- - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - - - - - - - - These are relevant to any codas processing of shipboard ADCP data Options are specified on the command line or in a file. (see below) help = False # print help varvals = False # print values about to be used, then exit # eg. quick_adcp.py --cntfile q_py.cnt --varvals vardoc = False # detailed use for each variable commands = None # print specific help # === directories and files === # # variable default # description # ------- ---------- # ----------------- # #---- required ----- datatype = None # choose what kind of data logging (and # hence which kind of data files # are being processed) # # default is "pingdata" # # name what # ---- ---- # "pingdata" implies DAS2.48 (or 2.49) NB # # "uhdas" implies known directory # structure for access # to raw data # "lta", "sta" VmDAS averages # sonar = None # eg. nb150, wh300, os75bb, os38nb yearbase = None # 4 digits (acquisition year) ens_len = None # seconds in an ensemble; default set in dbinfo cruisename = None # used for plot titles; required # cruise name is the same as procdir name # required in post-processing; beamangle = None # degrees (integer). # Reference layer smoothing: # three possibilities: # (1) bin-based reference layer; "smoothr" # (2) refavg decomposition (timeseries, # baroclinic, minimize error) "refsm" # (3) use_uvship: use average of ship speeds from # good profiles only. limitations: # - uhdas single-ping processing only # - must be set at the time of averaging dbname = None # traditionally # - start with "a" # - then append 4 characters # defined as the 'XXX' in 'adcpdb/XXXdir.blk' ## ---- end of required parameters --- cntfile = None # override defaults with values from this # control file. Format is the same as # command line options, but whitespace is # unimportant. Do not quote wildcard # characters in the cnt file (whereas # you would for the command line) # Defaults are overridden by this cntfile # Commandline options can override either. # additional parameters --- datadir = None # data path. defaults are: # (1) relative to scan or load directory # (2) full path # ../ping (for LTA, ENS, pingdata) # # for NON-UHDAS processing only. # use "sonar" and cruise_cfg.m for UHDAS datafile_glob = None #look for sequential data files. # (not for UHDAS data) # defaults are: # pingdata.??? (for pingdata) # *.LTA (for LTA files) # *.ENS (for ENS files) data_filelist = None # use data file paths in this text file pingpref # (only activated with these choices for --sonar: # os150, os75, os38 (i.e. without the pingtype specified) # - used to choose default ping type if interleaved # - otherwise it uses whatever is there # (whereas eg. os75bb would only use bb pings) #----- # Reference layer smoothing: # two possibilities: # (1) old: "smoothr" # - bin-based reference layer; # - simple averaging # (2) default: "refsm" # - refavg decomposition # - calculates timeseries+baroclinic, # - minimize error "refsm" # # additionally, supports: # - navigation from 'gps' or from # translated positions, based on # transducer offset from ADCP # - ship speed from # - 'nav' (traditional calculation # of ship speed (from first # difference of positions from # ensemble end-times) # - 'uvship' (new, EXPERIMENTAL) # average of ship speeds from # pings used, calculted during # single-ping processing # these two are set in quick_setup.py (check_ref_method) ref_method = 'refsm' ## Default: use "refsm" for reference layer # - positions inputted with "put_txy" # - ship speeds inputted with "put_tuv" ## other choice: use "smoothr" for reference layer # - ship speed and position inputted with "putnav" # Plots are done with smoothr, regardless ## these two combine in RefSmooth to create tuv.asc for "put_tuv" refuv_source = 'nav' # default = uvship from position file # otherwise EXPERIMENTAL: # specify 'uvship' to use # ship speeds from "uvship", i.e. # averaged from only those pings used refuv_smoothwin = 3 # default blackman filter half-width = 3 # (use 2*N-1 ensembles on each side for # reference-layer smoothing # (goes into Refsm as bl_half_width) # 0: no smoothing # 1: just use one point (same as "no smoothing") # 2: (less smoothing) #------------ # xducer_dx, xducer_dy # The next two variables use the offset # between transducer and gps to "realign" # the positions closer to the adcp. # POSTPROCESSING: run with "--steps2rerun" # and specify "navsteps:calib" # new fix file is dbname.agt # SINGLE-PING PYTHON PROCESSING: creates # .gps2 and .gpst2 files in load, # and cats to .gpst2 to dbname.gpst # for the fix file # xducer_dx = 0 # positive starboard distance from GPS to ADCP # This option is usually not necessary # xducer_dy = 0 # positive forward distance from GPS to ADCP # This option is usually not necessary fixfile = None # override the default fix file. defaults are: # if datatype is pingdata, default is # [dbname].ags (for pingdata) # [dbname].gps (for LTA, ENS, or uhraw) # fixfile is used as input to # - smoothr # - xducer_dx, xducer_dy ######## ub_type = '1920' # For NB DAS only: User buffer type: # 720 for demo; 1920 for recent cruises # # === processing options === # # variable default # description # ------- ---------- ----------------- rotate_amplitude = 1 # run "rotate" on the entire database with # amplitude (scale factor) = 1.0 rotate_angle = 0 # run "rotate" on the entire database with # this angle (phase), usially a tweak from # bottom track or watertrack calibration rl_startbin = 2 # first bin for reference layer: 1-nbins rl_endbin = 20 # last bin for reference layer : 1-nbins pgmin = 50 # only accept PG greater than this value # --> don't go below 30 <-- # default is 50 for pre-averaged datatypes # ('pingdata', 'lta', and 'sta') # default is 20 for single-ping datatypes # ('uhdas', 'enr', 'ens', 'enx') jitter = 15 # jitter cutoff (increase value to keep more data) # MATLAB: jitter is a parameterization of horizontal # and vertical second derivatives of u,v # PYTHON: jitter is the vertical average of median # filter applied to each bin in the ref. layer find_pflags = False # automatically find profile flags # apply editing (dbupdate, etc) # You should be familiar with gautoedit # before using this... # === REPROCESSING options === # # # variable default # description # ------- ---------- ----------------- steps2rerun = '' # colon-separated list of the following: # 'rotate:apply_edit:navsteps:calib:matfiles' # designed for batch mode; assumes codasdb # already in place, operates on entire # database. # # 'rotate' is: # apply amplitude and phase corrections # using these (if specified): # rotate_angle (contstant angle) # rotate_amplitude (scale factor) # Apply time-dependent correction manually # # 'navsteps' is: # [adcpsect+refabs+smoothr+refplots] # and reference layer smoothing by # refsm (default; uses put_txy, put_tuv) # or smoothr (uses putnav) # # 'apply_edit' is: # badbin, dbupdate, set_lgb, setflags # # 'calib' is: # botmtrk (refabsbt, btcaluv) # watertrk (adcpsect, timslip, adcpcal) # # 'matfiles' is: # adcpsect for vector and contour # Always use "sonar" for defaults # (specify top_plotbin for better results # IF you have codas python extensions) # or use "firstdepth" to tweak top values # # 'write_report' is: # write a summary of cruise metadata # - lands in "cruise_info.txt" # ONLY use this option to generate a cruise # report for a cruise without one; check for # "cruise_info.txt" before running in this mode ### === Data extraction options === numbins = 128 # max number of bins to extract for editing firstdepth = None # depth of shallowest bin for adcpsect extraction ## === specialized processing options === auto = False # 1: whiz along (do not prompt); do all # requested steps (default is all step) # 0 to prompt at each step ############## for UHDAS processing only #################### # batch or incremental # proc_engine = 'python' # default -- no choice # "python" : requires matplotlib; # matlab is not used cfgpath = 'config' # UHDAS only # Find cfg files (*_cfg.m, *_proc.m) here. # NOTE: path should be absolute or can be # relative root processing directory # (if relative, rendered absolute # before being used, to remove ambiguity) # NOTE: cruisename is the prefix for these files configtype = 'python' # default (no choice) 'python' python processing badbeam = None # badbeam for 3-beam data (beam=1,2,3,4) max_search_depth = 0 # use predicted topography as follows: # 0 = always use amp to identify the bottom # and remove velocities below the bottom # -1 = never look for the bottom using amplitude # therefore never edit data below the 'bottom' # positive integer: # - if predicted topo is deeper than this # depth, then we are in deep water and do # not expect to find the bottom. Therefore # DO NOT try and identify the bottom # (eg. do not idenfity strong # scattering layers in deep water) # - impacts weak-profile editing # - used to be "use_topo4edit" with a search # depth of 1000 max_BLKprofiles= 300 # max number of profiles per block. Might # want to make smaller to test incremental # processing (must be 512 or less) update_gbin = False # UHDAS; update gbin files py_gbindirbase = None # defaults to uhdas_dir/gbin for python IO ############## for UHDAS processing only, incremental ################## dday_bailout = None # may be useful for testing (UHDAS only) # (bail out of averaging at this time) ping_headcorr = False # UHDAS only. apply heading corrections on-the-fly # installation for other backends top_plotbin = None # shallowest bin to use for data extraction # bins are 1,2,3,... # --> overrides 'firstdepth' if both ar chosen # --> requires codas python extensions #