CTD processing notes
====================
fb, 10/21/08
Prior to departing, Terry McKee showed me the two batch files
runctd.bat and runladcp.bat. We tried them out as far as we
could. While we did not get a fully processed station - we
figured the pressure binning crashed since our on-deck test data
did not have the changing pressure values required for the binning
to work - most of the processing steps ran.
----- as a side comment: ------------
One item struck me as odd: Terry mentioned that the last entry
in the .NAV file gives the CTD scan for the particular entry
(such as on-deck, start-down etc). However, the numbers appeared
too small to me to be scans (which are 24Hz). With more exact
numbers on hand from the log sheets of, say, station 3, it appears
clear now that at least for the CTD stations here, that entry
is in units of seconds, not scans; e.g; station 3 was close to 2 hours
long, and the last .NAV entry has around 5000 as the last item.
Not knowing how to properly set the starting scan (which should be
the scan number for when the CTD package starting going down), I
will just use "1". I understand that the error I make thereby may
affect the first depth bins (1-dbar averages) in that they may include
data from the CTD soaking prior to the start down.
------ end side comment ---------------
I selected station 2 for my first test runs of the batch
files. All our data files are in c:\data\449_6raw. Before
running my tests, I made a directory
c:\data\449-6raw\backup_for_testing and copied all station 2
files in there, for safe keeping.
Running "runctd.bat 449_6002 1", the program crashes
because it can not find the proper data files. I assume
this has to do with the fact that normally the data get saved
to c:\data, rather than to c:\data\449_6raw.
I create a new bat file called "runctd_fb.bat" which
looks for the data files in c:\data\449_6raw. It uses the file
v_ctd_wn_fb.txt which specifies c:\data\449_6raw as the input
directory.
One issue: the bottlesum program does not seem to
recognize the 449_6raw subdirectory when looking for the
.con file for input. I think that is a SeaBird bug, since the
line for the bottlesum step has the same argument
"/cc:\data\449_6raw\%1.con" as the previous line for the datcnv
step. To go around that little annoying "feature", I add a
line to the batch file to copy the .con file from
c:\data\449_6raw to c:\data.
======================================================
for the LADCP batch processing:
copy runladcp.bat to runladcp_fb.bat; work with the latter
runladcp.bat uses v_ladc_wn.txt; copy that to v_ladc_wn_fb.txt
and use the latter for runladcp_fb.bat
=======================================================
ran the following:
runctd_fb.bat 449_6001 1
runctd_fb.bat 449_6002 1
runctd_fb.bat 449_6003 1
runctd_fb.bat 449_6004 1
runctd_fb.bat 449_6005 1
runctd_fb.bat 449_6006 1
runladcp_fb.bat 449_6001 # for kicks
runladcp_fb.bat 449_6003 # our first LADCP station
10/22/08 local; 10/21/08 21:56GMT:
after receiving the confirmation email by Terry McKee, I
changed the configuration file that SeaSave is set to load
by default for this cruise (file SBE09-0901-20081018-hrnctd.con)
to "average" 1 scan (i.e., not average scans at all) instead
of the previous setting of averaging 24 scans.
for station 8: look at the .NAV file (c:\data\449_6raw\449_6008.NAV:
scan 13969 for start-down (second line, last entry)
runctd_fb.bat 449_6008 13969
runladcp_fb.bat 449_6008
10/23/08
I found out that that the down profiles of the earlier
1-Hz stations are noisy at the top bins, likely due to
incorporating data from the initial CTD soak prior to
the pump start. So I need to determine the start-down
"scan", which in this case will be the start-down second.
This effort is a bit hampered by the fact that
we were a bit lax with hitting the NAV button for the
early stations.
station 1: 2345, from the .NAV file, confirmed by the LADCP
1-second time series (looks like start down accorred
around second 2345 in that time series file).
station 2: very shallow cast - 50m only. The CTD went down
to 11m, soaked, but did not come back up to the surface.
station 3: down at 265, says the .NAV file. Confirmed
by the LADCP file
station 4: down at 937; confirmed from LADCP file
station 5: down at 1231; confirmed
station 6: down at 318; confirmed
station 7: down at 451; confirmed
===================================
also: find out why we have 2-dbar data in the processed
files, rather than 1 dbar data: with a text editor,
change the config file for bin averaging:
c:\data\config\v3_bin.psa
to
re-ran stations 1:7 with the above numbers for first scans.
As a first cut for Amy, also ran 8:19 with start scan 1,
since she was interested at a quick look at the deep data.
10/25/08
re-ran stations 9:19 as well with the first-scan settings
from the .NAV files. I made a batch file "call_runctdfbbat.bat"
to allow better tracking of the first scan settings used.
As it turns out, even though that batch file contains more
than one call to the batch file "runctd_fb.bat", it stops
each time after processing the first un-commented station,
i.e., it only executes the first executable (non-comment)
line. So calling a DOS batch file via a DOS batch file has
limited utility. However, it does serve the purpose of
documenting the used first-scan setting.
I use "call_runctdfbbat.bat" as follows:
- type in all the calls of runctd_fb.bat,
- execute call_runctdfb.bat; it processes the first non-comment line
- comment out the station thus processed
- run "call_runctdfbbat.bat" again to process the next station
=========== start listing of call_runctdfbbat.bat ======
rem batch file to call the batch file to process CTD data
rem sounds like overkill to have a batch file do this, but
rem it allows to better save the setting of the start down scan.
rem
rem see file "readme.txt" for further comments on the batch file setup.
rem
rem comment out the stations that were already run
rem
rem fb, 10/25/08
rem runctd_fb.bat 449_6001 2345
rem runctd_fb.bat 449_6002 1
rem runctd_fb.bat 449_6003 265
rem runctd_fb.bat 449_6004 937
rem runctd_fb.bat 449_6005 1231
rem runctd_fb.bat 449_6006 318
rem runctd_fb.bat 449_6007 451
rem
rem station 7 was the last with 1Hz raw data
rem
rem runctd_fb.bat 449_6008 13969
rem runctd_fb.bat 449_6009 43297
runctd_fb.bat 449_6010 6865
runctd_fb.bat 449_6011 17329
runctd_fb.bat 449_6012 39121
runctd_fb.bat 449_6013 12601
runctd_fb.bat 449_6014 13393
runctd_fb.bat 449_6015 12265
runctd_fb.bat 449_6016 12961
runctd_fb.bat 449_6017 27817
runctd_fb.bat 449_6018 19801
runctd_fb.bat 449_6019 14449
runctd_fb.bat 449_6020 13537
runctd_fb.bat 449_6021 10633
runctd_fb.bat 449_6022 12049
runctd_fb.bat 449_6023 10393
============ end listing of call_runctdfbbat.bat ======