#!/usr/bin/perl
#======================================================================
#                    L A D C P P R O C 
#                    doc: Thu Sep 16 20:36:10 2010
#                    dlm: Tue Oct 26 14:29:05 2010
#                    (c) 2010 A.M. Thurnherr & E. Firing
#                    uE-Info: 299 61 NIL 0 0 72 2 2 4 NIL ofnI
#======================================================================

$antsSummary = 'process LADCP data to get shear, time series';

# NOTES:
#	- THE CORE OF THIS CODE IS A SIMPLE TRANSCRIPTION OF MERGE.C WRITTEN BY ERIC FIRING
#	- comments starting with ## are taken from Eric's code
#	- CTD elapsed time is estimated from recno * CTD_sampint
#	- CTD_elapsed is undefined for records before instrument is in the water
#	- ITS-90 temp field in degC required
#	- salin field prequired
#	- pressure field in dbar required

# HISTORY:
#	Sep 16, 2010: - incepted
#	Oct 13, 2010: - first working version
#	Oct 14, 2010: - renamed from LADCPshear
#	Oct 19, 2010: - added -a)coustic backscatter profiles
#	Oct 20, 2010: - added -2)dary CTD sensors
#	Oct 23, 2010: - added magnetic-declination correction
#	Oct 26, 2010: - added tilt calculation

($ANTS) 	  = (`which list` =~ m{^(.*)/[^/]*$});
($PERL_TOOLS) = (`which mkProfile` =~ m{^(.*)/[^/]*$});
($LADCPPROC)  = ($0 =~ m{^(.*)/[^/]*$});

require "$ANTS/ants.pl";
require "$ANTS/libEOS83.pl";
require "$ANTS/libstats.pl";
require "$LADCPPROC/LADCPproc.bestLag";
require "$LADCPPROC/LADCPproc.BT";
require "$LADCPPROC/LADCPproc.backscatter";
require "$LADCPPROC/LADCPproc.UHcode";
require "$PERL_TOOLS/RDI_BB_Read.pl";
require "$PERL_TOOLS/RDI_Coords.pl";
require "$PERL_TOOLS/RDI_Utils.pl";

$antsParseHeader = 0;
&antsUsage('24ab:df:l:n:ops:t:w:',2,
	'[use -2)dary CTD sensor pair]',
	'[require -4)-beam LADCP solutions]',
	'[-s)etup <file>]',
	'[enable -p)PI editing]',
	'[-l)ag LADCP <by>] [auto-lag -w)indow <size[60s]>] [-n) <auto-lag windows[20]]',
	'[-d)iagnostic output]',
	'output: [-t)ime series <file>] [-f)lag <file>] [-b)ottom-track <file>]',
	'        [-a)coustic backscatter profiles] [b-o)toom-track profs]',
	'<RDI file> <SeaBird file>');

$RDI_Coords::minValidVels = 4 if ($opt_4);

&antsFloatOpt($opt_l);
&antsCardOpt(\$opt_w,60);
	# old default of -w 30 does not work if there are significant ambiguity-velocity
	# problems, as is the case, e.g., with 2010_DIMES_US2 station 142
&antsCardOpt(\$opt_n,20);

$LADCP_file = &antsFileArg();
$CTD_file 	= &antsFileArg();

&antsAddParams('LADCP_file',$LADCP_file,'CTD_file',$CTD_file);
&antsActivateOut();

#----------------------------------------------------------------------
# Step 1: Read Data
#----------------------------------------------------------------------

print(STDERR "Reading LADCP data ($LADCP_file)...");
readData($LADCP_file,\%LADCP);
printf(STDERR "\n\t%d ensembles\n",scalar(@{$LADCP{ENSEMBLE}}));

print(STDERR "Reading CTD data ($CTD_file)...");
open(F,$CTD_file) || croak("$CTD_file: $!\n");
while (1) {															# parse header
	chomp($hdr = <F>);
	$hdr =~ s/\r*$//;
	croak("$0: unexpected EOF (format error)\n") unless defined($hdr);
	last if ($hdr eq '*END*');
	
	$CTD_nfields = $',next if ($hdr =~ /nquan = /);					# Layout
	$CTD_nrecs = $',next if ($hdr =~ /nvalues = /);
	$pressF = $1,next if ($hdr =~ /name (\d+) = prDM:/);
	if ($opt_2) {
		$tempF  = $1,next if ($hdr =~ /name (\d+) = t190C:/);
		$salinF = $1,next if ($hdr =~ /name (\d+) = sal11:/);
	} else {
		$tempF  = $1,next if ($hdr =~ /name (\d+) = t090C:/);
		$salinF = $1,next if ($hdr =~ /name (\d+) = sal00:/);
	}

	&antsAddParams('start_time',$1),next							# selected metadata
		if ($hdr =~ /start_time = (.*)/);

	&antsAddParams('station',$1),next
		if ($hdr =~ /Station\s*:\s*(.*)/);
	&antsAddParams('ship',$1),next
		if ($hdr =~ /Ship\s*:\s*(.*)\s*$/);
	&antsAddParams('cruise',$1),next
		if ($hdr =~ /Cruise\s*:\s*(.*)\s*$/);
	&antsAddParams('time',$1),next
		if ($hdr =~ /Time\s*:\s*(.*)/);
	&antsAddParams('date',$1),next
		if ($hdr =~ /Date\s*:\s*(.*)/);

	if ($hdr =~ /Latitude\s*[=:]\s*/) {
		($deg,$min,$NS) = split(/ /,$');
		$lat = $deg + $min/60;
		$lat *= -1 if ($NS eq 'S');
		&antsAddParams('lat',$lat);
		next;
	}
	if ($hdr =~ /Longitude\s*[=:]\s*/) {
		($deg,$min,$EW) = split(/ /,$');
		$lon = $deg + $min/60;
		$lon *= -1 if ($EW eq 'W');
		&antsAddParams('lon',$lon);
		next;
	}
	
	if ($hdr =~ /interval = seconds: /) {
		$CTD_sampint = 1*$';
		&antsAddParams('CTD_interval',1/$CTD_sampint);
		next;
	}
	
	$CTD_badval = $',next
		if ($hdr =~ /bad_flag = /);	
	$CTD_file_type = $',next
		if ($hdr =~ /file_type = /);	
}

croak("$CTD_file: cannot determine CTD file layout\n")
	unless ($CTD_nfields && $CTD_nrecs);
croak("$CTD_file: cannot determine missing value\n")
	unless defined($CTD_badval);
croak("$CTD_file: not a CTD time series file\n")
	unless ($CTD_sampint);
croak("$CTD_file: no pressure field\n")
	unless defined($pressF);
croak("$CTD_file: no suitable temperature field\n")
	unless defined($tempF);
croak("$CTD_file: no suitable salinity field\n")
	unless defined($salinF);

croak("$0: unknown latitude\n") unless defined($lat);
croak("$0: unknown longitude\n") unless defined($lon);

&antsAddParams('ITS',$P{ITS} = 90);

if ($CTD_file_type eq 'ascii') {
	while (1) {
		last unless (@rec = &antsFileIn(F));
		push(@CTD_press,($rec[$pressF] == $CTD_badval) ? nan : $rec[$pressF]);
		push(@CTD_temp, ($rec[$tempF]  == $CTD_badval) ? nan : $rec[$tempF]);
		push(@CTD_salin,($rec[$salinF] == $CTD_badval) ? nan : $rec[$salinF]);
	}
} elsif ($CTD_file_type eq 'binary') {

	my($fbits) = 8 * length(pack('f',0));
	croak(sprintf("$0: incompatible native CPU float representation (%d instead of 32bits)\n",fbits))
		unless ($fbits == 32);	
		
	croak("$CTD_file: can't read binary data\n")
		unless (read(F,$dta,4*$CTD_nfields*$CTD_nrecs) == 4*$CTD_nfields*$CTD_nrecs);
	print(STDERR "$CTD_file: WARNING: extraneous data at EOF\n") unless eof(F);

	$dta = pack('V*',unpack('N*',$dta))				# big-endian CPU
		if (unpack('h*', pack('s', 1)) =~ /01/);	# c.f. perlport(1)
	
	@dta = unpack("f*",$dta);

	for ($r=0; $r<$CTD_nrecs; $r++) {
		push(@CTD_press,($dta[$r*$CTD_nfields+$pressF] == $CTD_badval) ? nan : $dta[$r*$CTD_nfields+$pressF]);
		push(@CTD_temp, ($dta[$r*$CTD_nfields+$tempF]  == $CTD_badval) ? nan : $dta[$r*$CTD_nfields+$tempF]);
		push(@CTD_salin,($dta[$r*$CTD_nfields+$salinF] == $CTD_badval) ? nan : $dta[$r*$CTD_nfields+$salinF]);
	}
} else {
	croak("$CTD_file: unknown CTD file type $CTD_file_type\n");
}

printf(STDERR "\n\t%d scans\n",scalar(@CTD_press));

#----------------------------------------------------------------------
# Step 2: Set Processing Parameters
#----------------------------------------------------------------------

print(STDERR "Setting processing parameters...\n");

printf(STDERR "\tloading $LADCPPROC/LADCPproc.defaults...\n");
require "$LADCPPROC/LADCPproc.defaults";

if (defined($opt_s)) {
	print(STDERR "\tloading $opt_s...\n");
	require $opt_s;
}

if ($LADCP{BLANKING_DISTANCE} == 0) {
	print(STDERR "\t\tBLANKING_DISTANCE == 0 => excluding all data from bin 1\n")
		if ($opt_d);
	$wbin_start = 2 unless ($wbin_start > 2);
	$ubin_start = 2 unless ($ubin_start > 2);
	$shbin_start = 2 unless ($shbin_start > 2);
}

&antsAddParams('ADCP_orientation',
		$dta->{ENSEMBLE}[0]->{XDUCER_FACING_UP} ? 'uplooker' : 'downlooker');

$SHEAR_PREGRID_DZ = 20;
$GRID_DZ = 5;

my($year)  = substr($LADCP{ENSEMBLE}[0]->{DATE},6,4);
my($month) = substr($LADCP{ENSEMBLE}[0]->{DATE},0,2);
my($dau  ) = substr($LADCP{ENSEMBLE}[0]->{DATE},3,2);
my($magdec,$maginc,$h_strength,$v_strength) = split('\s+',`magdec $lon $lat $year $month $day`);

croak("$0: unknown magnetic declination\n")
	unless defined($magdec);

&antsAddParams('magnetic_declination',$magdec);

#----------------------------------------------------------------------
# Step 3: Pre-Process CTD & LADCP Data
#----------------------------------------------------------------------

printf(STDERR "Pre-processing data...");
printf(STDERR "\n\tCTD...");

#------------------------
# clean CTD pressure data
#------------------------
my($pSpikes) = 0;
for (my($r)=1; $r<$CTD_nrecs; $r++) {
	$pSpikes++,$CTD_press[$r]=nan
		if (abs($CTD_press[$r]-$CTD_press[$r-1])/$CTD_sampint > 2);
}
print(STDERR "\n\t\t$pSpikes pressure spikes removed")
	if ($pSpikes>0 && $opt_d);

#------------------------------------
# calculate w and find deepest record
#------------------------------------
$CTD_maxpress = -9e99;
for (my($r)=1; $r<$CTD_nrecs-1; $r++) {
	$CTD_w[$r] = 0.99*($CTD_press[$r+1] - $CTD_press[$r-1]) / (2*$CTD_sampint);
	if ($CTD_press[$r] > $CTD_maxpress) {
		$CTD_maxpress = $CTD_press[$r];
		$CTD_bottom = $r;
    }										
}
print(STDERR "\n");

#----------------------------------------------------------------------
# Step 2b: Pre-Process LADCP Data
#----------------------------------------------------------------------

print(STDERR "\tLADCP...");

#-------------------------------------------
# transform to earth coordinates if required
#-------------------------------------------

$U = 0;		# velocity indices
$V = 1;
$W = 2;
$E = 3;

$LADCP{HEADING_BIAS} = -$magdec;

if ($LADCP{BEAM_COORDINATES}) {
	print(STDERR "\n\t\ttransforming beam to Earth coordinates...")
		if ($opt_d);
	for (my($ens)=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
		$LADCP{ENSEMBLE}[$ens]->{TILT} = &angle_from_vertical($LADCP{ENSEMBLE}[$ens]->{PITCH},$LADCP{ENSEMBLE}[$ens]->{ROLL});
		for (my($bin)=0; $bin<$LADCP{N_BINS}; $bin++) {
			@{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]} =
				velInstrumentToEarth(\%LADCP,$ens,velBeamToInstrument(\%LADCP,@{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]}));
			@{$LADCP{ENSEMBLE}[$ens]->{PERCENT_GOOD}[$bin]} =					# fake it to fool ref_lr_w
				(0,0,0,defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$W]) ? 100 : 0);
		}
	}
	$LADCP{BEAM_COORDINATES} = 0;
	$LADCP{EARTH_COORDINATES} = 1;
	unless ($opt_4) {
		print(STDERR "\n\t\t\t3-beam solutions: $RDI_Coords::threeBeam_1 $RDI_Coords::threeBeam_2 $RDI_Coords::threeBeam_3 $RDI_Coords::threeBeam_4")
			if ($opt_d);
		&antsAddParams('3_beam_solutions',"$RDI_Coords::threeBeam_1 $RDI_Coords::threeBeam_2 $RDI_Coords::threeBeam_3 $RDI_Coords::threeBeam_4");
	}
} elsif ($LADCP{EARTH_COORDINATES}) {
	printf(STDERR "\n\t\tcorrecting for magnetic declination of %.1f deg...",$magdec)
		if ($opt_d);
	for (my($ens)=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {
		$LADCP{ENSEMBLE}[$ens]->{TILT} = &angle_from_vertical($LADCP{ENSEMBLE}[$ens]->{PITCH},$LADCP{ENSEMBLE}[$ens]->{ROLL});
		for (my($bin)=0; $bin<$LADCP{N_BINS}; $bin++) {
			@{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]} =
				velApplyHdgBias(\%LADCP,$ens,@{$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin]});
		}
	}
} else {
	croak("$0: can only handle beam or earth coordinates\n")
}

print(STDERR "\n");

#------------------------------------------------------
# construct a depth-vs-time "profile" from the raw data
#------------------------------------------------------

print(STDERR "\t\tconstructing profile time series...")
	if ($opt_d);
	
($LADCP_start,$LADCP_end,$LADCP_bottom,$w_gap_time,$zErr,$maxz) =
    mk_prof(\%LADCP,0,undef,1,6,70,0.1,9999);
croak("\n$LADCP_file: no good ensembles found\n")
    unless defined($LADCP_start);

if ($opt_d) {
	printf(STDERR "\n\t\t\tStart of cast    : %s (#%5d) at %6.1fm\n",
	                    $LADCP{ENSEMBLE}[$LADCP_start]->{TIME},
	                    $LADCP{ENSEMBLE}[$LADCP_start]->{NUMBER},
	                    $LADCP{ENSEMBLE}[$LADCP_start]->{DEPTH});
	printf(STDERR "\t\t\tBottom of cast   : %s (#%5d) at %6.1fm\n",
	                    $LADCP{ENSEMBLE}[$LADCP_bottom]->{TIME},
	                    $LADCP{ENSEMBLE}[$LADCP_bottom]->{NUMBER},
	                    $LADCP{ENSEMBLE}[$LADCP_bottom]->{DEPTH});
	printf(STDERR "\t\t\tEnd of cast      : %s (#%5d) at %6.1fm",
	                    $LADCP{ENSEMBLE}[$LADCP_end]->{TIME},
	                    $LADCP{ENSEMBLE}[$LADCP_end]->{NUMBER},
	                    $LADCP{ENSEMBLE}[$LADCP_end]->{DEPTH});
}

print(STDERR "\n");

#----------------------------------------------------------------------
# Step 4: Add CTD to LADCP Data & correct velocities for sound speed
#	- {DEPTH} field is overwritten!
#----------------------------------------------------------------------

print(STDERR "Matching CTD to LADCP time series...");

$opt_l = &lagLADCP2CTD()
	unless defined($opt_l);

print(STDERR "Associating CTD data with LADCP ensembles...");

for (my($ens)=$LADCP_start; $ens<=$LADCP_end; $ens++) {
	my($r) = int(($LADCP{ENSEMBLE}[$ens]->{ELAPSED_TIME} - $opt_l) / $CTD_sampint);
	if ($r < 0 && $ens == $LADCP_start) {
		$r = int(($LADCP{ENSEMBLE}[++$ens]->{ELAPSED_TIME} - $opt_l) / $CTD_sampint)
			while ($r < 0);
		printf(STDERR "\n\tCTD data begin with instrument already in water => skipping %ds of LADCP data",
			$LADCP{ENSEMBLE}[$ens]->{ELAPSED_TIME}-$LADCP{ENSEMBLE}[$LADCP_start]->{ELAPSED_TIME});
		$LADCP_start = $ens;
	}
	if ($r > $#CTD_press) {
		printf(STDERR "\n\tCTD data end while instrument is still in water => truncating %ds of LADCP data",
			$LADCP{ENSEMBLE}[$LADCP_end]->{ELAPSED_TIME}-$LADCP{ENSEMBLE}[$ens]->{ELAPSED_TIME});
		$LADCP_end = $ens - 1;
		last;
	}
	my($dr);
	for ($dr=0; !numberp($CTD_press[$r+$dr]); $dr--) {}
	$LADCP{ENSEMBLE}[$ens]->{DEPTH} = depth($CTD_press[$r+$dr],$lat);
	$LADCP{ENSEMBLE}[$ens]->{CTD_W} = $CTD_w[$r];
	$LADCP{ENSEMBLE}[$ens]->{CTD_TEMP} = $CTD_temp[$r];
	$LADCP{ENSEMBLE}[$ens]->{CTD_SVEL} = sVel($CTD_salin[$r],$CTD_temp[$r],$CTD_press[$r+$dr]);
	my($sscorr) = $LADCP{ENSEMBLE}[$ens]->{CTD_SVEL} / $LADCP{ENSEMBLE}[$ens]->{SPEED_OF_SOUND};
	for (my($bin)=0; $bin<$LADCP{N_BINS}; $bin++) {
		next unless defined($LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$W]);
		$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$U] *= $sscorr;
		$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$V] *= $sscorr;
		$LADCP{ENSEMBLE}[$ens]->{VELOCITY}[$bin][$W] *= $sscorr;
    }
}

&antsAddParams('bottom_depth',round($LADCP{ENSEMBLE}[$LADCP_bottom]->{DEPTH}),
			   'start_date',$LADCP{ENSEMBLE}[$LADCP_start]->{DATE},
			   'start_time',$LADCP{ENSEMBLE}[$LADCP_start]->{TIME},
			   'bottom_date',$LADCP{ENSEMBLE}[$LADCP_bottom]->{DATE},
			   'bottom_time',$LADCP{ENSEMBLE}[$LADCP_bottom]->{TIME},
			   'end_date',$LADCP{ENSEMBLE}[$LADCP_end]->{DATE},
			   'end_time',$LADCP{ENSEMBLE}[$LADCP_end]->{TIME});

print(STDERR "\n");

#----------------------------------------------------------------------
# Step  : Calculate Acoustic Backscatter Profile
#----------------------------------------------------------------------

print(STDERR "Finding seabed in acoustic backscatter profiles...");

mk_backscatter_profs($LADCP_start,$LADCP_end);
($water_depth,$sig_water_depth) =
	find_backscatter_seabed($LADCP{ENSEMBLE}[$LADCP_bottom]->{DEPTH});

$min_hab = $water_depth - $LADCP{ENSEMBLE}[$LADCP_bottom]->{DEPTH};
printf(STDERR "\n\twater depth      = %d(+-%.1f)m",$water_depth,$sig_water_depth);
printf(STDERR "\n\tclosest approach = %dmab",$min_hab);

print(STDERR "\n");

#----------------------------------------------------------------------
# Step 5: Find Seabed
#----------------------------------------------------------------------

print(STDERR "Finding seabed in BT data...");

($BT_water_depth,$sig_BT_water_depth) = 
	find_seabed(\%LADCP,$LADCP_bottom,$LADCP{BEAM_COORDINATES});

if (defined($BT_water_depth)) {
	$min_hab = $BT_water_depth - $LADCP{ENSEMBLE}[$LADCP_bottom]->{DEPTH};
	printf(STDERR "\n\twater depth      = %d(+-%.1f)m",$BT_water_depth,$sig_BT_water_depth);
	printf(STDERR "\n\tclosest approach = %dmab",$min_hab);
#	$water_depth = $BT_water_depth;									# assume BT data are better
#	$sig_water_depth = $sig_BT_water_depth;							# (at least they are higher vertical resolution)
}

unless (defined($water_depth)) {
	print(STDERR "\n\tno seabed found\n");
	print(STDERR "\n\tunknown water depth => PPI editing disabled\n")
		if ($opt_d);
	$clip_margin = 0;
}

print(STDERR "\n");

#----------------------------------------------------------------------
# Step 6: Edit Data
#----------------------------------------------------------------------

print(STDERR "Calculating shear profiles...\n");

$LADCP_start = 1 if ($LADCP_start == 0);							# ensure that there is previous ensemble

print(STDERR "\tdowncast...");
edit_velocity($LADCP_start,$LADCP_bottom);							# downcast
calc_shear($LADCP_start,$LADCP_bottom,$SHEAR_PREGRID_DZ,0);			# pre-grid shear @SHEAR_PREGRID_DZm resolution
calc_shear($LADCP_start,$LADCP_bottom,$GRID_DZ,1);					# calculate final gridded shear profile

@dc_sh_n = @sh_n;													# save downcast results
@dc_ush_mu = @ush_mu; @dc_ush_sig = @ush_sig;
@dc_vsh_mu = @vsh_mu; @dc_vsh_sig = @vsh_sig;
@dc_wsh_mu = @wsh_mu; @dc_wsh_sig = @wsh_sig;

print(STDERR "\n\tupcast...");
edit_velocity($LADCP_end,$LADCP_bottom);							# upcast
calc_shear($LADCP_end,$LADCP_bottom,$SHEAR_PREGRID_DZ,0);
calc_shear($LADCP_end,$LADCP_bottom,$GRID_DZ,1);

print(STDERR "\n");

#----------------------------------------------------------------------
# Step 7: Get bottom track profile
#----------------------------------------------------------------------

print(STDERR "Getting BT profile...");
getBTprof($LADCP_start,$LADCP_end);
print(STDERR "\n");

#----------------------------------------------------------------------
# Step 8: Write Output
#----------------------------------------------------------------------

print(STDERR "Writing shear profiles...");

@antsNewLayout = ('depth','dc_nshear','dc_u_z','dc_u_z.sig','dc_v_z','dc_v_z.sig','dc_w_z','dc_w_z.sig',
						  'uc_nshear','uc_u_z','uc_u_z.sig','uc_v_z','uc_v_z.sig','uc_w_z','uc_w_z.sig');
						  
$commonParams = $antsCurParams;
&antsAddParams('ubin_start',$ubin_start,'ubin_end',$ubin_end,		# record processing params
			   'wbin_start',$wbin_start,'wbin_end',$wbin_end,
			   'shbin_start',$shbin_start,'shbin_end',$shbin_end,
			   'w_ref_bin',$w_ref_bin,'w_dif',$w_dif,
			   'wake_hd_dif',$wake_hd_dif,'wake_ang_min',$wake_ang_min,
			   'min_wake_w',$min_wake_w,'n_wake_bins',$n_wake_bins,
			   'e_max',$e_max,'min_cor',$min_cor,
			   'max_shdev',$max_shdev,'max_shdev_sum',$max_shdev_sum,
			   'water_depth',round($water_depth),'water_depth.sig',round($sig_water_depth),
			   'min_hab',round($min_hab),
			   'clip_margin',$clip_margin,'first_clip_bin',$first_clip_bin);

for (my($gi)=0; $gi<@ush_mu; $gi++) {
	&antsOut(depthOfGI($gi),										# depth in center of bin
			 $dc_sh_n[$gi],											# downcast
			 $dc_ush_mu[$gi],$dc_ush_sig[$gi],
			 $dc_vsh_mu[$gi],$dc_vsh_sig[$gi],
			 $dc_wsh_mu[$gi],$dc_wsh_sig[$gi],
			 $sh_n[$gi],											# upcast
			 $ush_mu[$gi],$ush_sig[$gi],
			 $vsh_mu[$gi],$vsh_sig[$gi],
			 $wsh_mu[$gi],$wsh_sig[$gi]);
}

print(STDERR "\n");

#----------------------------------------------------------------------

if (defined($opt_a)) {
	print(STDERR "Writing acoustic backscatter profiles...");

	for (my($bin)=0; $bin<$LADCP{N_BINS}; $bin++) {
		my($fn) = sprintf("bin%02d.Sv",$bin);
		print(STDERR " $fn");
		
		@antsNewLayout = ('depth','Sv');
		&antsOut('EOF');
		$antsCurParams = $commonParams;
		close(STDOUT);
		open(STDOUT,">$fn") || croak("$fn: $!\n");
	    
		for (my($gi)=0; $gi<@sSv; $gi++) {
		    &antsOut(depthOfGI($gi),
				     $nSv[$gi][$bin] ? $sSv[$gi][$bin]/ $nSv[$gi][$bin] : nan);
	    }
	}
	print(STDERR "\n");
}

#----------------------------------------------------------------------

if (defined($opt_t)) {
	print(STDERR "Writing time series to $opt_t...");
	
	@antsNewLayout = ('ens','elapsed','depth','CTD_w','LADCP_w');
	&antsOut('EOF');
	$antsCurParams = $commonParams;
	close(STDOUT);
	open(STDOUT,">$opt_t") || croak("$opt_t: $!\n");
	
	for (my($ens)=$LADCP_start; $ens<=$LADCP_end; $ens++) {
		&antsOut($LADCP{ENSEMBLE}[$ens]->{NUMBER},
				 $LADCP{ENSEMBLE}[$ens]->{ELAPSED_TIME},
				 $LADCP{ENSEMBLE}[$ens]->{DEPTH},
				 $LADCP{ENSEMBLE}[$ens]->{CTD_W},
				 $LADCP{ENSEMBLE}[$ens]->{W});
	}
	print(STDERR "\n");
}

#----------------------------------------------------------------------

if (defined($opt_b)) {
	print(STDERR "Writing bottom-track data to $opt_b...");
	
	@antsNewLayout = ('depth','u','v','w','u.sig','v.sig','w.sig','ndata');
	&antsOut('EOF');
	$antsCurParams = $commonParams;
	close(STDOUT);
	open(STDOUT,">$opt_b") || croak("$opt_b: $!\n");

	my($skipped);
	for (my($gi)=0; $gi<@BT_nsamp; $gi++) {
		$skipped = 1 if ($BT_nsamp[$gi] > 0);
		next unless ($skipped);
		&antsOut(depthOfGI($gi),$BTu[$gi],$BTv[$gi],$BTw[$gi],$BTu_sig[$gi],$BTv_sig[$gi],$BTw_sig[$gi],$BT_nsamp[$gi]);
	}
	print(STDERR "\n");
}

#----------------------------------------------------------------------

if (defined($opt_f)) {
	print(STDERR "Writing data flags to $opt_f...");
	
	@antsNewLayout = ('ens');
	for (my($i)=1; $i<=$LADCP{N_BINS}; $i++) {
		$antsNewLayout[$i] = "bin$i";
	}
	&antsOut('EOF');
	$antsCurParams = $commonParams;

	close(STDOUT);
	open(STDOUT,">$opt_f") || croak("$opt_f: $!\n");
	
	&antsPrintHeaders(STDOUT,@antsNewLayout);
	for (my($ens)=$LADCP_start; $ens<=$LADCP_end; $ens++) {
		printf('%4d  ',$LADCP{ENSEMBLE}[$ens]->{NUMBER});
		for (my($bin)=0; $bin<$LADCP{N_BINS}; $bin++) {
			printf("%02x ",$edit_flags[$ens][$bin]);
		}
		print($opt_R);
	}
	
	print(STDERR "\n");
}

&antsExit();