Matlab Gui tool for editing shipboard CODAS3
data, "gautoedit":
(pronounced "gee! autoedit!
")
I. Introduction
The "autoedit" package is a collection of programs for
extracting and displaying velocity and other ancillary data from a
codas database in panel plots, and creating ascii files of flags for
bad data. As with the original "waterfall" editing, the ascii
files containing information about bad data are then applied to the
database so that further data extraction will not include those
flagged values.
A new perl program (quick_adcp.prl) can set up the gautoedit files
and run through all the basic processing steps. It is useful for a
quick
look at a dataset and is sufficient for processing most shipboard ADCP
datasets. It can handle data from DAS (pingdata files) or from VmDAS
(LTA files), though the latter requires a separate load step.
Advantages to using quick_adcp.prl include (1) standardized names (2)
automatic setup of gautoedit
files (3) consistency in parameters (4) steps are recorded in a log
file (5) many parameters can be changed on the command line (6) it is
relatively
painless to delete a database and start over (7) runs under MS Windows.
Read this document for more
information.
Notes:
- Matlab can only run one "gautoedit" session at a time
- You can access the command line and do other matlab things while
running gautoedit, but you must be in the initial directory (edit/)
when you hit buttons on the gui tool or it will complain
- You can't see the effect of your editing until you've finished
and applied all the ascii files to the database and rerun the
navigation steps. Seeing the results immediately is on the list of
"things to do".
- You should AVOID resizing the figure windows while they are
drawing: matlab will sometimes draw the upcoming figure in whatever
window you're fiddling with, and you can end up with a plot inside your
gui tool. Don't worry - just kill that figure and start gautoedit again.
This html documentation is meant to give you an introduction to
tthe autoedit package and provide some guidance as to its use. It is
not a comprehensive editing tutorial, so some detail is lacking. Data
come from two sources: (1) the same pingfiles that were used in the
original "demo", and a much newer dataset that contains Ashtech
headings in the user buffer and some good illustrative editing
examples.
-------------------------------
Jules Hummon , 6/2002
II. Setting up gautoedit
Two text files exist describing the autoedit package and the gui
tool (gautoedit) to use it:
aREADME_basics.txt,
which describes how to configure up the setup files, and
aREADME_details.txt, which describes the editing parameters and
what they control.
Please read them in conjunction with this
document.
III. gautoedit: gui panel layout
The gui panel has four sections:
Gautoedit always
plots a panel figure with ocean velocities (rendered absolute via
navigation steps). By default it will also plot a vector plot of upper
ocean velocities overlaid on topography. This can be turned off. You
can choose to plot
amplitude and velocity in the forward direction. You can also
choose to plot error
velocity and an experimental parameter called "bias parameter"
(undocumented: indicator for underway bias in the presence of strong
scattering layers).
IV. Editing ADCP data
(1) starting out
- Run
gautoedit from the edit/ subdirectory of your adcp processing tree
- Choose the
number of days to display (based on your screen resolution), make
sure
you can see individual profiles.
- Choose your actual starting date so you don't have a big blank
spot at the beginning of the cruise
- Look at the
jitter cutoff: it should be just low enough to cut off the tops of
outliers
but not catch every little bump
- Press "show now" to load the data and get started
- Examples from two databases are here (1)
,
(2)
(2) a typical sequence of steps
- You might want to adjust the
jitter cutoff to see
whether the places with the highest jitter actually show up in the
velocity as anomalous profiles. If you can't see a difference in
character between the profile with the jitter spike and its neighbors,
chances are there is no reason to flag it
- You might have data with bottom tracking OFF but with the bottom
within the instrument's range. Try adjusting the three
bottom-detection
parameters. The "show amp and forward" button brings up a panel with
amplitude the next time you hit "show now", providing a useful context
for determining whether you're looking at the bottom or fish.
- You might have data with alot of bad "tails" (bias near the
bottoms of profiles). These are probably best removed with either "zap
edit" or "old edit". The two tools are different, and you may prefer
one to the other for this purpose. Zap editing is simply a rectangular
flagging of data; the old editing tool is fully interactive and
completely independent from gautoedit. The "old edit" button is
simply a way to invoke the waterfall editing from within
gautoedit. NOTE: you must have used "-zapsetup" during quick_adcp.prl
or edited the "setup.m" file yourself. You must run setup once before
"list".
- You might need to flag a whole time range as bad. If so, click on
"del time range" and select the start and end of the bad time
range. The profiles in that range will automatically be listed to
"abadprf.asc"
- You might want to see what the data look like without the
autoedit
parameters applied: if so, try turning on both "plot in new" and "do
not show (autoedit) editing", and then hit "show now". You will get a
new figure with the absolute velocity as it comes from the database,
(as well as any other figures you have turned on) with no autoediting
applied. This can be useful in determining howo to change parameter
values or what approach to take in editing the data.
- Make sure you do any deletion of time ranges or bad bins before
you move on, or you'll forget to come back to it.
- When you are satisfied with your editing parameters, hit "list to
disk" and the flags will be listed to ascii files a*.asc. Hit "show
next" and move on to the next panel.
(3) Other things to edit
(4) Interpretation: things to keep in mind
(5) finishing up
When you have gone through the whole dataset, you have a collection
of ascii files. You need to update the following before you attempt to
make any
plots or assess whethere anything more needs to be done:
applying the flags to the database: (in any order)
badbin ../adcpdb/edemo abadbin.asc
badbin ../adcpdb/edemo badbin.asc
dbupdate ../adcpdb/eemo abadtimes.asc
dbupdate ../adcpdb/edemo abottom.asc
dbupdate ../adcpdb/edemo badprf.asc
dbupdate ../adcpdb/edemo badtimes.asc
dbupdate ../adcpdb/edemo bottom.asc
dbupdate ../adcpdb/edemo abadprf.asc
and then, in order:
set_lgb ../adcpdb/ademo
setflags setflags.tmp
and finally, (in order) update the navigation :
refsm (or adcpsect and refabs and smoothr)
putnav putnav.tmp
Remember, you will still have to run adcpsect, refabs, and smoothr
before updating the reference layer plots or doing any watertrack
calibrations.