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whoosher version at beginning of FZ1
authorA.M. Thurnherr <ant@ldeo.columbia.edu>
Wed, 09 Jul 2014 15:19:27 -0400
changeset 16 29e867b3e070
parent 15 dfcb6bef9d42
child 17 fc83e436a800
whoosher version at beginning of FZ1
LADCP_w file | annotate | diff | comparison | revisions
LWplot_Sv file | annotate | diff | comparison | revisions
Plots/2014_P16_043.eps file | annotate | diff | comparison | revisions
defaults.pl file | annotate | diff | comparison | revisions
edit_data.pl file | annotate | diff | comparison | revisions
time_lag.pl file | annotate | diff | comparison | revisions 
--- a/LADCP_w	Tue May 20 09:08:43 2014 +0000
+++ b/LADCP_w	Wed Jul 09 15:19:27 2014 -0400
@@ -2,9 +2,9 @@
 #======================================================================
 #                    L A D C P _ W 
 #                    doc: Fri Dec 17 18:11:13 2010
-#                    dlm: Mon May 19 22:21:35 2014
+#                    dlm: Wed May 21 08:50:29 2014
 #                    (c) 2010 A.M. Thurnherr
-#                    uE-Info: 932 27 NIL 0 0 72 2 2 4 NIL ofnI
+#                    uE-Info: 680 96 NIL 0 0 72 2 2 4 NIL ofnI
 #======================================================================
 
 # TODO:
@@ -138,6 +138,9 @@
 #	Sep  5, 2013: - BUG: w12/w34 do not work for earth-coordinate data, of course
 #	Apr 17, 2014: - BUG: edit_tilt was never called when all recorded bins are valid
 #	Apr 21, 2014: - updated comments
+#	May 19, 2014: - began adding support for PPI filtering
+#	May 20, 2014: - changed volume_scattering_coeff to Sv in output
+#				  - added editPPI()
 
 # CTD REQUIREMENTS
 #	- elapsed		elapsed seconds; see note below
@@ -658,8 +661,7 @@
 # Construct sound-speed correction profile from CTD 1Hz downcast data
 #	very simple algorithm that stores the last value found
 #	in each 1m bin
-# For PPI filtering, a sound speed profile to the surface is required.
-# 	This is ensured by extrapolating the first value up to zero
+# For PPI filtering, a sound speed profile without gaps is required.
 #--------------------------------------------------------------------
 
 progress("Constructing sound-speed correction profile\n");
@@ -671,10 +673,15 @@
 	$min_depth = $s if ($s < $min_depth);
 	$sVelProf[int($CTD{DEPTH}[$s])] = $CTD{SVEL}[$s];
 }
-while ($min_depth > 0) {
+while ($min_depth > 0) {													# fill surface gap
 	$sVelProf[$min_depth-1] = $sVelProf[$min_depth];
 	$min_depth--;
 }
+for (my($d)=$min_depth+1; $d<=$#sVelProf; $d++) {							# fill interior gaps
+	$sVelProf[$d] = $sVelProf[$d-1]
+		unless defined($sVelProf[$d]);
+}
+	
 
 #-------------------
 # Determine time lag
@@ -904,16 +911,20 @@
 		($nvrm,$nerm) = editSideLobes($firstGoodEns,$lastGoodEns,$water_depth);
 		progress("\t$nvrm velocities from $nerm ensembles removed\n");
 
-		progress("Editing data to remove PPI from seabed...\n");
-		  progress("\tConstructing travel-time profile...\n");
-		  my($tt) = ($water_depth - $#sVelProf) / $sVelProf[$#sVelProf];  # $#sVelProf = max_depth(profile) in meters
-		  $ttProf[$#sVelProf] = $tt;
-		  for (my($d)=$#sVelProf-1; $d>=0; $d--) {
-			  $tt += 1 / $sVelProf[$d];
-			  $ttProf[$d] = $tt;
-          }
-		($nvrm,$nerm) = editPPI($firstGoodEns,$lastGoodEns,$water_depth);
-		progress("\t$nvrm velocities from $nerm ensembles removed\n");
+		if ($PPI_editing) {
+			progress("Editing data to remove PPI from seabed...\n");
+			  progress("\tConstructing depth-average soundspeed profile...\n");
+			  my($dz) = $water_depth - $#sVelProf;							# $#sVelProf = max_depth(profile) in meters
+			  my($sum) = $dz * $sVelProf[$#sVelProf];
+			  $DASSprof[$#sVelProf] = $sum/$dz;
+			  for (my($d)=$#sVelProf-1; $d>=0; $d--) {
+			  	$sum += $sVelProf[$d];
+			  	$dz++;
+				$DASSprof[$d] = $sum/$dz;
+			  }
+			($nvrm,$nerm) = editPPI($firstGoodEns,$lastGoodEns,$water_depth);
+	        progress("\t$nvrm velocities from $nerm ensembles removed\n");
+	    }
 	} else {
 		info("no seabed found in backscatter profiles --- cannot edit sidelobe or PPI\n");
 	}
@@ -925,16 +936,17 @@
 	($nvrm,$nerm) = editSideLobes($firstGoodEns,$lastGoodEns,undef);
 	progress("\t$nvrm velocities from $nerm ensembles removed\n");
 
-	progress("Editing data to remove PPI from sea surface...\n");
-	  progress("\tConstructing travel-time profile...\n");
-	  my($tt) = 0;
-	  $ttProf[0] = $tt;
-	  for (my($d)=1; $d<=$#sVelProf; $d++) {
-		  $tt += 1 / $sVelProf[$d];
-		  $ttProf[$d] = $tt;
-      }
-	($nvrm,$nerm) = editPPI($firstGoodEns,$lastGoodEns,undef);
-	progress("\t$nvrm velocities from $nerm ensembles removed\n");
+	if ($PPI_editing) {
+		progress("Editing data to remove PPI from sea surface...\n");
+		  progress("\tConstructing depth-average soundspeed profile...\n");
+		  $DASSprof[0] = my($sum) = 0;
+		  for (my($d)=1; $d<=$#sVelProf; $d++) {
+		  	$sum += $sVelProf[$d];
+			$DASSprof[$d] = $sum/$d;
+		  }
+		($nvrm,$nerm) = editPPI($firstGoodEns,$lastGoodEns,undef);
+	    progress("\t$nvrm velocities from $nerm ensembles removed\n");
+	}
 }
 
 #----------------------------------------------------------------------
@@ -1264,7 +1276,7 @@
 
 	@antsNewLayout = ('ensemble','bin','elapsed','depth','CTD_depth','downcast',
 					  'w','w12','w34','residual','CTD_w','CTD_w_tt','LADCP_w','errvel',
-					  'correlation','echo_amplitude','volume_scattering_coeff',
+					  'correlation','echo_amplitude','Sv',
 					  'pitch','roll','tilt','heading','3_beam','svel');
 
 	open(STDOUT,"$out_w") || croak("$out_w: $!\n");
--- a/LWplot_Sv	Tue May 20 09:08:43 2014 +0000
+++ b/LWplot_Sv	Wed Jul 09 15:19:27 2014 -0400
@@ -2,9 +2,9 @@
 #======================================================================
 #					 L W P L O T _ S V 
 #                    doc: Sat Oct 15 13:42:50 2011
-#                    dlm: Thu May 16 15:22:39 2013
+#                    dlm: Tue May 20 10:57:56 2014
 #                    (c) 2011 A.M. Thurnherr
-#                    uE-Info: 83 26 NIL 0 0 72 2 2 4 NIL ofnI
+#                    uE-Info: 17 57 NIL 0 0 72 2 2 4 NIL ofnI
 #======================================================================
 
 # HISTORY:
@@ -14,6 +14,7 @@
 #	Mar 12, 2012: - sh -> ksh as this does not work with /bin/sh on MacOSX 10.6.4
 #   Apr 12, 2012: - made re-entrant
 #	May 16, 2013: - adapted to file-layout changes
+#	May 20, 2013: - renamed volume_scattering_coeff to Sv
 
 #--------------------------------------------------
 # Usage
@@ -44,7 +45,7 @@
 done
 
 set -- $fields
-[ "$1" = ensemble -a "$4" = depth -a "${17}" = volume_scattering_coeff ] || {
+[ "$1" = ensemble -a "$4" = depth -a "${17}" = Sv ] || {
 	echo "$0: file layout error" >&2
 	exit 1
 }
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Plots/2014_P16_043.eps	Wed Jul 09 15:19:27 2014 -0400
@@ -0,0 +1,2039 @@
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+% End plot #4
+stroke
+LTb
+1980 13355 N
+0 -11591 V
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+Z stroke
+1.000 UP
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+end
+showpage
+%%Trailer
+cleartomark countdictstack exch sub { end } repeat restore
+%%EOF
--- a/defaults.pl	Tue May 20 09:08:43 2014 +0000
+++ b/defaults.pl	Wed Jul 09 15:19:27 2014 -0400
@@ -1,9 +1,9 @@
 #======================================================================
 #                    D E F A U L T S . P L 
 #                    doc: Tue Oct 11 17:11:21 2011
-#                    dlm: Thu Sep  5 22:46:45 2013
+#                    dlm: Wed May 21 12:59:09 2014
 #                    (c) 2011 A.M. Thurnherr
-#                    uE-Info: 37 55 NIL 0 0 72 0 2 4 NIL ofnI
+#                    uE-Info: 233 0 NIL 0 0 72 0 2 4 NIL ofnI
 #======================================================================
 
 # HISTORY:
@@ -23,7 +23,6 @@
 #	Oct 27, 2011: - modified ProcessingParam file loading
 #				  - added ${pitch,roll,heading}_bias
 #	Oct 11, 2012: - added .TL output to defaults
-#--- hg commit
 #	Oct 15, 2012: - removed support for TLhist
 #	Apr 22, 2013: - removed option variable aliases
 #	May 14, 2013: - opt_m => w_max_lim
@@ -35,6 +34,8 @@
 #	Jun  5, 2013: - made ProcessingParams (without .profiles) default file
 #	Sep  5, 2013: - also allow ProcessingParams.default
 #				  - added LWplot_spec to default output
+#	May 20, 2014: - added support for $PPI_editing
+#	May 21, 2014: - added $PPI_extend_upper_limit
 
 # Variable Names:
 #	- variables that are only used in a particular library are
@@ -213,6 +214,23 @@
 
 $surface_layer_depth = 25;
 
+
+# PPI editing as described in [edit_data.pl]
+#	- enabled by default for WH150 data
+#	- 2014 CLIVAR P16 #47 has a slight discontinuity at 4000m; this
+#	  discontinuity is there without PPI filtering but gets slightly
+#	  worse with PPI filtering. Setting $PPI_extend_upper_limit to 
+#	  1.03-1.05 partially removes the discontinuity but the profile
+#	  never gets better than the profile wihtout PPI editing. Note
+#	  the only reason why the upper PPI should be extended is if the
+#	  recorded ping intervals are inaccurate as the upper limit is
+#	  set by the shortest acoustic path between the ADCP and the 
+#	  seabed.
+
+$PPI_editing = ($LADCP{BEAM_FREQUENCY} < 300);
+
+#$PPI_extend_upper_limit = 1.03;		# arbitrarily increase calculated max dist from seabed by 3%
+
 #======================================================================
 # Time Lagging
 #======================================================================
--- a/edit_data.pl	Tue May 20 09:08:43 2014 +0000
+++ b/edit_data.pl	Wed Jul 09 15:19:27 2014 -0400
@@ -1,9 +1,9 @@
 #======================================================================
 #                    E D I T _ D A T A . P L 
 #                    doc: Sat May 22 21:35:55 2010
-#                    dlm: Mon May 19 22:24:40 2014
+#                    dlm: Wed May 21 13:00:35 2014
 #                    (c) 2010 A.M. Thurnherr
-#                    uE-Info: 285 28 NIL 0 0 72 2 2 4 NIL ofnI
+#                    uE-Info: 339 74 NIL 0 0 72 2 2 4 NIL ofnI
 #======================================================================
 
 # HISTORY:
@@ -28,6 +28,8 @@
 #	Oct 15, 2012: - BUG: editSurfLayer() counted also ensembles without CTD depth
 #	Nov 12, 2013: - added comments on editCorr_Earthcoords()
 #	Mar  4, 2013: - added support for missing PITCH/ROLL (TILT) & HEADING
+#	May 20, 2014: - added editPPI()
+#	May 21, 2014: - got it to work correctly
 
 # NOTES:
 #	- editCorr_Earthcoords() is overly conservative and removed most
@@ -241,11 +243,12 @@
 }
 
 #======================================================================
-# ($nvrm,$nerm) = editSideLobes($fromEns,$toEns,$range)
+# ($nvrm,$nerm) = editSideLobes($fromEns,$toEns,$water_depth)
 #
 # NOTES:
 #	1) When this code is executed the sound speed is known. No attempt is made to correct for
 #	   along-beam soundspeed variation, but the soundspeed at the transducer is accounted for.
+#	2) for UL, water_depth == undef
 #======================================================================
 
 sub editSideLobes($$$)
@@ -278,31 +281,103 @@
 
 
 #======================================================================
-# ($nvrm,$nerm) = editPPI($fromEns,$toEns,$range)
+# ($nvrm,$nerm) = editPPI($fromEns,$toEns,$water_depth)
 #
 # NOTES:
-#	1) When this code is executed the travel-time profile (@ttProf at 1m resolution)
-#	   has been constructed.
+#	- for UL, water_depth == undef; for DL water_depth is always defined,
+#	  or else editPPI is not called
+#	- when this code is executed a suitable UL or DL depth-average-soundspeed
+#	  profile (@DASSprof at 1m resolution) is available
+#	- PPI layer is defined by the shortest and longest acoustic paths
+#	  between transducer and seabed that contribute significantly to the
+#	  backscatter
+#		- shortest path (shallow limit):
+#			- distance to seabed => sidelobe
+#			- min_lim = water_depth - DASSprof[CTD_depth]*DeltaT/2
+#		- longest path (deep limit):
+#			- outer edge of main lobe of one of the beams (depending on 
+#			  instrument tilt)
+#			- nominal half-beam apertures at half peak signal strength
+#			  (-3dB), RDI BB Primer, pp. 35f (2ND COLUMN)
+#				WH1200	1.4		2.4
+#				WH600	1.5		2.5
+#				WH300	2.2		3.7
+#				WH150	4.0		6.7
+#				WH75	5.0	    8.4
+#			- for WH150, Fig. 23 indicates that half-beam-width 
+#			  at -5dB (<1% peak signal strength) is about 5/3 of same
+#			  at -3dB => PPI limit choice (3rd column above)
+#		- [Plots/2014_P16_043.eps]:
+#			- mean tilt of 2 degrees included in effects
+#			- finite pulse length means that there actually
+#			  is less elapsed time between the end of the sending
+#			  and the beginning of the reception than the ping
+#			  interval suggests; without it, the PPI peak depth
+#			  does not agree with the prediction
+#			- note that there is no PPI effect possible above
+#			  the dark blue line --- this is a hard limit
+#			  (I checked ping interval to within 0.001,
+#			  water depth is known better than 2m, sound
+#			  speed is accurately accounted for (as indicated
+#			  by the cyan line), so the variability above
+#			  is due to background variability, which is
+#			  consistent with the shape of the curve outside
+#			  the PPI layer
+#		  	=> PPI peak can be tightly bracketed but care has to
+#			   be taken to account for finite beam width & 
+#			   instrument beam_tilt = max(|pitch|,|roll|)
+#	- while the upper limit of the PPI layer is unambiguous, this
+#	  is only true if the recorded ping intervals are accurate
+#		- 2014 CLIVAR P16 #47 shows a slight discontinuity in dc_w near
+#		  the middle of the upper PPI layer (4000m)
+#		- the discontinuity is slightly more pronounced with PPI editing
+#	      enabled
+#		- setting $PPI_extend_upper_limit = 1.03 (or 1.04, 1.05, 1.1)
+#		  reduces the discontinuity to the level without PPI filtering, but
+#		  not any better
+#		- overall I am not convinced that the discontinuity is related
+#		  to PPI; therefore, $PPI_extend_upper_limit is not set by default
 #======================================================================
 
+{ my($bha);					# beam half aperture (static scope)
+
 sub editPPI($$$)
 {
 	my($fe,$te,$wd) = @_;	# first & last ens to process, water depth for downlooker
 	my($nvrm) = 0;			# of velocities removed
 	my($nerm) = 0;			# of ensembles affected
+
+	unless (defined($bha)) {
+		if    ($LADCP{BEAM_FREQUENCY} == 1200) { $bha = 2.4; }
+		elsif ($LADCP{BEAM_FREQUENCY} ==  600) { $bha = 2.5; }
+		elsif ($LADCP{BEAM_FREQUENCY} ==  300) { $bha = 3.7; }
+		elsif ($LADCP{BEAM_FREQUENCY} ==  150) { $bha = 6.7; }
+		elsif ($LADCP{BEAM_FREQUENCY} ==   75) { $bha = 8.4; }
+		else { croak("$0: unexpected transducer frequency $LADCP{BEAM_FREQUENCY}\n"); }
+	}
+	
 	for (my($e)=$fe; $e<=$te; $e++) {
 		next unless numberp($LADCP{ENSEMBLE}[$e]->{CTD_DEPTH});
-		my($range) = $LADCP{ENSEMBLE}[$e]->{XDUCER_FACING_UP}
-				   ? $LADCP{ENSEMBLE}[$e]->{CTD_DEPTH}
-				   : $wd - $LADCP{ENSEMBLE}[$e]->{CTD_DEPTH};
-		my($sscorr) = $CTD{SVEL}[$LADCP{ENSEMBLE}[$e]->{CTD_SCAN}] / 1500;
-		my($goodBins) =   ($range - $sscorr*$LADCP{DISTANCE_TO_BIN1_CENTER}) * cos(rad($LADCP{BEAM_ANGLE}))
-						/ ($sscorr*$LADCP{BIN_LENGTH})
-						- 1.5;
+		next unless ($e > 0);
+		
+		my($delta_t)   = $LADCP{ENSEMBLE}[$e]->{UNIX_TIME} - $LADCP{ENSEMBLE}[$e-1]->{UNIX_TIME};
+		my($dz_max)    = $DASSprof[int($LADCP{ENSEMBLE}[$e]->{CTD_DEPTH})]*$delta_t / 2;
+		my($beam_tilt) = max(abs($LADCP{ENSEMBLE}[$e]->{GIMBAL_PITCH}),
+							 abs($LADCP{ENSEMBLE}[$e]->{ROLL}));
+		my($dz_min)    = $dz_max * cos(rad($LADCP{BEAM_ANGLE} + $beam_tilt + $bha));
+		my(@bd) = calc_binDepths($e);
+
+		$dz_max *= $PPI_extend_upper_limit
+			if numberp($PPI_extend_upper_limit);
 
 		my($dirty) = 0;
-		for (my($bin)=int($goodBins); $bin<$LADCP{N_BINS}; $bin++) { 	# NB: 2 good bins implies that bin 2 is bad
-			next unless ($bin>=0 && defined($LADCP{ENSEMBLE}[$e]->{W}[$bin]));
+		for (my($bin)=$LADCP_firstBin-1; $bin<$LADCP_lastBin; $bin++) {
+			next unless (defined($LADCP{ENSEMBLE}[$e]->{W}[$bin]));
+			if (defined($wd)) {															# DL
+				next unless ($bd[$bin] >= $wd-$dz_max && $bd[$bin] <= $wd-$dz_min);
+			} else {																	# UL
+				next unless ($bd[$bin] <= $dz_max && $bd[$bin] >= $dz_min);
+			}
 			$dirty = 1;
 			$nvrm++;
 			undef($LADCP{ENSEMBLE}[$e]->{W}[$bin]);
@@ -313,6 +388,8 @@
 	return ($nvrm,$nerm);
 }
 
+} # static scope for $bha
+
 
 #======================================================================
 # $nerm = editSurfLayer($fromEns,$toEns,$surface_layer_depth)
--- a/time_lag.pl	Tue May 20 09:08:43 2014 +0000
+++ b/time_lag.pl	Wed Jul 09 15:19:27 2014 -0400
@@ -1,9 +1,9 @@
 #======================================================================
 #                    T I M E _ L A G . P L 
 #                    doc: Fri Dec 17 21:59:07 2010
-#                    dlm: Thu Apr 17 08:54:30 2014
+#                    dlm: Fri May 23 09:24:38 2014
 #                    (c) 2010 A.M. Thurnherr
-#                    uE-Info: 74 0 NIL 0 0 72 0 2 4 NIL ofnI
+#                    uE-Info: 54 59 NIL 0 0 72 0 2 4 NIL ofnI
 #======================================================================
 
 # HISTORY:
@@ -51,6 +51,7 @@
 #	Apr 22, 2013: - replaced $max_allowed_w by $opt_m, $TL_required_top_three_fraction by $opt_3
 #	May 14, 2013: - opt_m => w_max_lim
 #	Mar  3, 2014: - BUG: var-name typo
+#	May 23, 2014: - BUG: $s range check required in mad_w()
 
 # DIFFICULT STATIONS:
 #	NBP0901#131		this requires the search-radius doubling heuristic
@@ -68,6 +69,7 @@
 	my($LADCP_mean_w,$CTD_mean_w,$nsamp) = (0,0,0);
 	for (my($e)=$fe; $e<=$le; $e++) {			# first, calculate mean w in window
 		my($s) = int(($LADCP{ENSEMBLE}[$e]->{ELAPSED} + $CTD{TIME_LAG} - $CTD{ELAPSED}[0]) / $CTD{DT} + 0.5);
+		next unless ($s>=0 && $s<=$#{$CTD{ELAPSED}});
 		die("assertion failed\n" .
 			"\ttest: abs($LADCP{ENSEMBLE}[$e]->{ELAPSED} + $CTD{TIME_LAG} - $CTD{ELAPSED}[$s]) <= $CTD{DT}/2\n" .
 			"\te = $e, s = $s, ensemble = $LADCP{ENSEMBLE}[$e]->{NUMBER}"
LADCP_w