new file mode 100755
--- /dev/null
+++ b/listBins
@@ -0,0 +1,330 @@
+#!/usr/bin/perl
+#======================================================================
+# L I S T B I N S
+# doc: Fri Aug 25 15:57:05 2006
+# dlm: Sat May 23 16:34:30 2009
+# (c) 2006 A.M. Thurnherr
+# uE-Info: 269 0 NIL 0 0 72 2 2 4 NIL ofnI
+#======================================================================
+
+# Split data file into per-bin time series.
+
+# HISTORY:
+# Aug 25, 2006: - created from [listEns]
+# Aug 26, 2006: - added -M)agdecl
+# - changed -b to -f
+# Aug 27, 2006: - added %bin
+# Aug 28, 2006: - BUG: options were confused
+# Jan 4, 2007: - improved usage message for -a
+# - added %mag_decl
+# - BUG: roundoff error in %pct_good_vels
+# Sep 19, 2007: - adapted to new [RDI_BB_Read.pl]
+# Feb 7, 2008: - added sound-speed correction
+# - enabled 3-beam solutions
+# Feb 8, 2008: - added -d)iscard <beam>
+# - added -b)eam coordinate output
+# Feb 12, 2008: - modified 3-beam output
+# - added -p)ct_good <min>
+# Feb 13, 2008: - various improvements
+# Feb 19, 2008: - BUG: division by zero
+# BUG: min() did not work with 1st elt undef
+# Feb 21, 2008: - BUG: had forgotten to undo debugging changes
+# - removed missing magdecl warning on -b
+# Feb 22, 2008: - moved ssCorr() to [RDI_Utils.pl]
+# - BUG: %d complete ensembles was written to STDOUT
+# - BUG: %N_ensembles was total number of ensembles, not
+# only the ones used
+# - BUG: 0 errvel was output for 3-beam solutions =>
+# wrong time-average statistics
+# May 19, 2009: - added -w to calculate vertical velocities from
+# two beam pairs separately
+# May 21, 2009: - added horizontal beampair velocities on -w
+# - -P)itchRoll <bias/bias>
+# May 22, 2009: - added -B) <bias/bias/bias/bias>
+# May 23, 2009: - adapted to changed beampair-velocity fun name
+
+# General Notes:
+# - everything (e.g. beams) is numbered from 1
+# - no support for BT data
+
+# Soundspeed Correction:
+# - applied as described in the RDI coord-trans manual
+# - sound-speed variation over range is ignored (valid for small gradients)
+# => - same simple correction for all velocity components
+# - simple correction for cell depths
+
+# Min %-good (min_pcg):
+# - nan for records w/o valid velocities
+# - min(%-good) of the beams used for the velocity solution
+# - min_pcg does not have to decrease monotonically with distance,
+# at least when 3-beam solutions are allowed and when -p is used to
+# edit the data
+# - non-monotonic min_pcg is particularly obvious with the DYNAMUCK BM_ADCP
+# data, where one of the beams performed much worse than the others
+
+require "getopts.pl";
+$0 =~ m{(.*/)[^/]+};
+require "$1RDI_BB_Read.pl";
+require "$1RDI_Coords.pl";
+require "$1RDI_Utils.pl";
+
+die("Usage: $0 [-r)ange <first_ens,last_ens>] " .
+ "[output -f)ile <pat[bin%d.raw]>] " .
+ "[-a)ll ens (not just those with good vels)] " .
+ "[-M)agnetic <declination>] " .
+ "[-S)oundspeed correction <salin|*,temp|*,depth|*> " .
+ "[-P)itch/Roll <bias/bias>] [-B)eamvel <bias/bias/bias/bias>] " .
+ "[require -4)-beam solutions] [-d)iscard <beam#>] " .
+ "[-%)good <min>] " .
+ "[output -b)eam coordinates] [output two separate -w) estimates] " .
+ "<RDI file>\n")
+ unless (&Getopts("4abB:d:f:M:p:r:P:S:w") && @ARGV == 1);
+
+($P{pitch_bias},$P{roll_bias}) = split('[,/]',$opt_P);
+($P{velbias_b1},$P{velbias_b2},$P{velbias_b3},$P{velbias_b4}) = split('[,/]',$opt_B);
+
+die("$0: -4 and -d are mutually exclusive\n")
+ if ($opt_4 && defined($opt_d));
+
+die("$0: -p and -b are mutually exclusive\n")
+ if ($opt_b && defined($opt_p));
+
+$opt_p = 0 unless defined($opt_p);
+
+$RDI_Coords::minValidVels = 4 if ($opt_4); # no 3-beam solutions
+
+print(STDERR "WARNING: magnetic declination not set!\n")
+ unless defined($opt_M) || defined($opt_b);
+
+$opt_f = 'bin%d.raw' unless defined($opt_f);
+$ifn = $ARGV[0];
+
+($first_ens,$last_ens) = split(',',$opt_r)
+ if defined($opt_r);
+
+($SS_salin,$SS_temp,$SS_depth) = split(',',$opt_S)
+ if defined($opt_S);
+$variable_ssCorr = ($SS_salin eq '*' || $SS_temp eq '*' || $SS_depth eq '*');
+
+#----------------------------------------------------------------------
+
+sub min(@) # return minimum
+{
+ my($min) = 99e99;
+ for (my($i)=0; $i<=$#_; $i++) {
+ $min = $_[$i] if defined($_[$i]) && ($_[$i] < $min);
+ }
+ return ($min == 99e99) ? nan : $min;
+}
+
+sub dumpBin($$$) # write time series of single bin
+{
+ my($b,$fe,$le) = @_;
+ my($file) = sprintf($opt_f,$b+1);
+
+ open(P,">$file") || die("$file: $!\n");
+ print(P "#ANTS#PARAMS# ");
+ foreach my $k (keys(%P)) {
+ print(P "$k\{$P{$k}\} ");
+ }
+ if ($opt_b) {
+ printf(STDERR "%.0f%% ",100*$good_vels[$b]/($le-$fe+1));
+ } else {
+ my($pct3b) = ($good_vels[$b] > 0) ? 100*$three_beam[$b]/$good_vels[$b] : nan;
+ printf(STDERR "%.0f%%/%.0f%% ",100*$good_vels[$b]/($le-$fe+1),$pct3b);
+ printf(P "pct_3_beam{%.0f} ",$pct3b);
+ }
+ printf(P "pct_good_vels{%.0f} ",100*$good_vels[$b]/($le-$fe+1));
+ printf(P "bin{%d}",$b+1);
+ printf(P " soundspeed_correction{%s}",defined($opt_S) ? $opt_S : 'NONE!');
+ printf(P " dz{%g}",$dz[$b] *
+ (defined($opt_S) ? ssCorr($dta{ENSEMBLE}[$fe],$SS_salin,$SS_temp,$SS_depth) : 1)
+ ) unless ($variable_ssCorr);
+ print( P "\n");
+
+ print(P "#ANTS#FIELDS# " .
+ "{ensemble} {date} {time} {elapsed} " .
+ "{heading} {pitch} {roll} " .
+ "{sig_heading} {sig_pitch} {sig_roll} " .
+ "{xmit_current} {xmit_voltage} " .
+ "{temp} " .
+ ($opt_b ? "{v1} {v2} {v3} {v4} " : "{u} {v} {w} {err_vel} ") .
+ ($opt_w ? "{v12} {w12} {v34} {w34} " : "" ) .
+ "{corr1} {corr2} {corr3} {corr4} " .
+ "{amp1} {amp2} {amp3} {amp4} " .
+ ($opt_b ? "{pcg1} {pcg2} {pcg3} {pcg4}" : "{3_beam} {min_pcg}")
+ );
+ print(P " {dz}") if ($variable_ssCorr);
+ print(P "\n");
+
+ my($t0) = $dta{ENSEMBLE}[$fe]->{UNIX_TIME};
+ for (my($e)=$fe; $e<=$le; $e++) {
+ next unless ($opt_a || $dta{ENSEMBLE}[$e]->{GOOD_VEL}[$b]);
+
+ my($ssCorr) = defined($opt_S) ? ssCorr($dta{ENSEMBLE}[$e],$SS_salin,$SS_temp,$SS_depth) : 1;
+
+ print(P "$dta{ENSEMBLE}[$e]->{NUMBER} ");
+ print(P "$dta{ENSEMBLE}[$e]->{DATE} ");
+ print(P "$dta{ENSEMBLE}[$e]->{TIME} ");
+ printf(P "%d ",$dta{ENSEMBLE}[$e]->{UNIX_TIME}-$t0);
+ print(P "$dta{ENSEMBLE}[$e]->{HEADING} ");
+ print(P "$dta{ENSEMBLE}[$e]->{PITCH} ");
+ print(P "$dta{ENSEMBLE}[$e]->{ROLL} ");
+ print(P "$dta{ENSEMBLE}[$e]->{HEADING_STDDEV} ");
+ print(P "$dta{ENSEMBLE}[$e]->{PITCH_STDDEV} ");
+ print(P "$dta{ENSEMBLE}[$e]->{ROLL_STDDEV} ");
+ print(P "$dta{ENSEMBLE}[$e]->{ADC_XMIT_CURRENT} ");
+ print(P "$dta{ENSEMBLE}[$e]->{ADC_XMIT_VOLTAGE} ");
+ print(P "$dta{ENSEMBLE}[$e]->{TEMPERATURE} ");
+ if ($dta{ENSEMBLE}[$e]->{GOOD_VEL}[$b]) {
+ printf(P "%g ",$dta{ENSEMBLE}[$e]->{VELOCITY}[$b][0] * $ssCorr);
+ printf(P "%g ",$dta{ENSEMBLE}[$e]->{VELOCITY}[$b][1] * $ssCorr);
+ printf(P "%g ",$dta{ENSEMBLE}[$e]->{VELOCITY}[$b][2] * $ssCorr);
+ if ($dta{ENSEMBLE}[$e]->{THREE_BEAM}[$b]) {
+ print(P "nan ");
+ } else {
+ printf(P "%g ",$dta{ENSEMBLE}[$e]->{VELOCITY}[$b][3] * $ssCorr);
+ }
+ if ($opt_w) {
+ printf(P defined($dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][0]) ? "%g " : "nan ",
+ $dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][0]);
+ printf(P defined($dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][1]) ? "%g " : "nan ",
+ $dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][1]);
+ printf(P defined($dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][2]) ? "%g " : "nan ",
+ $dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][2]);
+ printf(P defined($dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][3]) ? "%g " : "nan ",
+ $dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b][3]);
+ }
+ } else {
+ print(P "nan nan nan nan ");
+ print(P "nan nan nan nan ") if ($opt_w);
+ }
+ print(P "@{$dta{ENSEMBLE}[$e]->{CORRELATION}[$b]} ");
+ print(P "@{$dta{ENSEMBLE}[$e]->{ECHO_AMPLITUDE}[$b]} ");
+ if ($opt_b) {
+ print(P "@{$dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b]} ");
+ } else {
+ printf(P "%d ",$dta{ENSEMBLE}[$e]->{THREE_BEAM}[$b]);
+ printf(P "%s ",min(@{$dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b]}));
+ }
+ printf(P "%g ",$dz[$b]*$ssCorr) if ($variable_ssCorr);
+ print(P "\n");
+ }
+ close(P);
+}
+
+#----------------------------------------------------------------------
+# MAIN
+#----------------------------------------------------------------------
+
+$P{RDI_file} = $ifn;
+$P{mag_decl} = $opt_M if defined($opt_M);
+
+readData($ifn,\%dta);
+printf(STDERR "%d complete ensembles...\n",scalar(@{$dta{ENSEMBLE}}));
+$dta{HEADING_BIAS} = -$opt_M; # magnetic declination
+
+if ($dta{BEAM_COORDINATES}) { # coords
+ $beamCoords = 1;
+} else {
+ die("$0: -b requires input in beam coordinates\n")
+ if ($opt_b);
+ die("$ifn: only beam and earth coordinates implemented so far\n")
+ if (!$dta{EARTH_COORDINATES});
+}
+
+for (my($b)=0; $b<$dta{N_BINS}; $b++) { # calc dz
+ $dz[$b] = $dta{DISTANCE_TO_BIN1_CENTER} + $b*$dta{BIN_LENGTH};
+}
+
+$lastGoodBin = 0;
+for ($e=0; $e<=$#{$dta{ENSEMBLE}}; $e++) { # check/transform velocities
+ next if (defined($first_ens) &&
+ $dta{ENSEMBLE}[$e]->{NUMBER} < $first_ens);
+
+ $dta{ENSEMBLE}[$e]->{PITCH} -= $P{pitch_bias};
+ $dta{ENSEMBLE}[$e]->{ROLL} -= $P{roll_bias};
+
+ $P{first_ens} = $dta{ENSEMBLE}[$e]->{NUMBER},$fe = $e
+ unless defined($P{first_ens});
+ last if (defined($last_ens) &&
+ $dta{ENSEMBLE}[$e]->{NUMBER} > $last_ens);
+ $P{last_ens} = $dta{ENSEMBLE}[$e]->{NUMBER};
+ $le = $e;
+
+ die("3-beams used in ensemble #$dta{ENSEMBLE}[$e]->{NUMBER}\n")
+ if ($dta{ENSEMBLE}[$e]->{N_BEAMS_USED} < 4);
+ die("BIT error in ensemble $dta{ENSEMBLE}[$e]->{NUMBER}\n")
+ if defined($dta{ENSEMBLE}[$e]->{BUILT_IN_TEST_ERROR});
+ die("Low gain in ensemble #$dta{ENSEMBLE}[$e]->{NUMBER}\n")
+ if ($dta{ENSEMBLE}[$e]->{LOW_GAIN});
+
+ for (my($b)=0; $b<$dta{N_BINS}; $b++) {
+ $dta{ENSEMBLE}[$e]->{VELOCITY}[$b][0] -= $P{velbias_b1};
+ $dta{ENSEMBLE}[$e]->{VELOCITY}[$b][1] -= $P{velbias_b2};
+ $dta{ENSEMBLE}[$e]->{VELOCITY}[$b][2] -= $P{velbias_b3};
+ $dta{ENSEMBLE}[$e]->{VELOCITY}[$b][3] -= $P{velbias_b4};
+ if ($opt_w) {
+ @{$dta{ENSEMBLE}[$e]->{BEAMPAIR_VELOCITY}[$b]} =
+ velBeamToBPEarth(\%dta,$e,@{$dta{ENSEMBLE}[$e]->{VELOCITY}[$b]});
+ }
+
+ if (defined($opt_d)) {
+ undef($dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b][$opt_d-1]);
+ undef($dta{ENSEMBLE}[$e]->{VELOCITY}[$b][$opt_d-1]);
+ }
+ for (my($i)=0; $i<4; $i++) {
+ if ($dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b][$i] < $opt_p) {
+ undef($dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b][$i]);
+ undef($dta{ENSEMBLE}[$e]->{VELOCITY}[$b][$i]);
+ }
+ }
+ @{$dta{ENSEMBLE}[$e]->{VELOCITY}[$b]} = $beamCoords
+ ? velInstrumentToEarth(\%dta,$e,
+ velBeamToInstrument(\%dta,@{$dta{ENSEMBLE}[$e]->{VELOCITY}[$b]})
+ )
+ : velApplyHdgBias(\%dta,$e,@{$dta{ENSEMBLE}[$e]->{VELOCITY}[$b]})
+ unless ($opt_b);
+ unless (defined($dta{ENSEMBLE}[$e]->{VELOCITY}[$b][0])) {
+ undef(@{$dta{ENSEMBLE}[$e]->{PERCENT_GOOD}[$b]});
+ next;
+ }
+ $dta{ENSEMBLE}[$e]->{THREE_BEAM}[$b] = $RDI_Coords::threeBeamFlag;
+ $three_beam[$b] += $RDI_Coords::threeBeamFlag;
+ $dta{ENSEMBLE}[$e]->{GOOD_VEL}[$b] = 1;
+ $good_vels[$b]++;
+ $lastGoodBin = $b if ($b > $lastGoodBin);
+ $firstGoodEns = $e unless defined($firstGoodEns);
+ $lastGoodEns = $e;
+ }
+}
+
+unless (defined($opt_r)) {
+ $fe = $firstGoodEns;
+ $le = $lastGoodEns;
+}
+
+$P{N_ensembles} = $le - $fe + 1;
+
+$firstBin = 0;
+$lastBin = $lastGoodBin;
+
+print( STDERR "Start : $dta{ENSEMBLE}[$fe]->{DATE} $dta{ENSEMBLE}[$fe]->{TIME}\n");
+print( STDERR "End : $dta{ENSEMBLE}[$le]->{DATE} $dta{ENSEMBLE}[$le]->{TIME}\n");
+printf(STDERR "Bins : %d-%d\n",$firstBin+1,$lastBin+1);
+if ($opt_b) {
+ print(STDERR "Good : ");
+} else {
+ printf(STDERR "3-Beam : %d %d %d %d\n",$RDI_Coords::threeBeam_1,
+ $RDI_Coords::threeBeam_2,
+ $RDI_Coords::threeBeam_3,
+ $RDI_Coords::threeBeam_4);
+
+ print(STDERR "Good/3-beam: ");
+}
+for ($b=$firstBin; $b<=$lastBin; $b++) { # generate output
+ dumpBin($b,$fe,$le);
+}
+print(STDERR "\n");
+
+exit(0);