#!/usr/bin/perl

#======================================================================

#                    L A D C P P R O C 

#                    doc: Thu Sep 16 20:36:10 2010

#                    (c) 2010 A.M. Thurnherr & E. Firing

#======================================================================

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

# NOTES:

#	- this code is based on merge.c written by Eric Firing

#	- comments starting with ## are taken from Eric's code

#	- for SeaBird files, 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

#	- -i should be set to the number that's added to LADCP_elapsed to make the two

#	  time series overplot nicely

# 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

#	Dec  9, 2010: - added support for ASCII CTD files

#	Dec 10, 2010: - change -w) default to 120s

#				  - changed nshear output to 0 from nan when there are no samples

#	Dec 27, 2010: - changed sign of -l to accept lag output from [LADCP_w]

#	Jan 10, 2011: - -o => -k added new -o

#				  - added code to fill CTD sound vel gaps

#	Jan 22, 2011: - added -g) lat,lon

#				  - added -c)ompass corr

#	Jun 15, 2011: - added mean backscatter profile to default output

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

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

($LADCPPROC)  = ($0 =~ m{^(.*)/[^/]*$});

require "$ANTS/ants.pl";

require "$ANTS/libEOS83.pl";

require "$ANTS/libstats.pl";

require "$LADCPPROC/LADCPproc.loadCTD";

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;

	'[use -2)dary CTD sensor pair]',

	'[require -4)-beam LADCP solutions]',

	'[-s)etup <file>] [-g)ps <lat,lon>]',

	'[-c)ompass-corr <offset,cos-fac,sin-fac>]',

	'[enable -p)PI editing]',

	'[-o)utput grid <resolution[5m]>]',

	'[-i)nitial LADCP time lag <guestimate>]',

	'[-l)ag LADCP <by>] [auto-lag -w)indow <size[120s]>] [-n) <auto-lag windows[20]]',

	'[-d)iagnostic output]',

	'output: [-t)ime series <file>] [-f)lag <file>] [-b)ottom-track <file>]',

	'<RDI file> <SeaBird file>');

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

&antsFloatOpt($opt_l);

&antsCardOpt(\$opt_w,120);

	# 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

	# old default of -w 60 did not work for DIMES_UK2 station 4 (DL), possibly again

	# related to ambiguity velocity

&antsCardOpt(\$opt_n,20);

&antsFileOpt($opt_s);

&antsFloatOpt($opt_i);

&antsCardOpt($opt_o);

if (defined($opt_g)) {

	($CTD{lat},$CTD{lon}) = split(',',$opt_g);

	croak("$0: cannot decode -g $opt_g\n")

		unless numberp($CTD{lat}) && numberp($CTD{lon});

}

if (defined($opt_c)) {

	($CC_offset,$CC_cos_fac,$CC_sin_fac) = split(',',$opt_c);

	croak("$0: cannot decode -c $opt_c\n")

		unless numberp($CC_offset) && numberp($CC_cos_fac) && numberp($CC_sin_fac);

}

$LADCP_file = &antsFileArg();

$CTD_file 	= &antsFileArg();

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

&antsActivateOut();

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

# Step 1: Read LADCP Data

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

print(STDERR "Reading LADCP data ($LADCP_file)...");

readData($LADCP_file,\%LADCP);

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

# 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',

$SHEAR_PREGRID_DZ = 20;

$GRID_DZ = defined($opt_o) ? $opt_o : 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 $CTD{lon} $CTD{lat} $year $month $day`);

croak("$0: unknown magnetic declination\n")

	unless defined($magdec);

&antsAddParams('magnetic_declination',$magdec);

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

# Step 3: Read CTD data

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

print(STDERR "Reading CTD data ($CTD_file)...");

readCTD($CTD_file,\%CTD);

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

# Step 4: Pre-Process CTD & LADCP Data

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

printf(STDERR "Pre-processing data...");

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

# clean CTD pressure data

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

my($pSpikes) = 0;

for (my($r)=1; $r<@{$CTD{press}}; $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{press}}-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{atbottom} = $r;

    }										

}

printf(STDERR "\n\t\tmax pressure [%ddbar] at scan#%d",$CTD{maxpress},$CTD{atbottom})

	if $opt_d;

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

# Step 4b: Pre-Process LADCP Data

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

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

# 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\n")

			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}) {

	if ($opt_d) {

		if ($opt_c) {

			printf(STDERR "\n\t\tcalculating tilt and correcting for compass error and magnetic declination of %.1f deg...\n",$magdec);

		} else {

			printf(STDERR "\n\t\tcalculating tilt and correcting for magnetic declination of %.1f deg...\n",$magdec);

		}

	}

	for (my($ens)=0; $ens<=$#{$LADCP{ENSEMBLE}}; $ens++) {

		$LADCP{ENSEMBLE}[$ens]->{TILT} = &angle_from_vertical($LADCP{ENSEMBLE}[$ens]->{PITCH},$LADCP{ENSEMBLE}[$ens]->{ROLL});

		my($hdg) = rad($LADCP{ENSEMBLE}[$ens]->{HEADING});

		$LADCP{HEADING_BIAS} = ($CC_offset + $CC_cos_fac*cos($hdg) + $CC_sin_fac*sin($hdg)) - $magdec

			if ($opt_c);

		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")

}

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

# 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 5: Add CTD to LADCP Data & correct velocities for sound speed

#	- {DEPTH} field is overwritten!

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

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

$opt_l = defined($opt_l) ? -$opt_l : &lagLADCP2CTD();

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

	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_end = $ens - 1;

		last;

	}

	my($dr);

	for ($dr=0; !numberp($CTD{press}[$r+$dr]); $dr--) {}

	$LADCP{ENSEMBLE}[$ens]->{DEPTH} = depth($CTD{press}[$r+$dr],$CTD{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]);

	if (numberp($LADCP{ENSEMBLE}[$ens]->{CTD_SVEL})) {

		$lastSvel = $LADCP{ENSEMBLE}[$ens]->{CTD_SVEL};

	} else {

		$LADCP{ENSEMBLE}[$ens]->{CTD_SVEL} = $lastSvel;

	}

	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;

    }

}

			   '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 6: Calculate Acoustic Backscatter Profile

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

mk_backscatter_profs($LADCP_start,$LADCP_end);

print(STDERR "\n");

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

# Step 7: Find Seabed

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

	printf(STDERR "\n\tclosest approach = %dmab",$min_hab);

}

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

# Step 8: Edit Data

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

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

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;

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);

@uc_sh_n = @sh_n;													# save upcast results

@uc_ush_mu = @ush_mu; @uc_ush_sig = @ush_sig;

@uc_vsh_mu = @vsh_mu; @uc_vsh_sig = @vsh_sig;

@uc_wsh_mu = @wsh_mu; @uc_wsh_sig = @wsh_sig;

for (my($gi)=0; $gi<@dc_ush_mu; $gi++) {

	if ($dc_sh_n[$gi]>0 && $uc_sh_n[$gi]>0) {

		$sh_n[$gi] = $dc_sh_n[$gi] + $uc_sh_n[$gi];

		$ush_mu[$gi] = ($dc_sh_n[$gi]*$dc_ush_mu[$gi] + $uc_sh_n[$gi]*$uc_ush_mu[$gi]) / $sh_n[$gi];

		$vsh_mu[$gi] = ($dc_sh_n[$gi]*$dc_vsh_mu[$gi] + $uc_sh_n[$gi]*$uc_vsh_mu[$gi]) / $sh_n[$gi];

		$wsh_mu[$gi] = ($dc_sh_n[$gi]*$dc_wsh_mu[$gi] + $uc_sh_n[$gi]*$uc_wsh_mu[$gi]) / $sh_n[$gi];

		$ush_sig[$gi] = sqrt(($dc_sh_n[$gi]*$dc_ush_sig[$gi]**2 + $uc_sh_n[$gi]*$uc_ush_sig[$gi]**2) / $sh_n[$gi]);

		$vsh_sig[$gi] = sqrt(($dc_sh_n[$gi]*$dc_vsh_sig[$gi]**2 + $uc_sh_n[$gi]*$uc_vsh_sig[$gi]**2) / $sh_n[$gi]);

		$wsh_sig[$gi] = sqrt(($dc_sh_n[$gi]*$dc_wsh_sig[$gi]**2 + $uc_sh_n[$gi]*$uc_wsh_sig[$gi]**2) / $sh_n[$gi]);

	} elsif ($dc_sh_n[$gi] > 0) {

		$sh_n[$gi] = $dc_sh_n[$gi];

		$ush_mu[$gi]  = $dc_ush_mu[$gi];  $vsh_mu[$gi]  = $dc_vsh_mu[$gi];  $wsh_mu[$gi]  = $dc_wsh_mu[$gi];

		$ush_sig[$gi] = $dc_ush_sig[$gi]; $vsh_sig[$gi] = $dc_vsh_sig[$gi]; $wsh_sig[$gi] = $dc_wsh_sig[$gi];

	} elsif ($uc_sh_n[$gi] > 0) {

		$sh_n[$gi] = $uc_sh_n[$gi];

		$ush_mu[$gi]  = $uc_ush_mu[$gi];  $vsh_mu[$gi]  = $uc_vsh_mu[$gi];  $wsh_mu[$gi]  = $uc_wsh_mu[$gi];

		$ush_sig[$gi] = $uc_ush_sig[$gi]; $vsh_sig[$gi] = $uc_vsh_sig[$gi]; $wsh_sig[$gi] = $uc_wsh_sig[$gi];

	} else {

		$sh_n[$gi] = 0;

		$ush_mu[$gi]  = $vsh_mu[$gi]  = $wsh_mu[$gi]  = nan;

		$ush_sig[$gi] = $vsh_sig[$gi] = $wsh_sig[$gi] = nan;

	}

}

print(STDERR "\n");

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

# Step 9: Get bottom track profile

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

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

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

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',

						  'nshear','u_z','u_z.sig','v_z','v_z.sig','w_z','w_z.sig','Sv','Sv.n');

$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

			 numberp($dc_sh_n[$gi])?$dc_sh_n[$gi]:0,				# 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],

			 numberp($uc_sh_n[$gi])?$uc_sh_n[$gi]:0,				# upcast

			 $uc_ush_mu[$gi],$uc_ush_sig[$gi],

			 $uc_vsh_mu[$gi],$uc_vsh_sig[$gi],

			 $uc_wsh_mu[$gi],$uc_wsh_sig[$gi],

			 $sh_n[$gi],											# combined