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.. UHDAS/CODAS restructured text document
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Changes and Updates
-------------------
(2009/05/01)
Improvements:
* corrected but in gautoedit and set_lgb that had bottom masking
(from side-lobe interference) hardwired at 30deg.
* added documentation about this and more about editing in general
(2008/06/31)
Changes:
* additional reorganization of python files
* work continues with python tools for access and plotting codas data
Improvements:
* continued efforts to improvement documentation
* added more variables to "getmat"
* added 64bit linux support
* more improvements to single-ping editing
(2007/05/31)
Improvements:
* improvements to documentation organization (including this page)
* added "persistence" of heading correction over small gaps (UHDAS data)
* added a distinction between yearbase (for date calculation) and
proc_yearbase (in case it was specified badly, or to join two UHDAS
cruises that span a year boundary)
* More improvements to single-ping editing
Bug Fixes:
* rewrote sonar variable specifications for HDSS so they work with
Matlab R2007a
(2006/10/25)
Changes:
* The entire directory tree is being reorganized to allow for
better version control. This slightly changes the installation
instructions (mostly the user's executable and python paths).
* We are embarking on an effort to move away from the use of
Matlab in processing and display software. Over time, routines
presently performed in Matlab will be ported to Python. We will
attempt to keep the Matlab code running as Mathworks changes
Matlab, but some things will falter, and eventually we will not
maintain them. The present examples of this include the
placement of a colorbar with gautoedit, and some aspects of
color mapping.
Improvements:
* Gautoedit polygon zapping and bottom editing tool was improved
for use with Matlab R14
* Codas database now stores cleaned averaged amplitude under 'amp'
and stores individual beam amplitudes under 'rawamp'; both are
accessible with "getmat"
* A new build system is being tested that uses python-based
`scons `_. If you wish to compile
the binaries for your system,
download codas3_declspec.zip and contact us for more information
about gotchas and what to expect. If you embark on this route
you will be a beta tester.
Bug fixes:
* Fixed: a bug in treatment of bottom depth resulted in databases
with noisy bottom depths were sometimes too large.
* Fixed: reference layers depths behaved badly if chosen to be
shallow
* Fixed: inconsistent treatment of ensemble length caused problems
for some long LTA averages
(2006/03/30)
New Additions:
* UHDAS documentation (acquisition, processing) added
(2005/10/17)
New Additions:
* improved heading-correction code
* split python processing scripts and executables into two groups
for cleaner updates
(2005/05/16)
* experimental HDSS tools (see `notes `_)
* UHDAS processing demo (in q_demos.zip)
* improving documentation for single ping data
(2004/12/30)
Major upgrades:
* Support for Matlab R14 (see `notes `_)
* Support for Macintosh OSX binaries (download binosx.zip)
Minor changes:
* fixed a recent bug in quick_adcp.py that made 'steps2rerun' fail
with VmDAS data
* gautoedit buttons are more visible for 1024x768 screens
Features introduced in earlier distributions:
(2004/05/18)
* `Online `_
documentation of Codas3 and ADCP processing. This
documentation is also present in the zip file distribution
"doc.zip", so you will have it on your disk once you download
all the appropriate zip files. When creating a processing
directory, there will also be an html file
"adcp_processing.html" containing a link to the local processing
documentation.
* A new variable-depth raference layer scheme "refsm" is now the
official standard for data with non-dithered GPS fixes and only
short gaps. It works well with cruises that have steep
topography or patchy depth loss due to bubbles or hull noise. It
does not do well if there are missing navigation points, as it
currently interpolates missing positions. "Smoothr" is still
required for watertrack calibration and reference layer
plotting, and can still be used for navigation.
* A new python program (`quick_adcp.py
`_) 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 averaged
data from DAS2.48 (pingdata files) or VmDAS (LTA or STA files),
and can perform configurable single-ping editing on UHDAS or
VMDAS single-ping data (for example ENX). Quick_adcp.py can be
run at sea on a unix machine at regular intervals, creating an
up-to-date codas database for scientists. Editing of the
averaged data in the CODAS database can be automated under these
circumstances. Advantages to using quick_adcp.prl include:
1. standardized names
2. impliments the new refsm reference-layer calculation
3. automatic setup of gautoedit files
4. works with pingdata or LTA files
5. works with ENX or UHDAS single-ping files
6. consistency in parameters
7. steps are recorded in a log file
8. many parameters can be changed on the command line or
in a control file
9. makes it relatively painless to delete a database and start over
10. runs under MS Windows
* Improvements to the new editing package " gautoedit" pronounced
`**Gee! Autoedi** `_
include improved automatic bottom detection,
manual bottom editing, and rectangle or polygon zap. This tool
is a graphical means of editing CODAS ADCP data (i.e. averaged
velocities) in user-determined time chunks (eg, 2-4 hours for
messy data; 1-3 days for clean data and a high resolution
monitor). This tool was designed to screen data for things like
ringing, on-station wire interference, jittery navigation, and
bottom interference when bottom tracking was not on. The old
editing (best done 20-30 profiels at a time) can still be used
for fine-tuning single-bin editing. This is also a useful tool
for simply looking at a dataset, even if you don't use it for
editing.
* Single-ping or averaged VmDAS data can be read directly into
matlab, allowing scientists to access specfic time ranges to
comput shears or to look at the backscatter amplitude. This
`readme `_ may help.
* The older perl script (quick_adcp.prl) is no longer
supported. It has been ported to Python, and additional
functionality has been added.
other tools:
* A fairly comprehensive but undocumented and unsupported plotting
tool called "gplot" is available in our matlab distribution. Add
the "guiplots" subdirectory to your path. Default paths are
configured with the expectation that you will be running it from
the adcp processing directory. Specifically, it will need to
load adcpsect output files (\*_xy.mat) from a contour or vector
subdirectory, and can make nice panel plots of percent good and
other parameters assuming your database is in an adcpdb
subdirectory.
Caveats:
* Both adcptree.py and quick_adcp.py work under Unix and Windows
systems. For Windows users, there are .BAT files supplied which
access these two programs: adcptree_py.bat (for adcptree.py),
and quickadcp_py.bat (for quick_adcp.py)
* Refsm should only be used with 5-minute averages and high
quality GPS data (i.e. not Selective Availability, and no
gaps). Smoothr still works fine if you are stuck with jittery
fixes.
refsm will interpolate across gaps in navigation. This is
probably OK for 1-2 points. If the gap is 3-6 points, and if the
ship is not maneuvering, you can substitute the positions from
smoothr. For longer gaps, substitute navigation from other
source. If you have no navigation, edit the out profiles. Refsm
leaves a log "refsm_interp.log" in the current directory ("nav"
if processing, "edit" when editing)
Updates:
* 2003/02/27: gautoedit now has an additional red button to allow
flagging of the bottom. Output is written directly to
abottom.asc
* 2003/02/27:a new setup program, "adcptree.prl" allows
specification of data type so that the directory can be created
to process VmDAS LTA files as well as ENS files. (Processing of
ENS files is not ready).
* 2003/02/27:A new Python program joins the processing toolbox:
"quick_adcp.py". This has all the features of quick_adcp.prl
as well as features such as: o keywords to rerun specific
steps (eg. nav steps, or calibration) o can process LTA
files as easily as pingdata files
* 2003/03/03: gautoedit
now has an additional gray bar which turns off smoothing of
navigational prior to calculating ocean velocity. This might
be useful if you think that ocean velocity artifacts are
caused by navigation or navigational smoothing.
* 2003/04/03: gautoedit now has one more manual editing
buttons, "pzap", bringing the number of buttons that
immediately write to ascii files to four (the others being
"Trange" and "rzap", and "bottom"). Documentation for these
buttons was updated.
* 2003/05/05: fixed a bug in which
on-station error velocity was actually being applied when
underway also (i.e. there was no difference between
on-station and underway error velocity: both were applied
always).
* 2003/05/05: added a field to adjust the
tolerance when deleting low shallow PG. This editing is
designed to identify probable ringing and delete the
offending bins. You may want to adjust it or disable it, and
now you can do that in the gautoedit window. Smaller numbers
mean alot of PG are deleted. Larger numbers make it less
effective.
* quick_adcp.prl batch processing for pingdata (no longer supported)
* using quick_adcp.prl to process ADCP data