Pnb - User contributions [en]

File:AC9 cal proc inst.PDF

2016-05-31T19:44:39Z

Eriks: Cal processing instructions which are still helpful, and old PnB processing instructions which are not really relevant.

Cal processing instructions which are still helpful, and old PnB processing instructions which are not really relevant.

Old AC9 cal process instructions

2016-05-31T19:42:57Z

Eriks: Created page with "File:AC9_cal_proc_inst.PDF"

[[File:AC9_cal_proc_inst.PDF]]

AC-9 specific instructions

2016-05-31T19:41:50Z

Eriks:

1. Copy wtr_d_030113a.dat wtr_d_030113b.dat wtr_d_030113c.dat into calibration working directory(three files made per cal)

2. Working directory will be /home/eriks/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/2016/20160204/X_Calproc

3. Symbolic link files and rename for a and c channels
ln -s wtr_d_030113a.dat wtr_a_030113a.dat
ln -s wtr_d_030113a.dat wtr_c_030113a.dat

4. Update 184_watertemp.txt

5. Start matlab in the X_Calproc directory and type ac9cal

6. In the GUI, get list > Find > Add all wtr_a_xxx files, select Wtr and "a" radio buttons > save qcal_a.txt

7. Main GUI, select AC9 instrument, latest factory calibration date, 'a' radio button, 'use list file'

8. Hit CALVIEW and zoom on good section of each cal plot, then hit "GO" in the main GUI

9 Save and override qcal_a_txt, do for every spectra, then save means and quit.

10. Select "Auto adv" and hit calspec in main GUI, and override qcal_a.txt again

11. Hit ts_cal in the main GUI, if one of the spectra don't look good, you can "Comment line out" and it will add a # sign, then run through the processing again.

12. Lastly, link the ts_cal_dat files to wtr_....ave.txt file
ln -s a_ts_cal.dat wtr_a_030113_ave.txt

13. Repeat steps for c-calibration channel.

To review entire cal time series, go to /home/eriks/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/cal_analysis
and modify qcal_a/c files and a/c_ts_cal.dat files by appending data from the individual cal you just did.
run ac9cal again, and go to the last step "ts_cal" running in the cal_analysis folder.

[[old_AC9_cal_process_instructions]]

AC-9 specific instructions

2016-05-31T19:24:33Z

Eriks: Created page with "1. Copy wtr_d_030113a.dat wtr_d_030113b.dat wtr_d_030113c.dat into calibration working directory(three files made per cal) 2. Working directory will be /home/eriks/CALIBRATIO..."

Calibration process procedures

2016-05-31T18:50:14Z

Eriks:

'''After calibration processing of calibration files'''

<big>AC-9</big>

As of October 2012, AC-9 calibrations have been reprocessed with new 'Sit' values from Wetlabs AC meter protocol document, rev.Q. The processing directory for AC9 calibrations is ''/pb/AC9/cals/ '' instrument number(184) ''/QWATER/'' year/date folder.

Each time the instrument is sent back for a factory calibration, the new disc should be checked for updated temp and sal correction coefficients and calibration history should be updated in the ac9cal.txt inside of the ''/cals/0184/DeviceFiles/'' directory. Note that if coefficients have changed, goac9.par will need to be updated in the fallowing cruise processing.

To process the calibration files, the device number _watertemp.txt file must be updated with the latest temperature value and .dat files must be present in the folder you wish to process in. ac9cal.m sources ac9cal_def.par in the ''AC9/cals/LIST'' folder. This should be updated when new 'Sit' are created.

[[AC-9 specific instructions]]

'''Directory update 6-25-2014'''

Calibration directories have been updated
AC9 example ==> /home/oceancolor/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/2014/140109/

For above example, qcal.txt will need to look in /home/oceancolor/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/2014/140109/X_Calproc/

To process the cals for PnB AC9 proc, make folder X_Calproc in same directory and copy/paste cal files to keep originals.

'''Reviewing calibrations'''

After processing, it is good to compare the latest calibration processed values with previous ones. For this, data from the _ave.txt files(which should be linked by you from the .txt files in the year/date folder) is added to the qcal_a_yy_yy.txt and qcal_c_yy_yy.txt files. ac9cal.m is restarted and the qcal file is now the *yy_yy.txt folder. Hit the last button ts_cal to view the whole time series.

[[File:achannel_cal_AC9.png]]

[[File:cchannel_cal_AC9.png]]

<big>HS-6</big>

Visual inspection of Kexp values for the HS6 cal files is the current method of verifying calibration.

back to [[Main Page]]

Support Material

2016-05-31T18:45:33Z

Eriks:

Mission files and other data are stored on the oceancolor/glider197..or oceancolor/glider197/glider_missions_material

[[File:Glider operators handbook.pdf]]

[[File:slocum_manual.pdf]]

[[File:Doc Server User Guide.pdf]]

[[File:TWR_AUV_Course_notes_2010.pdf]]
Course notes taken by Stuart Halewood at Teledyne course 2010

[[Nortek 1Mhz Aquadopp ADCP]]

Calibration tracking:

Science bay was sent to Teledyne 10-30-2012

[[Main Page]]

Ac9tosb E.m

2016-05-31T18:41:52Z

Eriks:

Modified by ES 5-31-2016

<pre>
function ac9tosb_E(cruise)
% useage: ac9tosb('pb##');
%latest
% This file loads up the mat file produced in the ac9 processing and
% produces a flat ascii file needed for producing SEABASS files for the
% ac9. .sbin files are written to a folder in the "final" folder location
% of the ac9 files.

%ac9_path=strcat('/home/data65/pb/AC9/',cruise,'/final/');
disp('Run this script in the AC9 "final" folder that contains .mat files')
pause(3);
%ac9_path = strcat('/home/eriks/OCEANCOLOR_PNB/Plumes_and_Blooms/AC9/',cruise,'/final/');
ac9_path = pwd;
ac9matfiles =[];
matfiles=what(ac9_path)
for i=1:size(matfiles.mat,1),
isdowncast=findstr(char(matfiles.mat(i)),'.lcd.1.');
if isempty(isdowncast)==0
ac9matfiles=[ac9matfiles; char(matfiles.mat(i))];
end
end

for i=1:size(ac9matfiles,1),
eval(['load ',strcat(ac9_path,'/',ac9matfiles(i,:))]);
use_ac9struct(ac9,ac9matfiles(i,:),cruise);

end

function use_ac9struct(str,filename,cruise)
wv_hdr=str.debug.par.wavelength;
other_fields=cellstr('depth');
for i=1:size(wv_hdr,2),
a_fields(i)=cellstr(strcat('a',num2str(wv_hdr(i))));
c_fields(i)=cellstr(strcat('c',num2str(wv_hdr(i))));
end
fields=[other_fields a_fields c_fields cellstr('bin_depth')];
%matrix_out=[str.ac9data.rac9depth str.out.a_cal, str.out.c_cal ...
%str.ac9data.intdepth]; %This line chnaged by Tiho
matrix_out=[str.ac9data.rac9depth str.out.a_scorr1, str.out.c_corr ...
str.ac9data.intdepth];
yr=filename(6:7);
mon=filename(8:9);
dy=filename(10:11);
st=filename(12:12);
mkdir([pwd,'/sbin']);
outpath = [pwd,'/sbin/'];
outname=strcat('ac9_',yr,mon,dy,st,'_',cruise,'.sbin');
%outpath='/home/data65/pb/SEABASS/ac9/sbin/';
%outpath='/home/eriks/OCEANCOLOR_PNB/Plumes_and_Blooms/SEABASS/AC9/sbin/'
%mkdir('../','sbin');
%fid=fopen(strcat(outpath,outname),'w');
fid = fopen(strcat(outpath,outname),'w');
fprintf(fid,'#%s\n',filename);
for i=1:size(fields,2)
fprintf(fid,'#%s\n',char(fields(i)));
end
for i=1:size(matrix_out,1),
for j=1:size(matrix_out,2),
fprintf(fid,'%e ',matrix_out(i,j));
end
fprintf(fid,'\n','');
end
display(['Printing to file ',strcat(outpath,outname)]);
fclose(fid);

</pre>

[[ac9tosb_E]]

SeaBASS Processing

2016-05-31T18:39:13Z

Eriks:

SeaBASS files are submitted to NASA in specific format with .sbin extension. AC9 and HS6 files use ac92sb_E.pl and hs2sb_E.pl files. The AC9 also requires the matlab script ac9tosb_E('pb###'). Syntax for the pl scripts run in the unix prompt are as92sb_E filename pb

For AC9:
Complete processing as normal in matlab, then cd into the final output folder for the AC9 and type ac9tosb_E('pb###')
[[ac9tosb_E]]

ex. perl /home/eriks/Erik_perl_seabass/hs2sb_E.pl pb228

This example is also found under commandline_syntax.txt in the file /home/eriks/Erik_perl_seabass/

For PRR SeaBASS written by DBC
<pre>From the directory in which you want to do the processing, you'll need to do the following:
1) create a list of calibration files that will be applied to the raw data
example: calibration
0 /home/data65/pb/PRR/CAL_INFO/CAL_Files/9628_0_130411.cfl
1 /home/data65/pb/PRR/CAL_INFO/CAL_Files/9628_1_130411.cfl
2 /home/data65/pb/PRR/CAL_INFO/CAL_Files/9629_2_130411.cfl

2) type: /home/oceancolor/Plumes_and_Blooms/processing_scripts/PRR/prr2lcd -ccalfile rawfile
note the syntax "-ccalfile" this is not a typo

If you are going to copy the binary to your own workspace and run it from there, you will need to change the permissions and the syntax will be:
./prr2lcd -ccalfile rawfile

All this should be done in your own workspace. You do not want to be doing any processing in the raw data folders

A good method is to link the raw data to your workspace.
Example: ln -s /home/oceancolor/Plumes_and_Blooms/cruise_data/pb248/PRR/raw/* .</pre>

C-OPS processing

2016-05-26T22:21:04Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

'''To determine system serial number, open BSI-generated CFG file, or file containing serial numbers column'''

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------
'''NOTE'''
Before running matlab script, open LCD files and check for errors, C-OPS processing expects a "FrameCount" or "LINECOUNT" and "LuZDepth" column. "LINECOUNT" is inserted by the perl script and has no real data bearing. If "FrameCount" is specified in the auto_bt function input, the function will default to a simple integer counter if LINECOUNT is what's used in the lcd file.

------------
Start matlab in your file directory, then type "process_COPS('**')" where ** are the two prefix letters of the file to process

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

[[File:C-OPSprocessing_instructions.pdf]]

'''For system #23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

File:C-OPSprocessing instructions.pdf

2016-05-26T22:16:46Z

Eriks: Eriks uploaded a new version of File:C-OPSprocessing instructions.pdf

Processing supplemental

File:C-OPSprocessing instructions.pdf

2016-05-26T22:15:29Z

Eriks: Processing supplemental

Processing supplemental

C-OPS processing

2016-05-26T22:10:01Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

'''To determine system serial number, open BSI-generated CFG file, or file containing serial numbers column'''

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------
'''NOTE'''
Before running matlab script, open LCD files and check for errors, C-OPS processing expects a "FrameCount" or "LINECOUNT" and "LuZDepth" column. "LINECOUNT" is inserted by the perl script and has no real data bearing. If "FrameCount" is specified in the auto_bt function input, the function will default to a simple integer counter if LINECOUNT is what's used in the lcd file.

------------
Start matlab in your file directory, then type "process_COPS('**')" where ** are the two prefix letters of the file to process

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

[[File:C-OPSprocessing_instructions.docx]]

'''For system #23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

Plumes and Blooms Project

2016-05-26T21:39:47Z

Eriks:

= '''Plumes and Blooms Data Processing''' =

[[About PnB Calibration Processing]]

[[About PnB Processing]]

<big>'''--PnB Matlab Calibration Processing Scripts--'''</big>

Latest version of M files is in /home/oceancolor/PnB/processing_scripts

<big>[[Calibration process procedures]]</big>

<big>[[AC-9 Calibration Mfiles]]</big>

<big>[[Coefficient update records]]</big>

<big>[[C-OPS/CERBERUS]]</big>

<big>'''--PnB Matlab Processing Scripts--'''</big>

<big>[[Hydroscat Mfiles]]</big>

<big>[[AC-9/AC-S Mfiles]]</big>

<big>[[AC-9 SeaBASS Mfiles]]</big>

<big>[[SeaBASS Processing]]</big>

<big>[[PRR-600 Mfiles]]</big>

<big>[[C-OPS/CERBERUS Mfiles]]</big>

<big>'''--PnB Processing Support--'''</big>

<big>[[AC-9 processing instructions]]</big>

<big>[[Analyzing processed AC-9 files]]</big>

<big>[[HS-6 processing instructions]]</big>

<big>[[Analyzing processed HS-6 files]]</big>

<big>[[LISST processing instructions]]</big>

<big>[[PRR processing instructions]]</big>

<big>[[C-OPS processing]]</big>

<big>[[CERBERUS processing]]</big>

<big>[[pb# cruise notes]]</big>

NOTE: MFILES ARE SUBJECT TO CHANGE

back to [[Main Page]]

HS-6 processing instructions

2016-05-26T21:36:22Z

Eriks:

In April 2010 the HS-6 underwent a calibration and wavelength change. 420 442 470 510 589 700
Original wavelengths were 442 470 510 589 671 870

Processing HS6 is generally the same procedure as the AC-9. See AC-9 processing instructions for more detailed information. The "X" cast is not processed for the HS6.

Hydroscat files must be initially removed from the DH4, then processed through Hydrosoft software on a Windows PC. Files from the DH4 will have a .LOG extension, files processed through Hydrosoft will have a .DAT extension.

The optimum/traditional directory structure for HS6

HYDROSCAT/pb#/
dat
final
from_DH4

-Open Hydrosoft, processing tab, then select Process Raw Files. Select appropriate calibration file from the oceancolor calibration directory, and input/output directories.

Start matlab in the directory you want to process the files in and run process_hs6(pb#). Directory should be parent to those listed above.

Once finished running process_hs6(pb#), correct bb values from AC-9 a and b values by running sigmacorrect_bb(pb#) in same directory as processing takes place. Sigmacorrect_bb.m needs to be updated to newest HS6 Kexp calibration coefficients ~about line 139 of the script. Kexp coefficient values are found by opening the HS6 .cal files and looking for "Kexp" under each channel. Channels are ordered low to long wavelength when Kexp values are entered in sigmacorrect_bb.

Sigma correction is an adjustment to improve the accuracy of
backscattering measurements in highly-attenuating water. Some light that would
otherwise be detected as backscattering is lost to attenuation in the water between
the instrument and the detection volume, causing backscattering to be
underestimated. The correction needs attenuation measurements Kbb = a + .4b where b = c-a from AC instrument.

Look at values after processing by running plot_bbp_final(pb###). When opening the file to look at, look in the "final" directory. Files are "ds_##"

[[plot_bbp_final]]

HS-6 processing instructions

2016-05-26T21:34:37Z

Eriks:

In April 2010 the HS-6 underwent a calibration and wavelength change. 420 442 470 510 589 700
Original wavelengths were 442 470 510 589 671 870

Processing HS6 is generally the same procedure as the AC-9. See AC-9 processing instructions for more detailed information. The "X" cast is not processed for the HS6.

Hydroscat files must be initially removed from the DH4, then processed through Hydrosoft software on a Windows PC. Files from the DH4 will have a .LOG extension, files processed through Hydrosoft will have a .DAT extension.

The optimum/traditional directory structure for HS6

HYDROSCAT/pb#/
dat
final
from_DH4

-Open Hydrosoft, processing tab, then select Process Raw Files. Select appropriate calibration file from the oceancolor calibration directory, and input/output directories.

Start matlab in the directory you want to process the files in and run process_hs6(pb#). Directory should be parent to those listed above.

Once finished running process_hs6(pb#), correct bb values from AC-9 a and b values by running sigmacorrect_bb(pb#) in same directory as processing takes place. Sigmacorrect_bb.m needs to be updated to newest HS6 Kexp calibration coefficients ~about line 139 of the script.

Sigma correction is an adjustment to improve the accuracy of
backscattering measurements in highly-attenuating water. Some light that would
otherwise be detected as backscattering is lost to attenuation in the water between
the instrument and the detection volume, causing backscattering to be
underestimated. The correction needs attenuation measurements Kbb = a + .4b where b = c-a from AC instrument.

Look at values after processing by running plot_bbp_final(pb###). When opening the file to look at, look in the "final" directory. Files are "ds_##"

[[plot_bbp_final]]

HS-6 processing instructions

2016-05-26T21:32:32Z

Eriks:

In April 2010 the HS-6 underwent a calibration and wavelength change. 420 442 470 510 589 700
Original wavelengths were 442 470 510 589 671 870

Processing HS6 is generally the same procedure as the AC-9. See AC-9 processing instructions for more detailed information. The "X" cast is not processed for the HS6.

Hydroscat files must be initially removed from the DH4, then processed through Hydrosoft software on a Windows PC. Files from the DH4 will have a .LOG extension, files processed through Hydrosoft will have a .DAT extension.

The optimum/traditional directory structure for HS6

HYDROSCAT/pb#/
dat
final
from_DH4

-Open Hydrosoft, processing tab, then select Process Raw Files. Select appropriate calibration file from the oceancolor calibration directory, and input/output directories.

Start matlab in the directory you want to process the files in and run process_hs6(pb#). Directory should be parent to those listed above.

Once finished running process_hs6(pb#), correct bb values from AC-9 a and b values by running sigmacorrect_bb(pb#) in same directory as processing takes place.

Sigma correction is an adjustment to improve the accuracy of
backscattering measurements in highly-attenuating water. Some light that would
otherwise be detected as backscattering is lost to attenuation in the water between
the instrument and the detection volume, causing backscattering to be
underestimated. The correction needs attenuation measurements Kbb = a + .4b where b = c-a from AC instrument.

Look at values after processing by running plot_bbp_final(pb###). When opening the file to look at, look in the "final" directory. Files are "ds_##"

[[plot_bbp_final]]

AC-9 processing instructions

2016-05-26T21:28:00Z

Eriks:

[[Media:AC9_HS6_proc_instructions.pdf]]
Original processing instructions.

NOTE: There are unix commands in these scripts.

'''NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.'''

New processing protocol:
Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
HYDROSCAT/pb#/
dat
final
from_DH4
AC-9/pb#/
final
processing
raw
SEABASS

With these directory structures, matlab processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
CD to these directories in UNIX, making sure you have X window forwarding or VNC viewer for matlab graphical piping.
Once in the directory, type "matlab" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until
CTD SeaBASS files are created.

AC9 files are extracted from the DH4, and then run through wetlabs software on a PC. Open Wetlabs, Wetview program, then tab, open device file and select device file from the oceancolor/calibrations/...Factory_Calibrations directory. Once appropriate device file is selected, choose to process .RAW files and select appropriate folder and .raw file. This needs to be done with every station. Output files from Wetlabs will be .dat extension format by you. Those can reside in the raw folder as well in your working directory.

move into processing directory in the correct pb# folder and start matlab with graphics.

type "process_ac9('pb235')or process_hs6('pb235')

You will be instructed to pick the bottoms and tops of the up and down casts. This is different than that radiometer processing where only
downcasts are picked.

[[== Check goac9.par and qcal.txt files when processing AC9. ==]]

NOTE: Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

goac9.par is used in a critical ac9 temp correction script:
It contains information on indexes for merged ac9 to ctd files.

Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

Method 1 subtracting a715 baseline

Method 2 .16 * c - a channels

Method 3 a - (a/c -a)*(c-a)

== example ==
:pb231

offset.iop [25 34 43 51] look in merged file for this info

25
m-d-d-a412(the start of AC data)
34
m-d-d-c412
43
a412ref
51
c412ref
-------
pnb.offset.itemp[60]
temp
------
pnb.offset.rac9depth[61]
1depth
-------

offset.phys [2 8 7 13 20 23]
2 timeJ
8 wetstarflour
7 wetBtrans
13 t068
19 sigmat-00
23 sal00

C-OPS processing

2016-05-25T21:18:32Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

'''To determine system serial number, open BSI-generated CFG file, or file containing serial numbers column'''

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------
'''NOTE'''
Before running matlab script, open LCD files and check for errors, C-OPS processing expects a "FrameCount" or "LINECOUNT" and "LuZDepth" column. "LINECOUNT" is inserted by the perl script and has no real data bearing. If "FrameCount" is specified in the auto_bt function input, the function will default to a simple integer counter if LINECOUNT is what's used in the lcd file.

------------
Start matlab in your file directory, then type "process_COPS('**')" where ** are the two prefix letters of the file to process

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

'''For system #23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

AC-9 processing instructions

2016-05-25T20:34:44Z

Eriks:

[[Media:AC9_HS6_proc_instructions.pdf]]
Original processing instructions.

NOTE: There are unix commands in these scripts.

'''NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.'''

New processing protocol:
Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
HYDROSCAT/pb#/
dat
final
from_DH4
AC-9/pb#/
final
processing
raw
SEABASS

With these directory structures, matlab processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
CD to these directories in UNIX, making sure you have X window forwarding or VNC viewer for matlab graphical piping.
Once in the directory, type "matlab" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until
CTD SeaBASS files are created.

AC9 files are extracted from the DH4, and then run through wetlabs software on a PC. Open Wetlabs, Wetview program, then tab, open device file and select device file from the oceancolor/calibrations/...Factory_Calibrations directory. Once appropriate device file is selected, choose to process .RAW files and select appropriate folder and .raw file. This needs to be done with every station. Output files from Wetlabs will be .dat extension format by you. Those can reside in the raw folder as well in your working directory.

move into processing directory in the correct pb# folder and start matlab with graphics.

type "process_ac9('pb235')or process_hs6('pb235')

[[== Check goac9.par and qcal.txt files when processing AC9. ==]]

NOTE: Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

goac9.par is used in a critical ac9 temp correction script:
It contains information on indexes for merged ac9 to ctd files.

Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

Method 1 subtracting a715 baseline

Method 2 .16 * c - a channels

Method 3 a - (a/c -a)*(c-a)

== example ==
:pb231

offset.iop [25 34 43 51] look in merged file for this info

25
m-d-d-a412(the start of AC data)
34
m-d-d-c412
43
a412ref
51
c412ref
-------
pnb.offset.itemp[60]
temp
------
pnb.offset.rac9depth[61]
1depth
-------

offset.phys [2 8 7 13 20 23]
2 timeJ
8 wetstarflour
7 wetBtrans
13 t068
19 sigmat-00
23 sal00

AC-9 processing instructions

2016-05-25T19:03:16Z

Eriks:

[[Media:AC9_HS6_proc_instructions.pdf]]
Original processing instructions.

NOTE: There are unix commands in these scripts.

'''NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.'''

New processing protocol:
Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
HYDROSCAT/pb#/
dat
final
from_DH4
AC-9/pb#/
final
processing
raw
SEABASS

With these directory structures, matlab processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
CD to these directories in UNIX, making sure you have X window forwarding or VNC viewer for matlab graphical piping.
Once in the directory, type "matlab" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until
CTD SeaBASS files are created.

AC9 files are extracted from the DH4, and then run through wetlabs software on a PC. Open Wetlabs, Wetview program, then tab, open device file and select device file from the oceancolor/calibrations/...Factory_Calibrations directory. Once appropriate device file is selected, choose to process .RAW files and select appropriate folder and .raw file. This needs to be done with every station. Output files from Wetlabs will be .dat format. Those can reside in the raw folder as well in your working directory.

move into processing directory in the correct pb# folder and start matlab with graphics.

type "process_ac9('pb235')or process_hs6('pb235')

[[== Check goac9.par and qcal.txt files when processing AC9. ==]]

NOTE: Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

goac9.par is used in a critical ac9 temp correction script:
It contains information on indexes for merged ac9 to ctd files.

Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

Method 1 subtracting a715 baseline

Method 2 .16 * c - a channels

Method 3 a - (a/c -a)*(c-a)

== example ==
:pb231

offset.iop [25 34 43 51] look in merged file for this info

25
m-d-d-a412(the start of AC data)
34
m-d-d-c412
43
a412ref
51
c412ref
-------
pnb.offset.itemp[60]
temp
------
pnb.offset.rac9depth[61]
1depth
-------

offset.phys [2 8 7 13 20 23]
2 timeJ
8 wetstarflour
7 wetBtrans
13 t068
19 sigmat-00
23 sal00

HS-6 processing instructions

2016-05-25T18:08:46Z

Eriks:

In April 2010 the HS-6 underwent a calibration and wavelength change. 420 442 470 510 589 700
Original wavelengths were 442 470 510 589 671 870

Processing HS6 is generally the same procedure as the AC-9. See AC-9 processing instructions for more detailed information. The "X" cast is not processed for the HS6.

Hydroscat files must be initially removed from the DH4, then processed through Hydrosoft software on a Windows PC. Files from the DH4 will have a .LOG extension, files processed through Hydrosoft will have a .DAT extension.

The optimum/traditional directory structure for HS6

dat

final

from_DH4

-Open Hydrosoft, processing tab, then select Process Raw Files. Select appropriate calibration file from the oceancolor calibration directory, and input/output directories.

Start matlab in the directory you want to process the files in and run process_hs6(pb#). Directory should be parent to those listed above.

Once finished running process_hs6(pb#), correct bb values from AC-9 a and b values by running sigmacorrect_bb(pb#) in same directory as processing takes place.

Sigma correction is an adjustment to improve the accuracy of
backscattering measurements in highly-attenuating water. Some light that would
otherwise be detected as backscattering is lost to attenuation in the water between
the instrument and the detection volume, causing backscattering to be
underestimated. The correction needs attenuation measurements Kbb = a + .4b where b = c-a from AC instrument.

Look at values after processing by running plot_bbp_final(pb###). When opening the file to look at, look in the "final" directory. Files are "ds_##"

[[plot_bbp_final]]

PRR processing instructions

2016-05-24T20:46:43Z

Eriks:

Change directory to where you want to process the files.

Review README_prr2lcd in /home/oceancolor/processing_scripts/PRR/ for creating lcd files.

Bring up a matlab prompt on the server in the file processing directory, type "process_prr('pb#')" and pick ud casts similar to AC9 or HS6.
typically these files are processed in a "lcd" folder.

The file rqclist.txt must be present in the directory you're processing in. This tells the scripts what channels to look for.
A copy of rqclist.txt is in the /home/oceancolor/processing_scripts/ directory.

<pre>#radq parameters for ED and LU were picked by examining
#a dozen profiles and picking where the profile turned to noise
#and averaging per wavelength
begin bbopradq parameters
-a 1ed412 0.0595
-a 1ed443 0.0353
-a 1ed490 0.1631
-a 1ed510 0.1197
-a 1ed555 0.0313
-a 1ed665 0.0125
-a 1lu412 0.0003
-a 1lu443 0.0020
-a 1lu490 0.0011
-a 1lu510 0.0007
-a 1lu555 0.0002
-a 1lu665 0.0000
-a 2es412 0
-a 2es443 0
-a 2es490 0
-a 2es510 0
-a 2es555 0
-a 2es665 0
</pre>

4-2014 updated new awk statement for prr_bt

4-2014 new QC being implemented for bad files

PRR processing instructions

2016-05-24T20:44:34Z

Eriks:

Change directory to where you want to process the files.

Review README_prr2lcd in /home/oceancolor/processing_scripts/PRR/ for creating lcd files.

Bring up a matlab prompt on the server in the file processing directory, type "process_prr('pb#')" and pick ud casts similar to AC9 or HS6.
typically these files are processed in a "lcd" folder.

The file rqclist.txt must be present in the directory you're processing in. This tells the scripts what channels to look for.

<pre>#radq parameters for ED and LU were picked by examining
#a dozen profiles and picking where the profile turned to noise
#and averaging per wavelength
begin bbopradq parameters
-a 1ed412 0.0595
-a 1ed443 0.0353
-a 1ed490 0.1631
-a 1ed510 0.1197
-a 1ed555 0.0313
-a 1ed665 0.0125
-a 1lu412 0.0003
-a 1lu443 0.0020
-a 1lu490 0.0011
-a 1lu510 0.0007
-a 1lu555 0.0002
-a 1lu665 0.0000
-a 2es412 0
-a 2es443 0
-a 2es490 0
-a 2es510 0
-a 2es555 0
-a 2es665 0
</pre>

4-2014 updated new awk statement for prr_bt

4-2014 new QC being implemented for bad files

PnB Cruise Notes

2016-05-23T20:55:36Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB271 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

01/28/2016 AC9 0187 returned with many parts replaced: filter wheel, a tube, new a detector, new bearing, windows

02/12/2016 AC9 0187 installed on rosette, transmissometer 146PR installed.

4/27/2016 PB277 Bad weather conditions, only a couple stations sampled

05/19/2016 PB278 CTD Electrical termination failed on station 5. C-OPS 23 used.

C-OPS processing

2016-05-23T20:31:17Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

'''To determine system serial number, open BSI-generated CFG file, or file containing serial numbers column'''

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------
'''NOTE'''
Before running matlab script, open LCD files and check for errors, C-OPS processing expects a "FrameCount" or "LINECOUNT" and "LuZDepth" column. "LINECOUNT" is inserted by the perl script and has no real data bearing. If "FrameCount" is specified in the auto_bt function input, the function will default to a simple integer counter if LINECOUNT is what's used in the lcd file.

------------
Start matlab in your file directory, then type "process_COPS"

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

'''For system #23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

PnB Cruise Notes

2016-05-23T18:56:24Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

01/28/2016 AC9 0187 returned with many parts replaced: filter wheel, a tube, new a detector, new bearing, windows

02/12/2016 AC9 0187 installed on rosette, transmissometer 146PR installed.

4/27/2016 PB277 Bad weather conditions, only a couple stations sampled

05/19/2016 PB278 CTD Electrical termination failed on station 5. C-OPS 23 used.

C-OPS processing

2016-05-23T18:20:02Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

'''To determine system serial number, open BSI-generated CFG file, or file containing serial numbers column'''

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------

Start matlab in your file directory, then type "process_COPS"

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

'''For system #23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

Coefficient update records

2016-05-23T17:53:56Z

Eriks:

AC9 Factory cal 10/2012
pb243 and on should have this cal.
*update goac9
*update ac9cal.txt
*check aw and bw data with cal CD
Tref 20.4C

Latest Factory Cal
pb275 1-08-2016
Tcal 18.1

HS-6 UC Calibration
09-2013 pb252 on should use this cal
*Check gain values in calibration file for sigmacorrect script
09/2013 kexp [.150 .148 .150 .150 .152 .150]

10/2014 kexp [.142 .141 .142 .143 .145 .141]

05/2015 kexp [.137 .137 .136 .139 .143 .136]

Calibration process procedures

2016-05-20T19:10:59Z

Eriks:

'''After calibration processing of calibration files'''

<big>AC-9</big>

As of October 2012, AC-9 calibrations have been reprocessed with new 'Sit' values from Wetlabs AC meter protocol document, rev.Q. The processing directory for AC9 calibrations is ''/pb/AC9/cals/ '' instrument number(184) ''/QWATER/'' year/date folder.

Each time the instrument is sent back for a factory calibration, the new disc should be checked for updated temp and sal correction coefficients and calibration history should be updated in the ac9cal.txt inside of the ''/cals/0184/DeviceFiles/'' directory. Note that if coefficients have changed, goac9.par will need to be updated in the fallowing cruise processing.

To process the calibration files, the device number _watertemp.txt file must be updated with the latest temperature value and .dat files must be present in the folder you wish to process in. ac9cal.m sources ac9cal_def.par in the ''AC9/cals/LIST'' folder. This should be updated when new 'Sit' are created.

'''Directory update 6-25-2014'''

Calibration directories have been updated
AC9 example ==> /home/oceancolor/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/2014/140109/

For above example, qcal.txt will need to look in /home/oceancolor/CALIBRATION/Wetlabs/AC-9/UCSB_Calibrations/AC-9_SN0184/2014/140109/X_Calproc/

To process the cals for PnB AC9 proc, make folder X_Calproc in same directory and copy/paste cal files to keep originals.

'''Reviewing calibrations'''

After processing, it is good to compare the latest calibration processed values with previous ones. For this, data from the _ave.txt files(which should be linked by you from the .txt files in the year/date folder) is added to the qcal_a_yy_yy.txt and qcal_c_yy_yy.txt files. ac9cal.m is restarted and the qcal file is now the *yy_yy.txt folder. Hit the last button ts_cal to view the whole time series.

[[File:achannel_cal_AC9.png]]

[[File:cchannel_cal_AC9.png]]

<big>HS-6</big>

Visual inspection of Kexp values for the HS6 cal files is the current method of verifying calibration.

back to [[Main Page]]

PRR processing instructions

2016-05-20T19:08:03Z

Eriks:

Change directory to where you want to process the files.

Review README_prr2lcd in /home/oceancolor/processing_scripts/PRR/ for creating lcd files.

Bring up a matlab prompt on the server in the file processing directory, type "process_prr('pb#')" and pick ud casts similar to AC9 or HS6.

The file rqclist.txt must be present in the directory you're processing in. This tells the scripts what channels to look for.

<pre>#radq parameters for ED and LU were picked by examining
#a dozen profiles and picking where the profile turned to noise
#and averaging per wavelength
begin bbopradq parameters
-a 1ed412 0.0595
-a 1ed443 0.0353
-a 1ed490 0.1631
-a 1ed510 0.1197
-a 1ed555 0.0313
-a 1ed665 0.0125
-a 1lu412 0.0003
-a 1lu443 0.0020
-a 1lu490 0.0011
-a 1lu510 0.0007
-a 1lu555 0.0002
-a 1lu665 0.0000
-a 2es412 0
-a 2es443 0
-a 2es490 0
-a 2es510 0
-a 2es555 0
-a 2es665 0
</pre>

4-2014 updated new awk statement for prr_bt

4-2014 new QC being implemented for bad files

Copsrcqlist.txt

2016-04-01T13:06:19Z

Eriks:

<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
</pre>

[[C-OPS processing]]

COPS bscalc window.txt

2016-04-01T13:04:43Z

Eriks:

<pre>
EdZ320 1 5
EdZ340 1 5
EdZ380 1 5
EdZ395 1 5
EdZ412 1 10
EdZ443 1 10
EdZ465 1 10
EdZ490 1 10
EdZ510 1 10
EdZ532 1 10
EdZ555 1 10
EdZ560 1 10
EdZ625 1 10
EdZ665 1 10
EdZ670 1 10
EdZ683 1 10
EdZ710 1 5
EdZ780 1 5
LuZ320 1 10
LuZ340 1 10
LuZ380 1 10
LuZ395 1 10
LuZ412 1 10
LuZ443 1 10
LuZ465 1 10
LuZ490 1 10
LuZ510 1 10
LuZ532 1 10
LuZ555 1 10
LuZ560 1 10
LuZ625 1 2
LuZ665 1 2
LuZ670 1 2
LuZ683 1 2
LuZ710 1 2
LuZ780 1 2</pre>

[[C-OPS processing]]

Calibrations.txt

2016-04-01T13:03:39Z

Eriks:

<pre>
channel immersion_coefficient sensitivity offset_high offset_medium offset_low
FrameCount 0 0 0 0 0
EdZRoll 0 0 0 0 0
EdZPitch 0 0 0 0 0
EdZ320 0.635 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.636 0.09229812 0.037 0.136 0.136
EdZ380 0.641 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.634 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.646 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.651 0.1830219 0.135 0.233 0.233
EdZ465 0.653 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.657 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.659 0.3828456 -0.025 0.081 0.08
EdZ532 0.662 0.4843704 -0.083 0.025 0.024
EdZ555 0.668 0.6248441 0.023 0.119 0.118
EdZ560 0.662 0.5728049 -0.041 0.059 0.058
EdZ625 0.669 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.662 1.423046 0.038 0.133 0.134
EdZ670 0.674 0.5043991 -0.05 0.074 0.073
EdZ683 0.68 1.001773 -0.194 -0.063 -0.065
EdZ710 0.684 1.158732 -0.037 0.112 0.111
EdZ780 0.692 1.495014 -0.3 -0.169 -0.17
EdZPAR 0.662 7062.271 -0.069 0.034 0.034
LuZDepth 0 0 0 0 0
LuZ320 0.5598 4.112603 -0.117 -0.019 -0.02
LuZ340 0.5624 2.528736 0.091 0.266 0.265
LuZ380 0.5665 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.5677 2.24874 -0.446 -0.164 -0.166
LuZ412 0.5689 2.439732 -0.139 0.066 0.064
LuZ443 0.5707 3.507107 -0.296 -1.25 -0.126
LuZ465 0.5719 2.577199 -0.054 0.104 0.103
LuZ490 0.573 6.130876 -0.057 0.053 0.052
LuZ510 0.5737 5.432522 -0.339 -0.147 -0.148
LuZ532 0.5745 5.947128 -0.177 -0.021 -0.021
LuZ555 0.5752 7.142782 -0.233 -0.091 -0.091
LuZ560 0.5754 6.520918 -0.226 -0.065 -0.064
LuZ625 0.577 10.92597 -0.565 -0.452 -0.452
LuZ665 0.5778 14.42576 0.031 0.211 0.21
LuZ670 0.5779 4.578427 -0.305 -0.148 -0.148
LuZ683 0.5781 10.67856 -0.125 0.047 0.048
LuZ710 0.5786 11.18393 -0.002 0.122 0.12
LuZ780 0.5795 13.74776 -0.511 -0.189 -0.191
Ed0320 -999 0.1468176 -0.177 -0.06 -0.061
Ed0340 -999 0.1296039 -0.076 0.054 0.053
Ed0380 -999 0.04120935 -0.392 -0.236 -0.236
Ed0395 -999 0.1586371 -0.172 -0.026 -0.027
Ed0412 -999 0.1568148 -0.117 -0.014 -0.015
Ed0443 -999 0.2382892 -0.031 0.087 0.087
Ed0465 -999 0.2087017 -0.412 -0.25 -0.251
Ed0490 -999 0.594159 -0.174 -0.062 -0.062
Ed0510 -999 0.5814521 -0.121 -0.004 -0.005
Ed0532 -999 0.6468537 -0.033 0.088 0.087
Ed0555 -999 0.8434793 -0.145 -0.015 -0.015
Ed0560 -999 0.7490816 -0.236 -0.124 -0.125
Ed0625 -999 1.122741 -0.044 0.064 0.063
Ed0665 -999 1.70267 0.008 0.126 0.125
Ed0670 -999 0.8276352 0.003 0.119 0.118
Ed0683 -999 1.374109 -0.066 0.05 0.049
Ed0710 -999 1.570383 -0.333 -0.204 -0.205
Ed0780 -999 2.187715 -0.174 -0.052 -0.053
Ed0PAR -999 10212.95 -0.122 -0.029 -0.029
Ed0Roll 0 0 0 0 0
Ed0Pitch 0 0 0 0 0
</pre>

[[C-OPS processing]]

Copsrcqlist.txt

2016-04-01T13:01:49Z

Eriks: Created page with "<pre> EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15 EdZ340 0.00040786 0.09229812 0.037 0.136 0.136 EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105 EdZ395 0.00040039 0.12..."

COPS bscalc window.txt

2016-04-01T13:00:33Z

Eriks: Created page with "<pre> EdZ320 1 5 EdZ340 1 5 EdZ380 1 5 EdZ395 1 5 EdZ412 1 10 EdZ443 1 10 EdZ465 1 10 EdZ490 1 10 EdZ510 1 10 EdZ532 1 10 EdZ555 1 10 EdZ560 1 10 EdZ625 1 10 EdZ665 1 10 EdZ67..."

Calibrations.txt

2016-04-01T12:58:25Z

Eriks: Created page with "<pre> channel immersion_coefficient sensitivity offset_high offset_medium offset_low FrameCount 0 0 0 0 0 EdZRoll 0 0 0 0 0 EdZPitch 0 0 0 0 0 EdZ320 0.635 0.1057925 -0.289 -0..."

C-OPS processing

2016-04-01T12:56:48Z

Eriks:

Processing Steps:

Place relevant processing files in directory you want to process in"

calibrations.txt
COPSbscalc_window.txt
Copsrqclist.txt

Convert C-OPS files by
cops2lcd.pl

-----------
for i in $(ls *P.csv) ; do perl cops2lcd.pl $i; done
-----------

Start matlab in your file directory, then type "process_COPS"

Automatic processing will start.

NOTE: Auto_bt script will write two cast ID matrices if you attempt to call the script twice. The easiest way to re-process is to start with a clean
directory with only .lcd file extensions.

similar scripts to prr

Converting CERBERUS files to lcd format in unix command line.
-----------
for i in $(ls *P.csv) ; do perl cerberus-csv2lcd.pl $i; done
-----------

Second column is noise limits for each channel(radQC) picked from pb240stn4 averaged values at 60m over 200 data points. In the future more casts should be looked at.

Depth values can either be taken from Eu(CERBERUS) or Lu sensors. Careful as these values are not exactly the same. LCD files generated by DBC scripts take LuZ depth.

To review the profiles use plotCOPS_final.m

'''for system 23'''

[[calibrations.txt]]

[[COPS_bscalc_window.txt]]

[[Copsrcqlist.txt]]

[[plotCOPS_final]]

COPSradQC params
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053 </pre>

========================================================================

CERBERUS radQC params. Same but with EU
<pre>
EdZ320 0.00063993 0.1057925 -0.289 -0.15 -0.15
EdZ340 0.00040786 0.09229812 0.037 0.136 0.136
EdZ380 0.00214926 0.03190586 -0.232 -0.104 -0.105
EdZ395 0.00040039 0.1271224 -0.293 -0.164 -0.164
EdZ412 0.00055682 0.1383356 -0.272 -0.138 -0.138
EdZ443 0.00056002 0.1830219 0.135 0.233 0.233
EdZ465 0.00222684 0.1535409 -0.159 -0.056 -0.056
EdZ490 0.01217142 0.4508201 -0.316 -0.199 -0.199
EdZ510 0.00001690 0.3828456 -0.025 0.081 0.08
EdZ532 0.01527306 0.4843704 -0.083 0.025 0.024
EdZ555 0.01683447 0.6248441 0.023 0.119 0.118
EdZ560 0.01812439 0.5728049 -0.041 0.059 0.058
EdZ625 0.00010200 0.8248582 -0.185 -0.077 -0.078
EdZ665 0.00003937 1.423046 0.038 0.133 0.134
EdZ670 0.00020907 0.5043991 -0.05 0.074 0.073
EdZ683 0.00006593 1.001773 -0.194 -0.063 -0.065
EdZ710 0.00006305 1.158732 -0.037 0.112 0.111
EdZ780 0.00003961 1.495014 -0.3 -0.169 -0.17
LuZ320 0.00001181 4.112603 -0.117 -0.019 -0.02
LuZ340 0.00007107 2.528736 0.091 0.266 0.265
LuZ380 0.00029265 0.7300571 -0.31 -0.103 -1.04
LuZ395 0.00012805 2.24874 -0.446 -0.164 -0.166
LuZ412 0.00008520 2.439732 -0.139 0.066 0.064
LuZ443 0.00004279 3.507107 -0.296 -1.25 -0.126
LuZ465 0.00007125 2.577199 -0.054 0.104 0.103
LuZ490 0.00009057 6.130876 -0.057 0.053 0.052
LuZ510 0.00011126 5.432522 -0.339 -0.147 -0.148
LuZ532 0.00007556 5.947128 -0.177 -0.021 -0.021
LuZ555 0.00005829 7.142782 -0.233 -0.091 -0.091
LuZ560 0.00006101 6.520918 -0.226 -0.065 -0.064
LuZ625 0.00001042 10.92597 -0.565 -0.452 -0.452
LuZ665 0.00001206 14.42576 0.031 0.211 0.21
LuZ670 0.00003364 4.578427 -0.305 -0.148 -0.148
LuZ683 0.00001260 10.67856 -0.125 0.047 0.048
LuZ710 0.00001034 11.18393 -0.002 0.122 0.12
LuZ780 0.00002035 13.74776 -0.511 -0.189 -0.191
Ed0320 0.00000000 0.1468176 -0.177 -0.06 -0.061
Ed0340 0.00000000 0.1296039 -0.076 0.054 0.053
Ed0380 0.00000000 0.04120935 -0.392 -0.236 -0.236
Ed0395 0.00000000 0.1586371 -0.172 -0.026 -0.027
Ed0412 0.00000000 0.1568148 -0.117 -0.014 -0.015
Ed0443 0.00000000 0.2382892 -0.031 0.087 0.087
Ed0465 0.00000000 0.2087017 -0.412 -0.25 -0.251
Ed0490 0.00000000 0.594159 -0.174 -0.062 -0.062
Ed0510 0.00000000 0.5814521 -0.121 -0.004 -0.005
Ed0532 0.00000000 0.6468537 -0.033 0.088 0.087
Ed0555 0.00000000 0.8434793 -0.145 -0.015 -0.015
Ed0560 0.00000000 0.7490816 -0.236 -0.124 -0.125
Ed0625 0.00000000 1.122741 -0.044 0.064 0.063
Ed0665 0.00000000 1.70267 0.008 0.126 0.125
Ed0670 0.00000000 0.8276352 0.003 0.119 0.118
Ed0683 0.00000000 1.374109 -0.066 0.05 0.049
Ed0710 0.00000000 1.570383 -0.333 -0.204 -0.205
Ed0780 0.00000000 2.187715 -0.174 -0.052 -0.053
EuZ320 0.00143408 0.09791 0.033 0.157 0.156
EuZ340 0.013987571 0.08936 0.072 0.172 0.172
EuZ380 0.122181794 0.02819 -0.187 -0.034 -0.035
EuZ395 0.19546726 0.09209 0.068 0.176 0.175
EuZ412 0.337328837 0.10665 -0.098 0.019 0.019
EuZ443 0.555936739 0.16495 -0.014 0.1 0.1
EuZ465 0.883383569 0.17083 0.054 0.142 0.142
EuZ490 1.13230505 0.41978 0.071 0.171 0.17
EuZ510 0.935274001 0.41944 -0.149 -0.023 -0.024
EuZ532 0.783264663 0.45267 -0.464 -0.112 -0.113
EuZ555 0.516853004 0.60115 -0.152 0.007 0.007
EuZ560 0.461559671 0.55471 -0.165 0.002 -0.002
EuZ625 0.00594545 0.91131 -0.078 0.084 0.083
EuZ665 0.011046655 1.33934 -0.17 -0.006 -0.006
EuZ670 0.018466335 0.51449 -0.827 -0.121 -0.123
EuZ683 0.028129248 0.94644 -0.126 -0.001 -0.001
EuZ710 0.003167644 1.15732 -0.077 0.095 0.094
EuZ780 0.000154474 1.53149 -0.581 -0.136 -0.138
</pre>

'''C-OPS Software version notes(Also seen in oceancolor/CALIBRATION/Biospherical)'''

0.6.23 Original Version 8/3/2011

1.5.3: <1.5 had a problem where gps data were not being reported for UTC < 10. The installer for version 1.5.3 addresses this problem. 10/22/2014

1.6.17: This version is different from versions < 1.5, tabs have been rearranged. Multiple file formats can be written at once. 6/10/2014

1.7.20: Has the fix for the GPS problem. At some point I will need to update BuoyProfiler as well for this error. 4/21/2015

1.8.5: In the Misc tab select “None”. I will create a new version 1.8.6 without the Misc tab, which should be available next week and will send a follow up email then 8/14/2015

About PnB Processing

2016-03-14T18:59:21Z

Eriks:

<big>The PnB or Plumes and Blooms processing is used for processing data currently collected from the AC9, Hydroscat, and CTD deployed on the Plumes and Blooms cruises in the Santa Barbara Channel. Data from the instruments is originally in a raw format, where it is processed through instrument manufacturers software to get a basic data file. After each station is processed with the instrument manufacturers software, it is then processed with the scripts outlined in these pages.</big>

Current working Matlab scripts for Plumes and Blooms are located in: /home/oceancolor/Plumes_and_Blooms/processing_scripts/

Erik currently process PnB data with scripts in /home/eriks/workingmfiles/
These scripts will be run in matlab in the directory they need to be processed in:
For HS6: PnB/HYDROSCAT/pb#
For AC9: PnB/AC9/pb#/processing
For PRR: PnB/PRR/pb#/lcd

More specific information about the cruises and instruments can be found at the ICESS PnB [http://www.icess.ucsb.edu/PnB/PnB.html website]

[[Main Page]]

HS-6 processing instructions

2016-03-09T19:56:37Z

Eriks:

AC-9 processing instructions

2016-02-24T20:58:30Z

Eriks:

[[Media:AC9_HS6_proc_instructions.pdf]]
Original processing instructions.

NOTE: There are unix commands in these scripts.

'''NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.'''

New processing protocol:
Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
HYDROSCAT/pb#/
dat
final
from_DH4
AC-9/pb#/
final
processing
raw
SEABASS

With these directory structures, matlab processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
CD to these directories in UNIX, making sure you have X window forwarding or VNC viewer for matlab graphical piping.
Once in the directory, type "matlab" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until
CTD SeaBASS files are created.

type "process_ac9('pb235')or process_hs6('pb235')

[[== Check goac9.par and qcal.txt files when processing AC9. ==]]

NOTE: Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

goac9.par is used in a critical ac9 temp correction script:
It contains information on indexes for merged ac9 to ctd files.

Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

Method 1 subtracting a715 baseline

Method 2 .16 * c - a channels

Method 3 a - (a/c -a)*(c-a)

== example ==
:pb231

offset.iop [25 34 43 51] look in merged file for this info

25
m-d-d-a412(the start of AC data)
34
m-d-d-c412
43
a412ref
51
c412ref
-------
pnb.offset.itemp[60]
temp
------
pnb.offset.rac9depth[61]
1depth
-------

offset.phys [2 8 7 13 20 23]
2 timeJ
8 wetstarflour
7 wetBtrans
13 t068
19 sigmat-00
23 sal00

AC-9 processing instructions

2016-02-24T20:57:27Z

Eriks:

[[Media:AC9_HS6_proc_instructions.pdf]]
Original processing instructions.

NOTE: There are unix commands in these scripts.
NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.

New processing protocol:
Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
HYDROSCAT/pb#/
dat
final
from_DH4
AC-9/pb#/
final
processing
raw
SEABASS

With these directory structures, matlab processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
CD to these directories in UNIX, making sure you have X window forwarding or VNC viewer for matlab graphical piping.
Once in the directory, type "matlab" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until
CTD SeaBASS files are created.

type "process_ac9('pb235')or process_hs6('pb235')

[[== Check goac9.par and qcal.txt files when processing AC9. ==]]

NOTE: Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

goac9.par is used in a critical ac9 temp correction script:
It contains information on indexes for merged ac9 to ctd files.

Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

Method 1 subtracting a715 baseline

Method 2 .16 * c - a channels

Method 3 a - (a/c -a)*(c-a)

== example ==
:pb231

offset.iop [25 34 43 51] look in merged file for this info

25
m-d-d-a412(the start of AC data)
34
m-d-d-c412
43
a412ref
51
c412ref
-------
pnb.offset.itemp[60]
temp
------
pnb.offset.rac9depth[61]
1depth
-------

offset.phys [2 8 7 13 20 23]
2 timeJ
8 wetstarflour
7 wetBtrans
13 t068
19 sigmat-00
23 sal00

PnB Cruise Notes

2016-02-12T20:21:08Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

01/28/2016 AC9 0187 returned with many parts replaced: filter wheel, a tube, new a detector, new bearing, windows

02/12/2016 AC9 0187 installed on rosette, transmissometer 146PR installed.

Coefficient update records

2016-02-09T23:13:42Z

Eriks:

PnB Cruise Notes

2016-01-28T20:06:11Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

01/28/2016 AC9 0187 returned with many parts replaced: filter wheel, a tube, new a detector, new bearing, windows

PnB Cruise Notes

2016-01-28T20:05:53Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

01/28/2016 AC9 0187 returned with many parts replaced, filter wheel, a tube, new a detector, new bearing, windows

PnB Cruise Notes

2016-01-06T22:54:01Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

12/17/2015 Control box issue, only manual bottle fire control. More problems with C-OPS software. Reverted to very old version.

PnB Cruise Notes

2016-01-06T21:47:29Z

Eriks:

pb221
-Switched to Wetlabs DH-4

pb252
-no files recorded on DH4 for stn7 and stn4D

pb253
-double cast on station D. Cast #2 is good.
-Cast E on PRR is bad. Roll column is not correct.

pb255
-termination failure due to water ingress. Short and blown fuse. Decided to use alternative termination methods.

pb258
-2Amp fuse issue with CERB sys. 23 stn 4. no data collected. Fuse later replaced with correct 5A

<====================================================================>

02/??/2009 Bad HS-6 cal

09/??/2009 bad AC-9 cal

10/??/2012 AC-9 0187 Factory Service

09/24/2013 New DH4 lithium batteries.

01/10/2014 Noticing problems with LISST data jumping on pb253, beam C has been off since pb24#

02/6/2014 Noticed PRR 510 channel is off, and has been since pb250/pb251

02/7/2014 LISST 1284 depth offset reset +3.69m set to 0.0m in air.

03/2014 LISST 1284 LREF value does not match transmission.--Tau and Beam-C are off due to this. Sent into service.

04/22/2014 Alpha-Q may be producing high bubbles causing issues with ZSCAT and other Qwater standards.

09/09/2014 No Q-water zscat was performed for pb261. Used pb260. #1284 was swapped back on rosette after pb260. pb262 zscat done 9-9-2014

09/17/2014 Something strange with pb261 LISST files. Two short files and no defined "A" cast.

09/25/2014 pb263 suspected termination failure on stn 3. 120m profile. High winds. No PRR. Test uPro

10/21/2014 pb264 Y cable to temp and cond. sensor damaged, replaced with IOP frame spare. New Electrical termination on CTD.

11/26/2014 pb265 AC9 depth values seem suspect, LISST1284 depth off by 3.35m

12/18/2014 pb266 No AC9 data from stn 4 to stn 1. Suspect cable issue.

12/18/2014 pb266 LISST 1284 is -4m off. Needs reset.

01/05/2015 pb263++ File format for C-OPS on PnB needs to be consistent: PB#_STN#_Date_time_cast#.tsv

03/20/2015 CTD Y-cable Temp Sal (not on this date-still need replacement)

03/26/2015 PB267 Battery left on, no AC9 data for stn 4, 3, 2, 1

03/26/2015 PB267 No CERBERUS data recorded for stations 7 and 6

04/16/2015 PB268 Choppy conditions, no AC-9 3, 2, 1. Suspect DH4 battery failing.

08/26/2015 PB270 Wire Jumped shiv and pinched. No CTD casts. Cable was rusty. C-OPS#41 tested

09/01/2015 AC9 0159 swapped in place of 0184. 0184 went to Wetlabs for service.

09/24/2015 PB272 Observed temperature dependence of Transmisometer. Values are unreliable. C-OPS software version crashing 1.8.5

10/15/2015 PB273 Transmisometer swapped with backup, backup also shows same problems, Brandon Russell Spectroradiometer JPL

11/19/2015 PB274 Transmisometer seems to work now. Bottle firing issue with CTD, two casts on station 4, second is full cast. C-OPS 1.9.2 software crashed a lot. No logical LISST files. Date is incorrect in LISST sensor. No C-OPS for station 6.

12/14/2015 Electrical Re-termination. [[Termination docs]]

Field test notes

2015-12-14T22:47:32Z

Eriks:

[[File:CERBERUS_SYSTEM_Field_test_2.pdf ]]

01-03-2014 by S.H.

[[File:CERBERUS_SYSTEM_Field_test_3.pdf ]]

01-17-2014 by S.H.

[[File:CERBERUS_SYSTEM_Field_test_4.pdf ]]

04-24-2014 by S.H.

[[File:CERBERUS_Field_test_20141208.pdf]]

10-06-2015

No report draft currently.
System deployment and physical components worked as planned. Software crash issues.

------------------
Comments:
cooked 5A fuse on 12-08-2014 on full field test.

File:20151214 123929.jpg

2015-12-14T21:47:31Z

Eriks: Shearwater termination docs 12/11/2015

Shearwater termination docs 12/11/2015

File:20151214 123912.jpg

2015-12-14T21:44:55Z

Eriks: Wiring and test of Shearwater termination 12/11/2015

Wiring and test of Shearwater termination 12/11/2015