%This is a setup script to set the structure values used by aflagit.m % "pfc" is "profile flags config" % substuctures are: % flag (the value of the bad data) % cfg (configuration information) % % You either have good data and want to automate the old-fashioned editing, or % you have lousy data and want to cavalierly eliminate anything of dubious % character. Here is a table with suggested settings for a "good" or "bad" % dataset. The defaults for this file will start out for "good" data so you % don't lose too much right at the start. % % % field of structure "pfc" good dataset bad dataset % (eg. Kaimimoana) (eg. NBPalmer) % ----------------------- ------------ ----------- % pfc.refl_startbin config.rl_range(1) config.rl_range(1) % pfc.refl_endbin config.rl_range(2) config.rl_range(2) % pfc.yearbase config.yearbase config.yearbase % % pfc.cfg.bigtarget_amp 25 25 (data dependent) % pfc.cfg.bigtarget_offset 5 5 (data dependent) % pfc.cfg.bigtarget_avg 2 2 (data dependent) % pfc.cfg.pgcutoff 30 50 (data dependent) % pfc.cfg.maxpgbin_fudge -1 (disable) 3 (data dependent) % pfc.cfg.badpgrefl 50 50 (data dependent) % pfc.cfg.badpgrefl_nbins 1 (make small) 5 (data dependent) % pfc.cfg.trimtopbins 0 1 (data dependent) % pfc.cfg.amp_cutoff_atbin1 0 (disable) 130 (data dependent) % pfc.cfg.ampdecrperbin 10 (disable) 10 (data dependent) % pfc.cfg.ecutoff 100 100 (data dependent) % pfc.cfg.wire_ecutoff 70 70 (data dependent) % pfc.cfg.wire_onstation 2 2 (data dependent) % pfc.cfg.wire_binrange [1 20] [1 20](data dependent) % pfc.cfg.jitter_cutoff 5 5 (data dependent) % pfc.cfg.orphan_numbins 0 pfc.cfg.badpgrefl_nbins % pfc.cfg.orphan_slide 0 3 (data dependent) % pfc.cfg.underway 100 100(data dependent) %============================================================================= % initialize some useful information pfc.cfg.underway = 100; % threshold ship speed (m/s): discard any data % with ship speed higher than this value. % disable it initially (i.e. set really high) % use: May want to reject all underway profiles % if ashtech went out (for instance) pfc.refl_startbin = config.rl_range(1); % ref layer should match what was pfc.refl_endbin = config.rl_range(2); % used in smoothr (for consistency) % (get it from ../nav/as_nav.tmp or % ( ../nav/adcpsect.cnt) pfc.yearbase = config.yearbase; % (for labelling) %set the config information to impliment the editing %------------ for binwise glitch filtering over time ----------- % for each bin, flag glitches but only if accelerating pfc.cfg.agility = 3; % ship-dependent pfc.cfg.degperminute = 20; % really accelerating - true outliers pfc.cfg.glitchfactor = 2; % alittle conservative pfc.cfg.topglitchbin = 1; % use glitch flagging starting at this bin (and deeper) % ---------- for the bottom ---------- % looking for a high amplitude signal which SHOULD be the bottom. % these values might have to be changed if we end up flagging % scattering layers. These values are good for the bottom being deeper than % about bin 5. If the bottom gets really really shallow, try no smoothing % (pfc.cfg.bigtarget_avg = 0) and a small window (pfc.cfg.bigtarget_offset = 2), % and decrease the threshold (pfc.cfg.bigtarget_amp = 10) pfc.cfg.bigtarget_avg = 2; % A value of 1, 2, or 3 is for smoothing % the vertical amplitude profile with a % a running average of 3, 5, or 7 points % respectively. A value of zero is no % smoothing. pfc.cfg.bigtarget_amp = 25; % an amplitude bump bigger than this is % identified as the bottom (like % AMP_THRESHOLD in the zap editing) pfc.cfg.bigtarget_offset = 5; % calculate the value of the amplitude % bump by comparing the value at a given % bin to the value shallower and deeper % by this number of bins. %---------- percent good ---------- % percent good is used in three ways: % (1) low percent good: eliminate all bins with pg < pfc.cgf.pgcutoff % (2) ringing: identified by a near-surface maximum (caused by a decrease % in PG near the surface, then PG returns to its normal value deeper % down). We locate the shallowest bin where PG attains its maximum % and chop of everything shallower than that. Because PG may hover % near its maximum for several bins, we back off the strict requirement % of "the shallowest bin with the maximum pg" and instead look for % "the shallowest bin within pfc.cfg.maxpgbin_fudge of the the maximum" % (3) reference layer: eliminate profiles if there are too few reference layer % bins with sufficiently good PG. pfc.cfg.pgcutoff = 50; % (1) low percent good for all bins % (lowest allowable number is 30; % set it higher to be more selective) pfc.cfg.maxpgbin_fudge = 3; % (2) ringing (allow this much slop % in identifying the "maximum" PG % --> set to -1 to disable % --> set to 1-3 if ringing pfc.cfg.badpgrefl = 50; % (3) reference layer PG cutoff % (lowest allowable number is 30; % set it higher to be more selective) pfc.cfg.badpgrefl_nbins = 1; % (4) require this many bins of good PG in % reference layer (or else reject profile) % ---------- trim the top ---------- %There are two editing criteria in this section eliminate bad data at the top. %(1) remove top N bins from all profiles %(2) remove bins where low amplitude may be artificially inflating % signal/noise ratio. At the moment this is a linear amplitude % cutoff with bin. % pfc.cfg.trimtopbins = 0; %exclude top N bins anyway (make it more to trim top) %%% NOTE: the following two may not be useful and should be disabled. pfc.cfg.amp_cutoff_atbin1 = 0; %amplitude cutoff at bin 1 is this % SET THIS ONE TO ZERO TO DISABLE BOTH PIECES pfc.cfg.ampdecrperbin = 10; %relative to bin 1, lose this many amplitude %counts ber bin in depth % ---------- error velocity ---------- % error velocity is used in two ways: % (1) plain old error velocity cutoff % (2) wire interference: different criterion (?), only on station, remove % an additional bin left, right, up, and down from flagged bins % (disable by setting cutoff to a large value (eg 10^6)) pfc.cfg.ecutoff = 120; % (1) plain old error velocity cutoff pfc.cfg.wire_ecutoff = 90; % (2) wire interference cutoff pfc.cfg.wire_onstation = 2; % (only look when speed is less than this) pfc.cfg.wire_binrange = [1 20];% (only look in this bin range) % ---------- jitter flag ---------- % jitter in measurement as defined by a running std of (sm - refl) pfc.cfg.jitter_cutoff = 5; %cm/s % ---------- flag isolated profiles ---------- % %If the data are mostly bad, we want to eliminate isolated profiles as % suspect. We do this by requiring a profile to have a few good close % friends. NOTE: to disable, must set both of these to zero % % pfc.cfg.orphan_numbins = 0 ; % number of unflagged bins in ref layer % required to accept the profile % pfc.cfg.orphan_slide = 0; %half-width of isolation profile % i.e. slide left and right by this, % and accept the center of a run of 3 % or middle 3 if a run of 5