Gui interface for ADCP autoedit package ==================================================== "gautoedit", pronounced "gee! autoedit" ==================================================== See "autoedit.html" for a better description of the editing process. --------- Jules Hummon; Dec 2000 (called aREADME.verbose) May 2002, consolidating and clarifying, written for refsm ref layer; tailored for "demo" gautoedit requires Matlab 5.3 or higher quick_adcp.prl requires perl 4.0 or higher aREADME_basics.txt contents: (I) Introduction (II) Directions (easy start) (III) description of some useful autoedit programs ======================================================================= =========================== (I) Introduction ========================== ======================================================================= This document describes two new programs in the CODAS3 suite of processing code, "gautoedit" and "quick_adcp.prl". I will describe their use in the context of the "demo" cruise, which is already well-documented (see "process.txt"). *** New editing: "gautoedit" (a matlab gui tool for editing ADCP data in a CODAS database) This editing package arose from a need to apply some new editing parameters to a large number of cruises, many of which contained varying (but generally large) amounts of bad data. The editing scheme was patterned after the original waterfall editing used in conjuction with codas processing: i.e. (1) view a time range with some editing criteria, (2) list the ascii flag information to disk, (3) move on to the next segment and repeat. After you are finished listing all the ascii flag information to the disk, you apply the flags to the database. With both kinds of editing, the results are not seen in the database until you apply the editing to the database. With both kinds of editing, you can view the effects of the editing about to be applied and can view the data with or without the already-applied flags (if there are any). You should already be familiar with the original interactive editing which used waterfall plots in matlab before using autoedit (see process.txt). One reason for this requirement is that you can (from autoedit) jump back into the old waterfall editing and zap profiles or bins. It is very easy to get confused if you are not familiar with the old waterfall editing tool. The other reason is that the scheme is the same: data are tagged for rejection using editing criteria which are similar between the two schems, and the approach is the same: view, list, view next group, list, [repeat until the end], apply flags; check results. *** Standardized processing: "quick_adcp.prl" (query-driven program to set up and run adcp processing steps) Quick_adcp.prl is a command-line perl program that will set up and run all the standard processing steps for a Narrowband shipboard ADCP cruise, with various defaults accessible through switches on the command line. It is designed for batch-processing (i.e. the whole time range of the specified pingdata files). You can use it to quickly process a cruise to a point where you can look at the database to evaluate whether processing needs more intervention. If your cruise requires special treatment (eg. a time shift, no ashtech, etc) you can stop the process at any point and do something manually, and then go back to quick_adcp.prl and start after that step. Other advantages of using quick_adcp.prl: (1) standardized file names (2) records of what was done are left on the disk (3) sets up the files for gautoedit (4) contains documentation: quick_adcp.prl --help (lists commandline arguments and usage) quick_adcp.prl --howto (tells how to get started) quick_adcp.prl --overview (lists quick_adcp.prl processing steps) quick_adpc.prl --config_info (some tips on customization) *** Two more potentailly useful little scripts: - linkping.prl (unix only) links a list of pingdata files from a source directory to the ping/ subdirectory as unique, sequentially numbered filenames. This is particularly useful if there are repeated filenames (eg. from two legs, both starting at pingdata.000). - scanping.prl goes through a list of specified pingdata files and scans them (i.e. writes scanping.tmp and runs "scanping scanping.tmp"). This is particularly useful if you want the time range of the data, or if you have a bunch of pingdata files with unknown time ranges that need to be sorted out (scanping.prl on each individually with a unique output name) ---- Note about names: (1) Nomenclature: You have a directory root called "programs" which contains our "matlab" and "codas3" subdirectories. I will refer to this as PROGRAMS when I identify paths. (2) You have to run adcptree to start a processing directory; I will refer to the cruisename as "demo" (3) These perl programs reside in PROGRAMS/codas3/bin/scripts. Add this to your path. To run, type "perl -S " followed by the perl script name, followed by any switches. EG: perl -S quick_adpc.prl --help ======================================================================== ===================== (II) directions================================== ======================================================================== If you have run quick_adcp.prl, you have two programs in your ADCP processing tree in the edit/ directory: asetup.m (basic information to configure gautoedit) aflagit_setup.m (parameters used to set editing criteria defaults) If you are processing this cruise with quick_adpc.prl, use the "-zapsetup" switch and it will automatically create an appropriate "setup.m" file. If you are not processing this cruise with quick_adcp.prl, then copy the templates for these files from PROGRAMS/matlab/autoedit, and edit them for your cruise. You also need to edit setup.m (for the original interactive editing programs). Approach: You either have good data and want to automate the old-fashioned editing (eg. Kaimimoana), or you have lousy data and want to cavalierly eliminate anything of dubious character (eg. N.B. Palmer). The example is for decent data. (Examples of aflagit_setup.m for good and bad cruises are in goodcruise_ex/ and badcruise_ex/, respectively) in matlab, to start the gui tool, go the the edit/ subdirectory of your ADCP processing directory and run: gautoedit This gui runs asetup (to get path info, dates,...) and aflagit_setup (sets the editing parameters) and sets up gui tool to let you view the effects of the editing on a range of days, adjust the parameters and/or go into the old-fashioned editing scheme to trim bins or profiles, allows you to list the chosen flags, and move on. This tool was developed as a way to view and screen entire datasets for gross abnormalities and identify issues to deal with later. suggested iteration: - adjust the parameters which control bin and profile flagging - "show now" to see the data - "list flags to disk" to add the flags from the current panel to the ascii (a*.asc) files. - "show next" to see the next group in time tweaking: - "find PG [blk, prf]" will let you identify time, block, profile, and bin from the Percent Good data (for your notes) - "old edit" lets you identify a [block, profile] location in the Percent Good data and puts you into the older interactive editing scheme. You can access commands from the command line **NOTE: Make sure you "list" on the command line so your flags to to update the appropriate ascii files **NOTE: You must edit setup.m before you try to use "zap" editing so it can find your database NOTE that the reference layer and percent good cutoff can be changed in this program to let you choose what value will work best for a given time range. HOWEVER in general we have used one PG and one reference layer for an entire cruise. These parameters are set in other control files that are run when applying the editing and running the nav steps) More details are contained in the html documentation, at PROGRAMS/codas3/adcp/doc/edit_html/autoedit.html or at http://currents.soest.hawaii.edu/adcp_doc/edit_doc/edit_html/autoedit.html APPLY THE RESULTS: --> apply the editing from gautoedit: dbupdate ../adcpdb/dbname abottom.asc dbupdate ../adcpdb/dbname abadprf.asc badbin ../adcpdb/dbname abadbin.asc --> apply the editing from waterfall editing: dbupdate ../adcpdb/dbname bottom.asc dbupdate ../adcpdb/dbname badprf.asc badbin ../adcpdb/dbname badbin.asc --> always run these two in this order after applying any editing set_lgb ../adcpdb/dbname setflags setflags.cnt --> rerun the nav steps: cd ../nav (run these steps to redo watertrack calibrations and redo reference layer plots.) adcpsect as_nav.tmp refabs refabs.tmp smoothr smoothr.tmp (run these to update navigation) (in matlab) refsm (from the command line) putnav putnav.tmp cd ../edit examine the results, reiterate if necessary