active output when ANTS are not available

#                 - removed /bin/ksh requirement

#                 - BUG: error messages were not reported in the log file

#                 - made seabed detection code more flexible

#                 - made reference-layer w_ocean warning more severe

#                 - BUG: info() did not write anything into logfile when format string was used

#                 - BUG: LADCP_lastBin was set 1 too low

#   Apr 20, 2015: - improved comments

#                 - improved diagnostic messages (warning on missing CTD temp)

#                 - added support for empirical backscatter correction

#   Apr 21, 2015: - improved screen log output

#   Apr 22, 2015: - BUG: $realLastGoodEns could be undefined, breaking plotting routines

#   Apr 24, 2015: - removed @ARGS

#                 - added %profile_id

#   May 13, 2015: - loosened "insufficient valid velocities" test for short casts

#   May 15, 2015: - added $min_valid_vels

#                 - BUG: LADCP_atbottom could be less than firstGoodEns

#   May 18, 2015: - added %LADCP_pulse_length, %dnXX

#   May 20, 2015: - added $PROF as newer alternative to $STN

#                 - replaced "require ProcessingParams" by "do ProcessingParams"

#   Jun 15, 2015: - clarified warning message

#   Jul 26, 2015: - added %output_grid_dz %output_grid_minsamp for use by [LADCP_w_regrid]

#                 - began work on support for [libGMT.pl]

#                 - -v usage message had wrong default

#                 - added $outGrid_firstBin & $outGrid_lastBin

#   Jul 28, 2015: - added GMT plot support for all @out_ lists

#   Jul 29, 2015: - continue adaptation of code for new plotting system

#   Jul 30, 2015: - cosmetics

#   Sep  3, 2015: - changed out_w to out_wsamp

#   Sep 26, 2015: - replaced numberp($water_depth) by defined($water_depth) for consistency

#                 - implemented secondary sidelobe editing

#                 - allow for -h <filename>

#                 - allow $ID as alias for $PROF and $STN

#   Sep 27, 2015: - BUG: -h filename was broken when water_depth is not known

#   Oct 12, 2015: - upgraded missing water-depth warnings to L2

#                 - added -V)ersion

#   Nov 25, 2015: - made warning disappear on setting $ANTS_TOOLS_AVAILABLE

#   Nov 27, 2015: - changed RDI_BB_READ.pl to RDI_PD0_IO.pl

#   Jan  4, 2016: - decreased default vertical resolution to 20m

#   Jan  5, 2016: - adapted to [ADCP_tools_lib.pl]

#   Jan 22, 2016: - updated for improved mean_residuals plot

#                 - added per-bin residual quality check

#   Jan 25, 2016: - added antsAddParams() with version number

#   Jan 26, 2016: - added %processing_params, many others

#                 - expunged -d

#                 - implemented outGrid_firstBin eq '*' (also lastBin)

#   Jan 27, 2016: - BUG: outGrid_lastBin eq '*' did not work

#                 - removed large ref-lr w warning

#   Feb 14, 2016: - fiddled with ping-coherent residuals code, fixing

#                   0-2 potential (minor?) bugs related to outGrid_{first,last}Bin;

#                   output of new code checked against old code => identical

#   Feb 16, 2016: - BUG: per-bin-residual QC could cause division by zero

#   Feb 19, 2016: - added -l (disable time-lag filtering)

#   Mar  7, 2016: - added error message when -h is neither number nor file

#                 - BUG: -ve depth error message referred to obsolete -d

#                 - BUG: dn field name did not use zero filling for year number

#   Mar  8, 2016: - removed L0 water-depth-difference warning

#                 - added test for 1500m/s sound speed

#   Mar  9, 2016: - added hab field to .wprof output

#   Mar 13, 2016: - cleaned up warnings created before LADCP_file is defined

#                 - added sanity checks and warnings

#   Mar 17, 2016: - added {dc,uc}_rms_{tilt,w_pkg}

#                 - replaced a couple of **2 by &SQR()

#                 - replaced %ADCP_orientation values by DL & UL

#                 - {dc,uc}_rms_w_pkg => {dc,uc}_rms_accel_pkg for V1.2beta6

#   Mar 18, 2016: - added -l to %processing_options

#   Mar 24, 2016: - generalized plotting system (renamed variables)

#                 - made plotting system search current dir before LADCP_w dir

#                 - BUG: ProcessingParams syntax errors were not flagged

#                 - BUG: progress message in rarely used filter

#   Mar 25, 2016: - added -r)esidual rms filter

#                 - added -q -r to processing_options

#   Mar 26, 2016: - BUG: water_depth < CTD_maxdepth was allowed

#                 - round(CTD_depth)

#   Mar 29, 2016: - split [default_paths.pl] from [defaults.pl] to allow defaults

#                   to be read before usage

#				  - renamed _subdir to _dir variables

#				  - renamed post-process hook script to LADCP_w.PostProcess

#				  - added -r default (0.04m/s)

require "$WCALC/defaults.pl";												# load default/option parameters

&antsUsage('3:4a:b:c:e:g:h:i:k:lm:n:o:p:qr:s:t:uv:Vw:x:',0,

	"[print software -V)ersion] [-v)erbosity <level[$opt_v]>]",

	"[-q)uick (no single-ping denoising)]",

    "[require -4)-beam solutions] [apply beamvel-m)ask <file> if it exists]",

	"[valid LADCP -b)ins <bin,bin[$opt_b]>",

	"[-c)orrelation <min[$opt_c counts]>] [-t)ilt <max[$opt_t deg]> [-e)rr-vel <max[$opt_e m/s]>]",

	"[-r)esidual <rms.max[$opt_r m/s]>]",

	"[-h water <depth|filename>]",

	"[max LADCP time-series -g)ap <length[$opt_g s]>]",

	"[-i)nitial CTD time offset <guestimate> [-u)se as final]]",

	"[calculate -n) <lags,lags[$opt_n]>] [lag -w)indow <sz,sz[$opt_w s]>] [lag-p)iece <CTD_elapsed_min|+[,...]>]",

	"[require top-3) lags to account for <frac[$opt_3]> of all]",

	"[disable time-l)ag filtering]",

	"[pressure-sensor -a)cceleration correction <residual/CTD_w_tt>]",

	"[-o)utput bin <resolution[$opt_o m]>] [-k) require <min[$opt_k]> samples]",

	"[e-x)ecute <perl-expr>]",

	"<profile-id> [run-label]");

if ($opt_V) {

	printf(STDERR "+-------------------------+\n");

	printf(STDERR "| LADCP_w Software V%s	|\n",$VERSION);

	printf(STDERR "|(c) 2015- A.M. Thurnherr |\n");

	printf(STDERR "+-------------------------+\n");

	exit(0);

}

&antsUsageError() if ($opt_u && !defined($opt_i));

&antsUsageError() unless (@ARGV==1 || @ARGV==2);

&antsCardOpt(\$opt_s,0);												# skip # initial ensembles

$opt_p = '+' unless defined($opt_p);									# separate uc/dc time lagging

&antsFloatOpt(\$opt_a,1);												# pressure acceleration correction

$ID = $PROF = $STN = &antsCardArg();									# station id ($STN for compatibility)

if (@ARGV) {															# run label

	$RUN = $ARGV[0];

	shift;

} else {

	$RUN = 'profiles';

}

require "$WCALC/default_paths.pl";										# load default input/output paths

croak("$processing_param_file: $@")

	unless ($err = do "$processing_param_file");						# load processing parameters

$processing_options .= " -i $opt_i" if defined($opt_i);

$processing_options .= " -r $opt_r" if defined($opt_r);

$processing_options .= ' -l' if defined($opt_l);

$processing_options .= ' -q' if defined($opt_q);

croak("$0: \$out_basename undefined\n")									# plotting routines use this to label the plots