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

#                    D E F A U L T S . P L 

#                    doc: Tue Oct 11 17:11:21 2011

#                    (c) 2011 A.M. Thurnherr

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

# HISTORY:

#	Oct 11, 2011: - created

#	Oct 12, 2011: - added $processing_param_file

#	Oct 13, 2011: - added $out_basename, $TL_out, $TL_hist_out

#	Oct 14, 2011: - added $w_out, $profile_out

#				  - renamed _out to out_; out_basename to out_basename

#	Oct 17, 2011: - added {data,plot,log}_subdir

#				  - added $out_BR

#				  - adapted to new filter-plot scripts

#				  - changed -v default to 2

#	Oct 19, 2011: - added SS_max_allowed_range & renamed _min_

#	Oct 20, 2011: - added $out_timeseries default

#				  - added $per_bin_valid_frac_lim

#	Oct 26, 2011: - added $first_guess_timelag

#	Oct 27, 2011: - modified ProcessingParam file loading

#				  - added ${pitch,roll,heading}_bias

#	Oct 11, 2012: - added .TL output to defaults

#	Oct 15, 2012: - removed support for TLhist

#	Apr 22, 2013: - removed option variable aliases

#	May 14, 2013: - opt_m => w_max_lim

#				  - BUG: default processing params file was still .default

#	May 15, 2013: - changed default profile plot to show 2-beam solutions

#				  - BUG: out_TLhist entry was still there

#	May 16, 2013: - -a => -d

#	Jun  5, 2013: - renamed $discard_data_from_beam to $bad_beam

#	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

#	Oct 15, 2014: - investigated, modified and documented -t default

#	Oct 27, 2014: - removed CTD-acceleration-effects and w spectral plots

#				  - removed time-lagging stats output file by default

#	Oct 31, 2014: - re-arranged order of things

#				  - .w => .samp output

#	Nov  4, 2014: - BUG: PPI_editing did not work as advertised

#   Apr 16, 2015: - turned output specifies into lists (re-design of

#                   plotting sub-system)

#				  - croak -> error

#				  - added $SS_use_BT, $SS_min_signal, $SS_min_samp

#	Apr 20, 2015: - reduced value of $SS_min_allowed_range

#				  - added $Sv_ref_bin

#	Apr 21: 2015: - BUG: typo in $Sv_ref_bin

#				  - decreased default verbosity

#   May 15, 2015: - added $min_valid_vels

#	May 20, 2015: - STN -> PROF

#	Jul 26, 2015: - began adaptation to libGMT.pl

#				  - changed .prof output .wprof

#				  - -v docu was wrong

#				  - added $outGrid_firstBin, $outGrid_lastBin

#	Jul 28, 2015: - implemented new plotting system

#	Jul 29, 2015: - implemented new plotting system

#	Sep  3, 2015: - renamed wsamp output and plot

#   			  - changed out_w to out_wsamp

#	Sep 26, 2015: - added sidelobe editing params

#	Oct 13, 2015: - addded support for $ENV{VERB}

#	Jan  4, 2016: - decreased default vertical resolution to 20m

#	Jan 22, 2016: - changed outGrid_firstBin default to 1

#	Jan 26, 2016: - removed -d

#				  - changed outGrid_firstBin default to '*', also lastBin

#	Jan 27, 2016: - added documentation

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

# Data Input 

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

# Set $opt_4 to 1 (or use the -4 option) to suppress 3-beam LADCP 

# solutions

#$opt_4 = 1;

# The following variables allow bias-correcting the attiude 

# sensors.

# NB: heading is not used for vertical-velocity processing!

$pitch_bias 	= 0;

$roll_bias 		= 0;

$heading_bias 	= 0;

# The following variable defines the minimum valid velocities 

# required in a LADCP file. If there are fewer data, an

# error is produced

$min_valid_vels = 50;

# The -b option defines the range of bins to use in w calculations.

# The '*' indicates the last bin in the ADCP file. For data

# collected with non-zero blanking distance, -b '1,*' should 

# likely be used.

$opt_b = '2,*' unless defined($opt_b);

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

# Logging and Output

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

#	- there are 4 verbosity levels, selected by -v

#		0 :	errors

#		1*:	UNIX-like (warnings and info messages that are not produced for every cast; *DEFAULT)

#		2 :	progress messages and useful information

#		>2:	debug messges

#	- the most useful ones of these are 1 & 2

&antsCardOpt(\$opt_v,$ENV{VERB});

$opt_v = 1 unless numberp($opt_v);

# The "base name" of all output files (usually 0-padded 3-digits)

$out_basename = sprintf('%03d',$PROF);

# Output subdirectories

$data_subdir = $plot_subdir = $log_subdir = $RUN;

# The -k option defines the minimum number of w samples required in each 

# vertical-velocity bin. The following sets the default value.

&antsCardOpt(\$opt_k,20);

# The -o option sets the output grid resolution in meters. The following

# sets the default value.

&antsFloatOpt(\$opt_o,20);

# The following variables limit the bins used to grid w_oean

#	- in contrast to -b, the other bins are still used e.g. for BT 

#	- values recorded in %outgrid_firstbin, %outgrid_lastbin

#	- values beyond range are:

#		- greyed out in *_mean_residuals.ps

#		- not used in *_w.ps, *_residuals.ps

$outGrid_firstBin = '*';			# use $LADCP_firstBin (-b)

$outGrid_lastBin  = '*';			# use $LADCP_lastBin (-b)

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

# Data Editing

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

# The following sets the default correlation limit; measurements with

# correlations below this limit are discarded.

&antsFloatOpt(\$opt_c,70);

# The following sets the default limit for instrument attitude 

# (pitch/roll).

# 

# The default value was established with IWISE profiles 004, 005, 045

# and 049, which all show considerabe tilt-related discrepancies between

# the corresponding 2-beam solutions. The first and second pair of

# profiles were collected with 8 and 6m bins, respectively, without

# bin re-mapping. The original default of 15 degrees led to large

# beam-pair differences. Based on diagnostic plots it appears that

# only tilt angles smaller than 9 degrees or so are satisfactory. 

# In case of the IWISE data set, such a tight constraint causes

# too many data gaps. The compromise of 12 degrees seems to work

# quite well, based on the p0 vs epsilon correlation across 5

# data sets.

#

# NB: if this default is changed, the usage message in [LADCP_w]

#	  needs to be updated as well.

&antsFloatOpt(\$opt_t,12);

# The following sets the default error velocity limit; measurements 

# with error velocities below this limit are discarded.

&antsFloatOpt(\$opt_e,0.1);

# The following variable allows editing the velocities farthest

# from the transducer. It defines how many velocities are to be

# removed from each ensemble. 

$truncate_farthest_valid_bins = 0;

# The following variable allows editing all data from a given

# beam. Set to 1-4 to enable.

$bad_beam = 0;

# The following sets the maximum gap length in the w time series that

# is simply ignored.

&antsFloatOpt(\$opt_g,60);

# The following variable sets the max allowed vertical ocean velocity 

# in m/s. Measurements with |w| this limit are discarded.

$w_max_lim = 1;

# In each ensemble, vertical velocities differing more than this

# parameter times the mean absolute deviation from the median, are 

# considered outliers and removed.

$per_ens_outliers_mad_limit = 2;

# Data from bins with less valid velocities than the following parameter

# are considered bad and removed. It is not clear whether this really

# makes sense, but this editing is likely safe because it only affects

# ensebles with the largest ranges.

$per_bin_valid_frac_lim = 0.15;

# All ensembles recorded when the CTD is shallower than 

# the following parameter (depth in meters) are discarded.

# Possible contamination: ship's hull, thrusters, bubble clouds

# Inspired by 2011_IWISE station 8.

$surface_layer_depth = 25;

# Previous Ping Interference editing as described in [edit_data.pl]

#	- enabled by default for WH150 data

#	- the variable defines a string with a perl expression, which is

#	  evaluated once the data are loaded

#	- 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.

$PPI_editing_required = '($LADCP{BEAM_FREQUENCY} < 300)';

#$PPI_extend_upper_limit = 1.03;		# see comments above

# The following variables control the "non-obvious" sidelobe editing for

# contamination from the seabed for the UL and from the sea surface for the

# DL. Tests with DoMORE-2 data (WH150 DL, WH300 UL) strongly suggest that

# it is not necessary to edit DL data for surface contamination. However,

# at least for that instrument combination, UL (WH300) contamination from the

# seabed should clearly be removed.

$sidelobe_editing_DL_surface	= 0;

$sidelobe_editing_UL_seabed		= 1;

# The following variable sets the depth for sidelobe contamination

# from the surface. 

$vessel_draft					= 6;		# in meters

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

# Time Lagging

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

# The -i option allows defining an initial guess for the time lag between

# the LADCP and the CTD data.

# $opt_i = 567;

# The following variables define the bins used to calculate the reference-

# layer velocities used for time lagging.

($refLr_firstBin,$refLr_lastBin) = (2,6);

# The -n option defines the number of windows used to calculate

# the optimal time lag. There's one value for each time-lagging step.

$opt_n = '10,100' unless defined($opt_n);

# The -w option defines the width of the window (in seconds) used

# to calculate the optimal time lag. There's one value for each 

# time-lagging step.

$opt_w = '240,20' unless defined($opt_w);

# The following parameters control whether the top three time lags 

# are accepted or not.

# If the top 3 lags have spread greater than $TL_max_allowed_three_lag_spread

# (in CTD scans) they must account for at least $TL_required_timelag_top_three_fraction

# or an error is generated.

# Notes:

#	- $TL_max_allowed_three_lag_spread default was initially set to 2 but found to be 

#	  violated quite often during 2011_IWISE

# 	- large spread may indicate dropped CTD scans

# 	- the optimum value of $TL_max_allowed_three_lag_spread may be 

#	  cast-duration dependent

$TL_max_allowed_three_lag_spread = 3;

&antsFloatOpt(\$opt_3,0.6);

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

# Acoustic Backscatter and Seabed Search

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

# After applying the method of Deines (1999), an empirical correction

# for Sv is applied to the data. The following variable determines which

# bin is chosen to construct a reference profile for Sv. The bin number

# is automatically increased if the selected bin does not contain valid

# data, i.e. the default value of 1 ensures that the closest valid bin

# is used to construct the reference profile.

$Sv_ref_bin = 1; 

# Set to folloing variable to 1 to use ADCP BT data to detect seabed 

# instead of default code based on Sv (echo amplitude). I do not know

# which code is better.

$SS_use_BT = 0;

# The following variable defines the minimum Sv signal in a bin (max - min)

# required for reliable seabed detection FROM ECHO AMPLITUDES. A limit of 40dB is

# indicated based on GoM#13, where the seabed is only visible in the last 

# bin (#25). 30dB is chosen as the default to allow for variability. 

# This value may need to be changed for data not collected with WH300

# instruments with 8m bins, and perhaps also for different types of

# seafloor (soft sediments). To do this, set $SS_min_signal to a small value

# (e.g. 10) and inspect the \@SV_rng values reported in the log files.

# This parameter is only used when $SS_use_BT == 0.

$SS_min_signal = 30;

# Require at minimum nubmer of valid samples for seabed detection FROM ECHO

# AMPLITUDES. Each sample is a bin with a clear seabed maximum. With a proper 

# setting of $SS_min_signal, the algorithm is stable even with only a single

# sample (GoM#13). However, a default of 3 required samples is chosen

# to make seabed detection less sensitive to $SS_min_signal. 

# This parameter is only used when $SS_use_BT == 0.

$SS_min_samp = 3;

# The following numbers define the valid range of height-above bottom

# for seabed detection FROM ECHO AMPLITUDE. For data collected with WH300 

# instruments and 8m bins, the maximum range needs to be greater than 250m 

# (based on # GoM#13).

$SS_min_allowed_range = 0;

$SS_max_allowed_range = 350;

# Number of ensembles around bottom to search sabed IN BT DATA. 

# Only used with $SS_use_BT == 1.

$SS_search_window_halfwidth = 200;	 

# Maximum allowed distance of seabed from mode of distribution. 

# Only used with $SS_use_BT == 1.

$SS_max_allowed_depth_range = 10;

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

# Bottom Tracking

#	- at present, the ADCP BT data are ignored, i.e. "post-processed"

#	  BT data are used.

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

# Don't look for BT-referenced velocities if package is more than $BT_max_range

# above seabed. This parameter is frequency dependent and the current value is

# appropriate (if rather high) for 300kHz Workhorse intruments.

$BT_max_range = 300;

# The code only tries to bin BT-referenced velocities if a consistent bottom

# is available in all 4 beams. Ensembles where the range of bin numbers where

# the maximum echo is found is greater than $max_BIT_bin_range_diff are rejected.

# In addition to flukes this also rejects ensembles collected with large

# instrument tilts. The value of 3 is a first guess that has not been explored.

$BT_max_bin_range_diff = 3;

# If the difference between measured vertical velocity of the seabed (i.e.

# the package vertical velocity referenced by the seabed) and the vertical

# velocity of the CTD (from dp/dt) si greater than $BT_max_w_error the current

# ensemble is ignored and $nBTwFlag is increased. The value of

# 3cm/s is taken from listBT developed on A0304 cruise.

$BT_max_w_error = 0.03;

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

# ProcessingParams file selection

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

if (-r "ProcessingParams.$RUN") {

	$processing_param_file = "ProcessingParams.$RUN";

} elsif (-r "ProcessingParams.default") {

	$processing_param_file = "ProcessingParams.default";

} elsif (-r "ProcessingParams") {

	$processing_param_file = "ProcessingParams";

} else {

	error("$0: cannot find either <ProcessingParams.$RUN> or <ProcessingParams[.default]>\n");

}

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

# Processing log (diagnostic messages) output

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

$out_log = "$log_subdir/$out_basename.log";

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

# Vertical-velocity profile output and plots:

# Data:

#	*.wprof				vertical velocity profiles

# Standard Plots:

# 	*_wprof.ps			vertical velocity profiles (main output plot)

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

@out_profile = ("plot_wprof($plot_subdir/${out_basename}_wprof.ps)",

			    "$data_subdir/$out_basename.wprof");

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

# Vertical-velocity sample data output and plots:

# Data:

#	*.wsamp				w sample data

# Standard Plots:

#	*_wsamp.ps			vertical velocity time-depth plot

#	*_residuals.ps		residual vertical velocity time-depth plot

#	*_backscatter.ps	volume scattering coefficient time-depth plot

# Optional Plots:

#	*_correlation.ps	correlation time-depth plot

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

push(@out_wsamp,"$data_subdir/$out_basename.wsamp");

push(@out_wsamp,"plot_residuals($plot_subdir/${out_basename}_residuals.ps)");

push(@out_wsamp,"plot_backscatter($plot_subdir/${out_basename}_backscatter.ps)");

push(@out_wsamp,"plot_wsamp($plot_subdir/${out_basename}_wsamp.ps)");

#push(@out_wsamp,"plot_correlation($plot_subdir/${out_basename}_correlation.ps)");

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

# Time-series output

# Data:

#	*.tis			combined CTD/LADCP time-series data, including 

#					package- and LADCP reference layer w

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

@out_timeseries = ("$data_subdir/$out_basename.tis");

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

# Per-bin vertical-velocity residuals (plot only)

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

@out_BR	= ("plot_mean_residuals($plot_subdir/${out_basename}_mean_residuals.ps)");

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

# Time-lagging correlation statistics (plot only)

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

@out_TL = ("plot_time_lags($plot_subdir/${out_basename}_time_lags.ps)");