#!/usr/bin/perl
#======================================================================
# L A D C P _ W
# doc: Fri Dec 17 18:11:13 2010
# dlm: Sun Jul 3 12:58:19 2011
# (c) 2010 A.M. Thurnherr
# uE-Info: 844 45 NIL 0 0 72 2 2 4 NIL ofnI
#======================================================================
# TODO:
# make timelagging work for short casts (make sure 10% is not more than half window size)
# own seabed detection (P403)
# instrument tilt in sidelobe editing?
# make diagnostic output 3-beam field work for Earth coordinates
# read assumed ADCP soundspeed from data file, instead of assuming 1500m/s
# calculate CTD acceleration from CTD velocity; probably not useful
# 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
$antsSummary = 'calculate vertical velocities from LADCP & CTD time series';
# HISTORY:
# 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
# PROCESSING PARAMETER FILE
# - # is comment character
# - invalid entries ignored
# - valid entries begin with <ADCP-file>: (NO INITIAL SPACE ALLOWED)
# - remainder of line is added to usage before ADCP file and LADCP_w is restarted
# - no argument with spaces allowed!
# - -0 suppresses acting on -l
# CTD REQUIREMENTS
# - elapsed elapsed seconds; see note below
# - depth
# - ss sound speed
# - w ddepth/dt
# - w_t dw/dt
# - temp OPTIONAL; used for backscatter calculation (i.e. not very important)
# NUMERICAL OPTIONS
# - the first option in the list cannot be numerical!
# - if need be, use -v 1 as a dummy option
# ELAPSED TIMES
# - there are 2 different elapsed times used in this program:
# 1) elapsed based on firstgoodens in the LADCP time series
# 2) CTD elapsed time
# - CTD elapsed time does not have to start with zero!
# - do not use the Seabird elapsed field, which is only reported to
# 3 significant digits, causing significant jitter in dt; however,
# at least up to 2010 Seabird simply calculates elapsed time by
# assuming a 24Hz sampling rate and no record drop; therefore,
# it is best to calculate elapsed time as %RECNO/24
# - the elapsed field of the output is the elapsed time from the CTD
# file; this is required in order to be able to compare the times
# from the uplooker and downlooker-derived vertical velocity
# profiles
# - as a result, a profile only starts with elapsed==0 if the CTD
# is turned on when the LADCP is already in the water
# TIME LAGGING
# - occasionally, the time lagging algorithm fails, in particular if the CTD is turned on
# some time after the package enters the water
# - in this case, an initial guess can be provided with -i
# - e.g. plot 'CTD/24Hz/054.1Hz elapsed w','LADCP/raw/054UL.prof =$elapsed-850 w' => -i -850
# VELOCITY AMBIGUITY ERRORS
# - quite extensive tests with DIMES US2 station 146, which has a lot of
# ambiguity velocity errors, reveal that -m 1 catches those errors
# quite nicely
# - even when the errors are not filtered with -m 1, they do not
# affect the w profiles, as long as the median bin values are used
# SCREEN LOGGING
# - there are 4 verbosity levels, selected by -v
# 0: only print errors
# 1: default, UNIX-like (warnings and info messages that are not produced for every cast)
# 2: progress messages and useful information
# >2: debug messges
# - the most useful ones of these are 1 & 2
($WCALC) = ($0 =~ m{^(.*)/[^/]*$});
($ANTS) = (`which list` =~ m{^(.*)/[^/]*$});
($PERL_TOOLS) = (`which mkProfile` =~ m{^(.*)/[^/]*$});
require "$ANTS/ants.pl";
require "$ANTS/libstats.pl";
require "$WCALC/edit_data.pl";
require "$WCALC/time_series.pl";
require "$WCALC/time_lag.pl";
require "$WCALC/find_seabed.pl";
require "$WCALC/svel_corrections.pl";
require "$WCALC/acoustic_backscatter.pl";
require "$WCALC/bottom_tracking.pl";
require "$PERL_TOOLS/RDI_BB_Read.pl";
require "$PERL_TOOLS/RDI_Coords.pl";
@ARGS = @ARGV; # save opts & arguments
$antsParseHeader = 0;
&antsUsage('03:4a:b:c:d:e:f:g:h:i:l:m:n:o:r:s:t:uv:w:x:',1,
'[-l)oad processing parameters from <file>]',
'[-v)erbosity <level[1]>]',
'[require -4)-beam solutions]',
'[-r)ef-layer <bin[2],bin[6]>]',
'[-c)orrelation <min[70]>] [-t)ilt <max[10deg]> [-e)rr-vel <max[0.1m/s]>]',
'[-h water <depth>]',
'[max LADCP time-series -g)ap <length[60s]>]',
'[-m)ax vertical <velocity[1m/s]>',
'[-a)djust CTD depth <by[0m]>]',
'[-i)nitial CTD time offset <guestimate> [-u)se as final]]',
'[calculate -n) <lags,lags[10,100]>] [lag -w)indow <sz,sz[240s,20s]>]',
'[require top-3) lags to account for <frac[0.6]> of all]',
# '[-x <pkg_vel_corr_coeffs>]',
'[-x <beamvel-scale-fac>]',
'[valid LADCP -b)ins <bin[2],bin[*]>',
'[-o)utput bin <resolution[50m]>] [require -s)amples <min[20]>]',
# '[-f) write time-series <file>] [-d)ump depth-bins to <basename>] [-p)ackage-velocity effect <file>]',
'[-f) write time-series <file>] [output residual -d)iagnostics to <file>]',
'<LADCP-file> [CTD-file]');
&antsCardOpt(\$opt_v,1); # suppress regular info
$RDI_Coords::minValidVels = 4 if ($opt_4); # suppress 3-beam solutions
&antsFloatOpt(\$opt_c,70); # min correlation
&antsFloatOpt(\$opt_t,15); # max tilt (pitch/roll)
&antsFloatOpt(\$opt_e,0.1); # max err vel
&antsFloatOpt(\$opt_g,60); # max LADCP gap length
&antsFloatOpt(\$opt_m,1); # max allowed vertical velocity
&antsFloatOpt(\$opt_a,0); # CTD depth adjustment
&antsFloatOpt($opt_i); # externally supplied lag
&antsUsageError() if ($opt_u && !defined($opt_i));
$opt_n = '10,100' unless defined($opt_n); # number of time-lags to carry out
$opt_w = '240,20' unless defined($opt_w); # time-lag search window (full width)
&antsFloatOpt(\$opt_3,0.6);
&antsFloatOpt(\$opt_o,50); # output bin size
&antsCardOpt(\$opt_s,20); # min samples required
$opt_r = '2,6' unless defined($opt_r); # reference layer bins for w for time matching
$opt_b = '2,*' unless defined($opt_b); # bins to use in w calculations
@n_lags = split(',',$opt_n); # decode -n
croak("$0: cannot decode -n $opt_n\n")
unless numberp($n_lags[0]) && numberp($n_lags[1]);
@w_size = split(',',$opt_w); # decode -w
croak("$0: cannot decode -w $opt_w\n")
unless numberp($w_size[0]) && numberp($w_size[1]);
($refLr_firstBin,$refLr_lastBin) = split(',',$opt_r); # decode -r
croak("$0: cannot decode -r $opt_r\n")
unless numberp($refLr_firstBin) && numberp($refLr_lastBin);
($LADCP_firstBin,$LADCP_lastBin) = split(',',$opt_b); # decode -b
croak("$0: cannot decode -b $opt_b\n")
unless (numberp($LADCP_firstBin) &&
($LADCP_lastBin eq '*' || numberp($LADCP_lastBin)));
#if (defined($opt_x)) { # decode corrections
# (@pkg_vel_corr_poly) = split(',',$opt_x);
# croak("$0: cannot decode -x $opt_x\n")
# unless (@pkg_vel_corr_poly);
# &antsAddParams('pkg_vel_corr_intercept',$pkg_vel_corr_poly[0],'pkg_vel_corr_slope',$pkg_vel_corr_poly[1]);
#}
&antsFloatOpt(\$opt_x,1);
#if (defined($opt_d)) { # make sure output directory is clean
# croak("$0: old depth-bin files <${opt_d}[0-9][0-9][0-9].dncast> found --- remove before creating new ones!\n")
# if (glob("${opt_d}[0-9][0-9][0-9].dncast"));
# croak("$0: old depth-bin files <${opt_d}[0-9][0-9][0-9].upcast> found --- remove before creating new ones!\n")
# if (glob("${opt_d}[0-9][0-9][0-9].upcast"));
#}
$LADCP_file = &antsFileArg();
if (defined($opt_l) && !defined($opt_0)) { # load per-cast processing parameters
my(@cast_params);
open(PF,$opt_l) || croak("$opt_l: $!\n");
while (<PF>) {
s/#.*//;
@cast_params=split(/\s+/),last if /^$LADCP_file:/;
}
close(PF);
if (@cast_params) { # found valid entry
if ($ARGS[$#ARGS] eq $LADCP_file) { # CTD data on <stdin>
exec($0,@ARGS[0..$#ARGS-1],@cast_params[1..$#cast_params],'-0',$ARGS[$#ARGS]);
die("exec($0,@ARGS[0..$#ARGS-1],@cast_params[1..$#cast_params],'-0',$ARGS[$#ARGS]) failed!\n");
} else { # CTD file specified on cmdline
exec($0,@ARGS[0..$#ARGS-2],@cast_params[1..$#cast_params],'-0',$LADCP_file,$ARGS[$#ARGS]);
die("exec($0,@ARGS[0..$#ARGS-2],@cast_params[1..$#cast_params],'-0',$LADCP_file,$ARGS[$#ARGS]) failed!\n");
}
}
}
#----------------------------------------------------------------------
# Screen Logging
# - warning levels:
# 0 probably unimportant, e.g. nonsensical parameters that probably won't affect solution
# 1 may be somewhat important
# 2 important
#----------------------------------------------------------------------
sub progress(@)
{ printf(STDERR @_) if ($opt_v > 1); }
sub info(@)
{
print(STDERR ($opt_v > 1) ? "\t" : "$LADCP_file: ");
printf(STDERR @_) if ($opt_v > 0);
}
sub warning(@)
{
my($lvl,@msg) = @_;
return if ($opt_v == 0);
print(STDERR "\n") if ($opt_v > 1);
print(STDERR "WARNING (level $lvl): ");
printf(STDERR @msg);
print(STDERR "\n") if ($opt_v > 1);
}
sub debugmsg(@)
{ printf(STDERR @_) if ($opt_v > 2); }
#----------------
# Read LADCP data
#----------------
progress("Reading LADCP data ($LADCP_file)...\n");
readData($LADCP_file,\%LADCP);
progress("\t%d ensembles\n",scalar(@{$LADCP{ENSEMBLE}}));
croak("$LADCP_file: not enough LADCP bins ($LADCP{N_BINS}) for choice of -r\n")
unless ($LADCP{N_BINS} >= $refLr_lastBin);
croak("$0: first reference-layer bin outside valid range\n")
unless ($refLr_firstBin>=1 && $refLr_firstBin<=$LADCP{N_BINS});
croak("$0: last reference-layer bin outside valid range\n")
unless ($refLr_lastBin>=1 && $refLr_lastBin<=$LADCP{N_BINS});
croak("$0: first reference-layer bin > last reference-layer bin\n")
unless ($refLr_firstBin <= $refLr_lastBin);
$LADCP_lastBin = $LADCP{N_BINS}-1
if ($LADCP_lastBin eq '*');
croak("$0: first valid LADCP bin outside valid range\n")
unless ($LADCP_firstBin>=1 && $LADCP_firstBin<=$LADCP{N_BINS});
croak("$0: last valid LADCP bin outside valid range\n")
unless ($LADCP_lastBin>=1 && $LADCP_lastBin<=$LADCP{N_BINS});
croak("$0: first valid LADCP bin > last valid LADCP bin\n")
unless ($LADCP_firstBin <= $LADCP_lastBin);
warning(0,"first reference-layer bin < first valid LADCP bin\n")
unless ($refLr_firstBin >= $LADCP_firstBin);
warning(0,"last reference-layer bin > last valid LADCP bin\n")
unless ($refLr_lastBin <= $LADCP_lastBin);
warning(1,"if at all, bin 1 should not be used for short blank-after-transmit values\n")
if ($LADCP{BLANKING_DISTANCE}<$LADCP{BIN_LENGTH} && $refLr_firstBin==1);
#------------------------------------------------------------
# Edit beam-velocity data
# 1) correlation threshold
# 2) tilt threshold (also sets TILT field in all ensembles)
#------------------------------------------------------------
if ($LADCP{BEAM_COORDINATES}) {
progress("Editing beam-velocity data...\n");
$nvv = $cte = 0;
for ($ens=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
$nvv += countValidBeamVels($ens);
$cte += editCorr($ens,$opt_c);
$pte += editTilt($ens,$opt_t);
}
croak("$LADCP_file: no valid data\n") unless ($nvv > 0);
progress("\tcorrelation threshold (-c %d): %d velocites removed (%d%% of total)\n",$opt_c,$cte,round(100*$cte/$nvv));
progress("\tattitude threshold (-t %d): %d velocites removed (%d%% of total)\n",$opt_t,$pte,round(100*$pte/$nvv));
} else {
progress("Editing velocity data...\n");
$nvv = $cte = 0;
for ($ens=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
$nvv += countValidBeamVels($ens);
$cte += editCorr_Earthcoords($ens,$opt_c);
$pte += editTilt($ens,$opt_t);
}
croak("$LADCP_file: no valid data\n") unless ($nvv > 0);
progress("\tcorrelation threshold (-c %d): %d velocites removed (%d%% of total)\n",$opt_c,$cte,round(100*$cte/$nvv));
progress("\tattitude threshold (-t %d): %d velocites removed (%d%% of total)\n",$opt_t,$pte,round(100*$pte/$nvv));
}
#-------------------------------------------------------------------
# Calculate earth velocities
# - this is done for all bins (not just valid ones), to allow
# useless possibility that invalid bins are used for reflr calcs
# - also calculate separate beam-pair velocities
# - the UNEDITED velocities are saved for the BT calculations
# (W is required, U & V are only used for stats that have not
# been very useful so far)
#-------------------------------------------------------------------
if ($LADCP{BEAM_COORDINATES}) {
progress("Calculating earth-coordinate velocities...\n");
$nvw = 0;
for ($ens=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
for (my($bin)=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
for (my($beam)=0; $beam<4; $beam++) {
$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$beam] *= $opt_x # HACK
if defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$beam]);
}
($LADCP{ENSEMBLE}[$ens]->{U}[$bin],
$LADCP{ENSEMBLE}[$ens]->{V}[$bin],
$LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$LADCP{ENSEMBLE}[$ens]->{ERRVEL}[$bin]) =
velInstrumentToEarth(\%LADCP,$ens,
velBeamToInstrument(\%LADCP,
@{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]}));
$nvw += defined($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
$LADCP{ENSEMBLE}[$ens]->{GIMBAL_PITCH} =
gimbal_pitch($LADCP{ENSEMBLE}[$ens]->{PITCH},$LADCP{ENSEMBLE}[$ens]->{ROLL});
$LADCP{ENSEMBLE}[$ens]->{U_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{U}[$bin];
$LADCP{ENSEMBLE}[$ens]->{V_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{V}[$bin];
$LADCP{ENSEMBLE}[$ens]->{W_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{W}[$bin];
}
}
progress("\t$nvw valid velocities\n");
progress("\t3-beam solutions : $RDI_Coords::threeBeam_1 " .
"$RDI_Coords::threeBeam_2 " .
"$RDI_Coords::threeBeam_3 " .
"$RDI_Coords::threeBeam_4\n")
unless ($opt_4);
} else {
progress("Counting valid vertical velocities...\n");
$nvw = 0;
for ($ens=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
for (my($bin)=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
($LADCP{ENSEMBLE}[$ens]->{U}[$bin],
$LADCP{ENSEMBLE}[$ens]->{V}[$bin],
$LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$LADCP{ENSEMBLE}[$ens]->{ERRVEL}[$bin]) = @{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]};
$nvw += defined($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
$LADCP{ENSEMBLE}[$ens]->{U_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{U}[$bin];
$LADCP{ENSEMBLE}[$ens]->{V_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{V}[$bin];
$LADCP{ENSEMBLE}[$ens]->{W_UNEDITED}[$bin] = $LADCP{ENSEMBLE}[$ens]->{W}[$bin];
$LADCP{ENSEMBLE}[$ens]->{W}[$bin] *= $opt_x # HACK
if defined($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
}
}
progress("\t$nvw valid velocities\n");
}
#----------------------------------------------
# S1 STEP: Edit earth-coordinate -velocity data
# 1) error-velocity threshold
#----------------------------------------------
progress("Editing earth-coordinate velocity data...\n");
$ete = 0;
for ($ens=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
$ete += editErrVel($ens,$opt_e);
}
progress("\t error-velocity threshold (-e %.1f): %d velocites removed (%d%% of total)\n",
$opt_e,$ete,round(100*$ete/$nvw));
#----------------------------
# Calculate LADCP time series
#----------------------------
progress("Calculating LADCP time-series...\n");
($firstGoodEns,$lastGoodEns,$LADCP_atbottom,$LADCP_w_gap_time) =
calcLADCPts(\%LADCP,$refLr_firstBin,$refLr_lastBin,$opt_g);
croak("$LADCP_file: no good ensembles\n")
unless defined($firstGoodEns) && ($lastGoodEns-$firstGoodEns > 0);
my($cast_duration) = $LADCP{ENSEMBLE}[$lastGoodEns]->{ELAPSED} -
$LADCP{ENSEMBLE}[$firstGoodEns]->{ELAPSED};
croak("$0: implausibly short cast ($cast_duration seconds)\n")
unless ($cast_duration > 600);
$LADCP{MEAN_DT} = $cast_duration / ($lastGoodEns-$firstGoodEns-1);
progress("\tStart of cast : %s (#%5d)\n",
$LADCP{ENSEMBLE}[$firstGoodEns]->{TIME},
$LADCP{ENSEMBLE}[$firstGoodEns]->{NUMBER});
progress("\tBottom of cast : %s (#%5d) @ dz~%.1fm\n",
$LADCP{ENSEMBLE}[$LADCP_atbottom]->{TIME},
$LADCP{ENSEMBLE}[$LADCP_atbottom]->{NUMBER},
$LADCP{ENSEMBLE}[$LADCP_atbottom]->{DEPTH});
progress("\tEnd of cast : %s (#%5d)\n",
$LADCP{ENSEMBLE}[$lastGoodEns]->{TIME},
$LADCP{ENSEMBLE}[$lastGoodEns]->{NUMBER});
progress("\tCast duration : %.1f hours (pinging for %.1f hours)\n",
$cast_duration / 3600,
($LADCP{ENSEMBLE}[$#{$LADCP{ENSEMBLE}}]->{UNIX_TIME} -
$LADCP{ENSEMBLE}[0]->{UNIX_TIME}) / 3600);
progress("\tMean ping interval: %.1f seconds\n",$LADCP{MEAN_DT});
#--------------
# Read CTD data
#--------------
progress("Reading CTD data...\n");
croak("$0: no CTD data\n") unless (&antsIn());
undef($antsOldHeaders);
($CTD_elapsed,$CTD_depth,$CTD_svel,$CTD_w,$CTD_w_t) =
&fnr('elapsed','depth','ss','w','w_t');
$CTD_temp = &fnrNoErr('temp');
$CTD_maxdepth = -1;
do {
croak("$0: cannot deal with non-numeric CTD elapsed time\n")
unless &antsNumbers($CTD_elapsed);
push(@{$CTD{ELAPSED}},$ants_[0][$CTD_elapsed]);
push(@{$CTD{DEPTH}}, $ants_[0][$CTD_depth]+$opt_a);
push(@{$CTD{SVEL}}, $ants_[0][$CTD_svel]);
push(@{$CTD{W}}, $ants_[0][$CTD_w]);
push(@{$CTD{W_T}}, $ants_[0][$CTD_w_t]);
push(@{$CTD{TEMP}}, $ants_[0][$CTD_temp]) if defined($CTD_temp);
if ($ants_[0][$CTD_depth]+$opt_a > $CTD_maxdepth) {
$CTD_maxdepth = $ants_[0][$CTD_depth]+$opt_a;
$CTD_atbottom = $#{$CTD{DEPTH}};
}
} while (&antsIn());
$CTD{DT} = ($CTD{ELAPSED}[$#{$CTD{ELAPSED}}] - $CTD{ELAPSED}[0]) / $#{$CTD{ELAPSED}};
progress("\t%d scans at %.1fHz\n",scalar(@{$CTD{DEPTH}}),1/$CTD{DT});
progress("\tstart depth = %.1fm\n",$CTD{DEPTH}[0]);
croak("$0: CTD start depth must be numeric\n")
unless numberp($CTD{DEPTH}[0]);
progress("\tmax depth = %.1fm (# $CTD_atbottom)\n",$CTD_maxdepth);
#--------------------------------------------------------------------
# Construct sound-speed correction profile from CTD 1Hz downcast data
# very simple algorithm that stores the last value found
# in each 1m bin
#--------------------------------------------------------------------
progress("Constructing sound-speed correction profile\n");
my($scans_per_sec) = int(1/$CTD{DT}+0.5);
for (my($s)=0; $s<=$CTD_atbottom; $s+=$scans_per_sec) {
next unless ($CTD{DEPTH}[$s] >= 0 && numberp($CTD{SVEL}[$s]));
$sVelProf[int($CTD{DEPTH}[$s])] = $CTD{SVEL}[$s];
}
#-------------------
# Determine time lag
#-------------------
if (defined($opt_i)) {
progress("Setting initial time lag...\n");
$CTD{TIME_LAG} = $opt_i;
progress("\t-i => elapsed(CTD) ~ elapsed(LADCP) + %.1fs\n",$CTD{TIME_LAG});
} else {
progress("Guestimating time lag...\n");
my($CTD_10pct_down) = my($LADCP_10pct_down) = 0;
$CTD_10pct_down++
until ($CTD{DEPTH}[$CTD_10pct_down]-$CTD{DEPTH}[0] >= 0.1*($CTD_maxdepth-$CTD{DEPTH}[0]));
$LADCP_10pct_down++
until ($LADCP{ENSEMBLE}[$LADCP_10pct_down]->{DEPTH} >= 0.1*$LADCP{ENSEMBLE}[$LADCP_atbottom]->{DEPTH});
$CTD{TIME_LAG} = $CTD{ELAPSED}[$CTD_10pct_down] - $LADCP{ENSEMBLE}[$LADCP_10pct_down]->{ELAPSED};
progress("\telapsed(dz(CTD)=%.1fm) ~ elapsed(dz(LADCP)=%.1fm) + %.1fs\n",
$CTD{DEPTH}[$CTD_10pct_down]-$CTD{DEPTH}[0],$LADCP{ENSEMBLE}[$LADCP_10pct_down]->{DEPTH},$CTD{TIME_LAG});
}
if ($opt_u) {
progress("\tskipping time lagging\n");
} else {
$CTD{TIME_LAG} = calc_lag($n_lags[0],$w_size[0],int(1/$CTD{DT}+0.5));
progress("\telapsed(CTD) ~ elapsed(LADCP) + %.2fs\n",$CTD{TIME_LAG});
$CTD{TIME_LAG} = calc_lag($n_lags[1],$w_size[1],1);
progress("\telapsed(CTD) = elapsed(LADCP) + %.2fs\n",$CTD{TIME_LAG});
}
&antsAddParams('CTD_time_lag',$CTD{TIME_LAG});
#------------------------------------------------
# Merge CTD with LADCP data
# - after this step, reflr w is sound-speed corrected!!!
#------------------------------------------------
progress("Merging CTD with LADCP data...\n");
for (my($skipped)=0,my($ens)=$firstGoodEns; $ens<=$lastGoodEns; $ens++) {
my($scan) = int(($LADCP{ENSEMBLE}[$ens]->{ELAPSED} + $CTD{TIME_LAG} - $CTD{ELAPSED}[0]) / $CTD{DT} + 0.5);
if ($scan <= 0) { # NB: must be <=, rather than <, or assertion below sometimes fails
$skipped++;
$firstGoodEns = $ens+1;
next;
}
if ($skipped > 0) {
info("$skipped initial LADCP ensembles skipped because CTD data begin with LADCP in water\n");
$skipped = 0;
}
if ($scan > $#{$CTD{ELAPSED}}) {
info(sprintf("%d final LADCP ensembles skipped because CTD data end with LADCP in water\n",
$lastGoodEns-$ens+1));
$lastGoodEns = $ens-1;
last;
}
die("assertion failed!\n" .
"\ttest: abs($LADCP{ENSEMBLE}[$ens]->{ELAPSED} + $CTD{TIME_LAG} - $CTD{ELAPSED}[$scan]) <= $CTD{DT}/2\n" .
"\tens = $ens, scan = $scan\n" .
sprintf("\tadjusted LADCP time = %f\n",$LADCP{ENSEMBLE}[$ens]->{ELAPSED} + $CTD{TIME_LAG}) .
sprintf("\tCTD($scan) time = %f\n",$CTD{ELAPSED}[$scan]) .
"=> Did you use SeaBird elapsed time? Don't!"
) unless (abs($LADCP{ENSEMBLE}[$ens]->{ELAPSED} + $CTD{TIME_LAG} - $CTD{ELAPSED}[$scan]) <= $CTD{DT}/2);
$LADCP{ENSEMBLE}[$ens]->{CTD_ELAPSED} = $CTD{ELAPSED}[$scan]; # elapsed field for output
if (defined($LADCP{ENSEMBLE}[$ens]->{REFLR_W}) # not a gap
&& numberp($CTD{DEPTH}[$scan])) {
$LADCP{ENSEMBLE}[$ens]->{REFLR_W} *= $CTD{SVEL}[$scan]/1500; # correct (inadequately) for sound-speed variations
croak(sprintf("\n$0: negative depth (%.1fm) in CTD file at elapsed(CTD) = %.1fs (use -a?)\n",
$CTD{DEPTH}[$scan],$CTD{ELAPSED}[$scan]))
unless ($CTD{DEPTH}[$scan] >= 0);
$LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH} = $CTD{DEPTH}[$scan];
$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN} = $scan;
my($reflr_ocean_w) = $LADCP{ENSEMBLE}[$ens]->{REFLR_W} - $CTD{W}[$scan];
if (abs($reflr_ocean_w) <= $opt_m) {
$sumWsq += &SQR($reflr_ocean_w);
$nWsq++;
if ($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH} > 100 &&
$LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH} < $LADCP{ENSEMBLE}[$LADCP_atbottom]->{CTD_DEPTH}-100) {
$sumWsqI += &SQR($reflr_ocean_w);
$nWsqI++;
}
} else {
undef($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH}); # DON'T USE THIS ENSEMBLE LATER
}
} else{
undef($LADCP{ENSEMBLE}[$ens]->{REFLR_W}); # don't output in time-series file
undef($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH}); # old DEPTH from calcLADCPts()
}
}
if ($nWsq > 0 && $nWsqI > 0) {
&antsAddParams('rms_w_reflr_err',sqrt($sumWsq/$nWsq),'rms_w_reflr_err_interior',sqrt($sumWsqI/$nWsqI));
progress("\t%.2f cm/s rms reference-layer w_ocean, %.2f cm/s away from boundaries\n",
100*sqrt($sumWsq/$nWsq),100*sqrt($sumWsqI/$nWsqI));
warning(0,"%.2f cm/s reference-layer w_ocean away from boundaries\n",100*sqrt($sumWsqI/$nWsqI))
if (sqrt($sumWsqI/$nWsqI) > 0.05);
# croak("$0: rms reference-layer w_ocean is too large\n")
# unless (sqrt($sumWsqI/$nWsqI) < 0.07);
} elsif ($nWsq > 0) {
&antsAddParams('rms_w_reflr_err',sqrt($sumWsq/$nWsq),'rms_w_reflr_err_interior',nan);
progress("\t%.2f cm/s rms reference-layer w_ocean\n",100*sqrt($sumWsq/$nWsq));
} else {
croak("$0: no valid vertical velocities\n");
}
#----------------------------------------------------------------------------
# Remove data contaminated by sidelobe reflection from seabed and sea surface
#----------------------------------------------------------------------------
if ($LADCP{ENSEMBLE}[$LADCP_atbottom]->{XDUCER_FACING_DOWN}) {
&antsAddParams('ADCP_orientation','downlooker');
if (numberp($opt_h)) {
progress("Setting water depth (-h)\n");
$water_depth = $opt_h;
$sig_water_depth = 0;
} else {
progress("Finding seabed...\n");
calc_backscatter_profs($firstGoodEns,$lastGoodEns);
($water_depth,$sig_water_depth) =
find_backscatter_seabed($LADCP{ENSEMBLE}[$LADCP_atbottom]->{CTD_DEPTH});
($water_depth_BT,$sig_water_depth_BT) =
find_seabed(\%LADCP,$LADCP_atbottom,$LADCP{BEAM_COORDINATES});
if (defined($water_depth_BT)) {
my($dd) = abs($water_depth_BT - $water_depth);
warning(2,sprintf("Large RDI vs. own water-depth difference (%.1fm)\n",$dd))
if ($dd > 5);
}
}
&antsAddParams('water_depth',$water_depth,'water_depth.sig',$sig_water_depth);
if (defined($water_depth)) {
if (defined($water_depth_BT)) {
progress("\t%.1f(%.1f) m water depth (%.1f(%.1f)m from BT)\n",
$water_depth,$sig_water_depth,$water_depth_BT,$sig_water_depth_BT);
} else {
progress("\t%.1f(%.1f) m water depth\n",$water_depth,$sig_water_depth);
}
warning(1,sprintf("large uncertainty in water-depth estimation (%.1fm)\n",$sig_water_depth))
if ($sig_water_depth > $LADCP{BIN_LENGTH});
progress("Editing data to remove sidelobe interference from seabed...\n");
($nvrm,$nerm) = editSideLobes($firstGoodEns,$lastGoodEns,$water_depth);
progress("\t$nvrm velocities from $nerm ensembles removed\n");
} else {
info("no seabed found in backscatter profiles --- no sidelobe editing done\n");
}
} else {
&antsAddParams('ADCP_orientation','uplooker');
progress("Editing data to remove sidelobe interference from sea surface...\n");
($nvrm,$nerm) = editSideLobes($firstGoodEns,$lastGoodEns,undef);
progress("\t$nvrm velocities from $nerm ensembles removed\n");
}
#---------------------------------------------------------------------------
# Depth-bin LADCP velocity data
#
# NOTES:
# 1) ensemble and bin numbers are saved for maximum flexibility
# 2) only ensemble/bins with valid vertical velocities are saved
# 3) applying the full soundspeed correction to w is most likely pointless in
# practice, but hey!, CPU cycles are cheap; [in a cast in the Gulf of Mexico
# which has fairly pronounce soundspeed gradients, the max value of Kn
# is 1.00004160558372, which gives rise to a correction of less than 0.2mm/s
# at a winch+wave speed of 3m/s....]
# 4) as far as I can tell, the soundspeed correction for bin length also
# has only a minute effect
#---------------------------------------------------------------------------
progress("Binning velocities...\n");
progress("\tdowncast...\n");
for ($ens=$firstGoodEns; $ens<$LADCP_atbottom; $ens++) { # downcast
next unless numberp($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH});
my(@bindepth) = calc_binDepths($ens);
for ($bin=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
next unless numberp($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin] =
sscorr_w($LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH},
$bindepth[$bin]);
my($bi) = $bindepth[$bin]/$opt_o;
push(@{$DNCAST{ENSEMBLE}[$bi]},$ens);
push(@{$DNCAST{ELAPSED}[$bi]},$CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]);
push(@{$DNCAST{CTD_W}[$bi]},$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]);
push(@{$DNCAST{BIN}[$bi]},$bin);
push(@{$DNCAST{DEPTH}[$bi]},$bindepth[$bin]);
push(@{$DNCAST{W}[$bi]},$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin]);
# bin apparent ocean velocities as
# a function of package velocity
# push(@{$DNCAST{PKGCORR_W}[10*round($CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],0.1)+50]},
# $LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin])
# if defined($opt_p);
}
}
#if (defined($opt_x)) { # apply polynomial package-velocity correction
# progress("\t\tapplying package_velocity correction...\n");
# for (my($bi)=0; $bi<=$#{$DNCAST{ENSEMBLE}}; $bi++) {
# for (my($i)=0; $i<@{$DNCAST{W}[$bi]}; $i++) {
# for (my($e)=0; $e<@pkg_vel_corr_poly; $e++) {
# $DNCAST{W}[$bi][$i] -= $pkg_vel_corr_poly[$e] *
# $CTD{W}[$LADCP{ENSEMBLE}[$DNCAST{ENSEMBLE}[$bi][$i]]->{CTD_SCAN}]**$e;
# }
# }
# }
#}
for (my($bi)=0; $bi<=$#{$DNCAST{ENSEMBLE}}; $bi++) { # bin data
$DNCAST{MEAN_DEPTH}[$bi] = avg(@{$DNCAST{DEPTH}[$bi]});
$DNCAST{MEAN_ELAPSED}[$bi] = avg(@{$DNCAST{ELAPSED}[$bi]});
$DNCAST{MEDIAN_W}[$bi] = median(@{$DNCAST{W}[$bi]});
$DNCAST{MAD_W}[$bi] = mad2($DNCAST{MEDIAN_W}[$bi],@{$DNCAST{W}[$bi]});
$DNCAST{N_SAMP}[$bi] = @{$DNCAST{W}[$bi]};
}
progress("\tupcast...\n"); # upcast
for ($ens=$LADCP_atbottom; $ens<=$lastGoodEns; $ens++) {
next unless numberp($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH});
my(@bindepth) = calc_binDepths($ens);
for ($bin=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
next unless numberp($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin] =
sscorr_w($LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH},
$bindepth[$bin]);
my($bi) = $bindepth[$bin]/$opt_o;
push(@{$UPCAST{ENSEMBLE}[$bi]},$ens);
push(@{$UPCAST{ELAPSED}[$bi]},$CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]);
push(@{$UPCAST{CTD_W}[$bi]},$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]);
push(@{$UPCAST{BIN}[$bi]},$bin);
push(@{$UPCAST{DEPTH}[$bi]},$bindepth[$bin]);
push(@{$UPCAST{W}[$bi]},$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin]);
# push(@{$UPCAST{PKGCORR_W}[10*round($CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],0.1)+50]},
# $LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin])
# if defined($opt_p);
}
}
#if (defined($opt_x)) {
# progress("\t\tapplying package-velocity correction...\n");
# for (my($bi)=0; $bi<=$#{$UPCAST{ENSEMBLE}}; $bi++) {
# for (my($i)=0; $i<@{$UPCAST{W}[$bi]}; $i++) {
# for (my($e)=0; $e<@pkg_vel_corr_poly; $e++) {
# $UPCAST{W}[$bi][$i] -= $pkg_vel_corr_poly[$e] *
# $CTD{W}[$LADCP{ENSEMBLE}[$UPCAST{ENSEMBLE}[$bi][$i]]->{CTD_SCAN}]**$e;
# }
# }
# }
#}
for (my($bi)=0; $bi<=$#{$UPCAST{ENSEMBLE}}; $bi++) {
$UPCAST{MEAN_DEPTH}[$bi] = avg(@{$UPCAST{DEPTH}[$bi]});
$UPCAST{MEAN_ELAPSED}[$bi] = avg(@{$UPCAST{ELAPSED}[$bi]});
$UPCAST{MEDIAN_W}[$bi] = median(@{$UPCAST{W}[$bi]});
$UPCAST{MAD_W}[$bi] = mad2($UPCAST{MEDIAN_W}[$bi],@{$UPCAST{W}[$bi]});
$UPCAST{N_SAMP}[$bi] = @{$UPCAST{W}[$bi]};
}
#--------------------------------------------------
# Calculate BT-referenced vertical-velocity profile
#--------------------------------------------------
if (defined($water_depth)) {
progress("Calculating BT-referenced vertical velocities\n");
calc_BTprof($firstGoodEns,$lastGoodEns,$water_depth,$sig_water_depth);
my($sumSq) = my($n) = 0;
for (my($bi)=0; $bi<=$#{$BT{MEDIAN_W}}; $bi++) {
next unless defined($BT{MEDIAN_W}[$bi]);
next unless ($BT{N_SAMP}[$bi]>=$opt_s && $DNCAST{N_SAMP}[$bi]>=$opt_s && $UPCAST{N_SAMP}[$bi]>=$opt_s);
$sumSq += ($BT{MEDIAN_W}[$bi] - $DNCAST{MEDIAN_W}[$bi]/2 - $UPCAST{MEDIAN_W}[$bi]/2)**2;
$n++;
}
if ($n > 0) {
my($rms) = round(sqrt($sumSq/$n),0.001);
&antsAddParams('BT_rms_w_discrepancy',$rms);
progress("\t$rms m/s rms vertical-velocity discrepancy\n");
}
}
#---------------
# Output profile
#---------------
progress("Writing vertical-velocity profile...\n");
@antsNewLayout = ('depth','dc_depth','dc_elapsed','dc_w','dc_w.mad','dc_w.N',
'uc_depth','uc_elapsed','uc_w','uc_w.mad','uc_w.N',
'elapsed','w','w.mad','w.N',
'BT_w','BT_w.mad','BT_w.N');
for (my($bi)=0; $bi<=max($#{$DNCAST{ENSEMBLE}},$#{$UPCAST{ENSEMBLE}},$#{$BT{NSAMP}}); $bi++) {
&antsOut(($bi+0.5)*$opt_o, # nominal depth
$DNCAST{MEAN_DEPTH}[$bi],$DNCAST{MEAN_ELAPSED}[$bi],
$DNCAST{N_SAMP}[$bi]>=$opt_s?$DNCAST{MEDIAN_W}[$bi]:nan,
$DNCAST{MAD_W}[$bi],$DNCAST{N_SAMP}[$bi],
$UPCAST{MEAN_DEPTH}[$bi],$UPCAST{MEAN_ELAPSED}[$bi],
$UPCAST{N_SAMP}[$bi]>=$opt_s?$UPCAST{MEDIAN_W}[$bi]:nan,
$UPCAST{MAD_W}[$bi],$UPCAST{N_SAMP}[$bi],
$DNCAST{MEAN_ELAPSED}[$bi]/2+$UPCAST{MEAN_ELAPSED}[$bi]/2,
$DNCAST{N_SAMP}[$bi]+$UPCAST{N_SAMP}[$bi]>=$opt_s ?
($DNCAST{MEDIAN_W}[$bi]*$DNCAST{N_SAMP}[$bi]+$UPCAST{MEDIAN_W}[$bi]*$UPCAST{N_SAMP}[$bi]) / ($DNCAST{N_SAMP}[$bi]+$UPCAST{N_SAMP}[$bi]) :
nan,
$DNCAST{N_SAMP}[$bi]+$UPCAST{N_SAMP}[$bi]>=$opt_s ?
($DNCAST{MAD_W}[$bi]*$DNCAST{N_SAMP}[$bi]+$UPCAST{MAD_W}[$bi]*$UPCAST{N_SAMP}[$bi]) / ($DNCAST{N_SAMP}[$bi]+$UPCAST{N_SAMP}[$bi]) :
nan,
$DNCAST{N_SAMP}[$bi]+$UPCAST{N_SAMP}[$bi],
$BT{N_SAMP}[$bi]>=$opt_s?$BT{MEDIAN_W}[$bi]:nan,
$BT{MAD_W}[$bi],$BT{N_SAMP}[$bi]
);
}
#-------------------------------------
# diagnostic output with all residuals
#-------------------------------------
if (defined($opt_d)) {
progress("Writing residuals-diagnostic data to <$opt_d>...\n");
@antsNewLayout = ('ensemble','bin','elapsed','depth','downcast',
'w','residual','CTD_w','LADCP_w','errvel',
'pitch','roll','tilt','heading','3_beam','svel');
&antsOut('EOF');
close(STDOUT);
open(STDOUT,">$opt_d") || croak("$opt_d: $!\n");
for ($ens=$firstGoodEns; $ens<$LADCP_atbottom; $ens++) { # downcast
next unless numberp($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH});
my(@bindepth) = calc_binDepths($ens);
for ($bin=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
next unless numberp($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
my($bi) = $bindepth[$bin]/$opt_o;
&antsOut(
$ens,$bin,$CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$bindepth[$bin],$ens<=$LADCP_atbottom,
$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin],
$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin] - $DNCAST{MEDIAN_W}[$bi],
$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$LADCP{ENSEMBLE}[$ens]->{ERRVEL}[$bin],
$LADCP{ENSEMBLE}[$ens]->{PITCH},
$LADCP{ENSEMBLE}[$ens]->{ROLL},
$LADCP{ENSEMBLE}[$ens]->{TILT},
$LADCP{ENSEMBLE}[$ens]->{HEADING},
(defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][0]) + # only works for beam coords
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][1]) +
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][2]) +
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][3])) < 4,
$CTD{SVEL}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
);
}
}
for ($ens=$LADCP_atbottom; $ens<=$lastGoodEns; $ens++) { # upcast
next unless numberp($LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH});
my(@bindepth) = calc_binDepths($ens);
for ($bin=$LADCP_firstBin-1; $bin<=$LADCP_lastBin-1; $bin++) {
next unless numberp($LADCP{ENSEMBLE}[$ens]->{W}[$bin]);
my($bi) = $bindepth[$bin]/$opt_o;
&antsOut(
$ens,$bin,$CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$bindepth[$bin],
$LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin] - $UPCAST{MEDIAN_W}[$bi],
$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{W}[$bin],
$LADCP{ENSEMBLE}[$ens]->{ERRVEL}[$bin],
$LADCP{ENSEMBLE}[$ens]->{PITCH},
$LADCP{ENSEMBLE}[$ens]->{ROLL},
$LADCP{ENSEMBLE}[$ens]->{TILT},
$LADCP{ENSEMBLE}[$ens]->{HEADING},
(defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][0]) + # only works for beam coords
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][1]) +
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][2]) +
defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][3])) < 4,
$CTD{SVEL}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
);
}
}
}
#-----------------------------
# package-velocity effect file
#-----------------------------
#if (defined($opt_p)) {
# progress("Writing package-velocity effect data to <$opt_p>...\n");
#
# @antsNewLayout = ('CTD_w','dc_w','dc_w.mad','dc_w.N','uc_w','uc_w.mad','uc_w.N','dc_w_corr','uc_w_corr');
# &antsOut('EOF');
#
# close(STDOUT);
# open(STDOUT,">$opt_p") || croak("$opt_p: $!\n");
#
# for (my($bi)=0; $bi<=max($#{$DNCAST{PKGCORR_W}},$#{$UPCAST{PKGCORR_W}}); $bi++) {
# my($dc_N) = scalar(@{$DNCAST{PKGCORR_W}[$bi]});
# my($uc_N) = scalar(@{$UPCAST{PKGCORR_W}[$bi]});
# next unless ($dc_N>0 || $uc_N>0);
# my($dc_w) = median(@{$DNCAST{PKGCORR_W}[$bi]});
# my($uc_w) = median(@{$UPCAST{PKGCORR_W}[$bi]});
# my($w) = ($bi-50) / 10;
## if (defined($opt_x)) {
## my($dc_corr) = my($uc_corr) = 0;
## for (my($e)=0; $e<@pkg_vel_corr_poly; $e++) {
## $dc_corr += $pkg_vel_corr_poly[$e]*$w**$e;
## }
## for (my($e)=0; $e<@pkg_vel_corr_poly; $e++) {
## $uc_corr += $pkg_vel_corr_poly[$e]*$w**$e;
## }
## &antsOut($w,$dc_w,mad2($dc_w,@{$DNCAST{PKGCORR_W}[$bi]}),$dc_N,
## $uc_w,mad2($uc_w,@{$UPCAST{PKGCORR_W}[$bi]}),$uc_N,
## $dc_corr,$uc_corr);
## } else {
# &antsOut($w,$dc_w,mad2($dc_w,@{$DNCAST{PKGCORR_W}[$bi]}),$dc_N,
# $uc_w,mad2($uc_w,@{$UPCAST{PKGCORR_W}[$bi]}),$uc_N);
## }
# }
#}
#--------------------------------------
# write time-series output if requested
#--------------------------------------
if (defined($opt_f)) {
progress("Writing time-series data to <$opt_f>...\n");
@antsNewLayout = ('ens','elapsed',
'depth','sound_speed','pitch','gimbal_pitch','roll','tilt','heading',
'CTD_w','CTD_w_t','LADCP_reflr_w','LADCP_reflr_w_err',
'ocean_reflr_w');
&antsOut('EOF');
close(STDOUT);
open(STDOUT,">$opt_f") || croak("$opt_f: $!\n");
for ($ens=$firstGoodEns; $ens<=$lastGoodEns; $ens++) {
my($reflr_w) = defined($LADCP{ENSEMBLE}[$ens]->{REFLR_W})
? $LADCP{ENSEMBLE}[$ens]->{REFLR_W} - $CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]
: undef;
&antsOut($ens,
$CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{CTD_DEPTH},
$CTD{SVEL}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{PITCH},
$LADCP{ENSEMBLE}[$ens]->{GIMBAL_PITCH},
$LADCP{ENSEMBLE}[$ens]->{ROLL},
$LADCP{ENSEMBLE}[$ens]->{TILT},
$LADCP{ENSEMBLE}[$ens]->{HEADING},
$CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$CTD{W_T}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
$LADCP{ENSEMBLE}[$ens]->{REFLR_W},
$LADCP{ENSEMBLE}[$ens]->{REFLR_W_ERR},
$reflr_w);
}
close(STDOUT);
undef($antsHeadersPrinted);
}
#--------------------------------------------------------------------------------------------
# Output all bins as separate files if requested
# NB: - vertical LADCP velocities are corrected inaccurately for sound-speed variations!!!!
# - full correction is used, on the other hand, for ocean velocities (w)
#--------------------------------------------------------------------------------------------
#if (defined($opt_d)) {
#
# sub outProfBinRec($$$)
# {
# my($ens,$bin,$depth) = @_;
# my($sscorr) = $CTD{SVEL}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}]/1500;
#
# &antsOut($ens,
# $bin,
# $CTD{ELAPSED}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
# $depth,
# $CTD{SVEL}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
# $LADCP{ENSEMBLE}[$ens]->{PITCH},
# $LADCP{ENSEMBLE}[$ens]->{GIMBAL_PITCH},
# $LADCP{ENSEMBLE}[$ens]->{ROLL},
# $LADCP{ENSEMBLE}[$ens]->{TILT},
# $LADCP{ENSEMBLE}[$ens]->{HEADING},
# $CTD{W}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
# $CTD{W_T}[$LADCP{ENSEMBLE}[$ens]->{CTD_SCAN}],
# $LADCP{ENSEMBLE}[$ens]->{W}[$bin]*$sscorr,
# $LADCP{ENSEMBLE}[$ens]->{ERRVEL}[$bin],
# $LADCP{ENSEMBLE}[$ens]->{REFLR_W},
# $LADCP{ENSEMBLE}[$ens]->{REFLR_W_ERR},
# $LADCP{ENSEMBLE}[$ens]->{SSCORRECTED_OCEAN_W}[$bin]);
# }
#
# progress("Writing profile-bin data of downcast...\n");
#
# $commonParams = $antsCurParams;
# @antsNewLayout = ('ens','bin','elapsed','depth','sound_speed','pitch','gimbal_pitch',
# 'roll','tilt','heading','CTD_w','CTD_w_t','LADCP_w','LADCP_errvel',
# 'LADCP_reflr_w','LADCP_reflr_w_err','w');
#
# for (my($bi)=0; $bi<=$#{$DNCAST{ENSEMBLE}}; $bi++) {
# my($fn) = sprintf("$opt_d%03d.dncast",$bi);
# &antsOut('EOF');
# close(STDOUT);
# open(STDOUT,">$fn") || croak("$fn: $!\n");
# $antsCurParams = $commonParams;
# &antsAddParams('CTD_w',avg(@{$DNCAST{CTD_W}[$bi]}));
# for (my($eii)=0; $eii<=$#{$DNCAST{ENSEMBLE}[$bi]}; $eii++) {
# &outProfBinRec($DNCAST{ENSEMBLE}[$bi][$eii],$DNCAST{BIN}[$bi][$eii],$DNCAST{DEPTH}[$bi][$eii]);
# }
# }
#
# progress("Writing profile-bin data of upcast...\n");
#
# for (my($bi)=0; $bi<=$#{$UPCAST{ENSEMBLE}}; $bi++) {
# my($fn) = sprintf("$opt_d%03d.upcast",$bi);
# &antsOut('EOF');
# close(STDOUT);
# open(STDOUT,">$fn") || croak("$fn: $!\n");
# $antsCurParams = $commonParams;
# &antsAddParams('CTD_w',avg(@{$UPCAST{CTD_W}[$bi]}));
# for (my($eii)=0; $eii<=$#{$UPCAST{ENSEMBLE}[$bi]}; $eii++) {
# &outProfBinRec($UPCAST{ENSEMBLE}[$bi][$eii],$UPCAST{BIN}[$bi][$eii],$UPCAST{DEPTH}[$bi][$eii]);
# }
# close(STDOUT);
# }
#}
&antsExit();