new file mode 100755
--- /dev/null
+++ b/LADCPproc
@@ -0,0 +1,595 @@
+#!/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();
+