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% |
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| 2 |
% gliderOptode_Generate_L1_Data.m |
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| 3 |
% |
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| 4 |
% Purpose: Generate Level 1 data mat files that include optode DO data. |
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% |
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| 6 |
% Requires: |
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| 7 |
% MATLAB folder - contains util |
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| 8 |
% |
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| 9 |
% Authors: Adapted from William Stark by Harvey Seim and Chris Calloway |
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| 10 |
% Marine Sciences Department |
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| 11 |
% UNC-Chapel Hill |
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| 12 |
% |
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| 13 |
% Created: March 2013 |
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% |
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| 15 |
% |
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| 16 |
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| 17 |
clear all; |
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| 18 |
|
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| 19 |
% add paths for required files... |
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| 20 |
addpath('MATLAB/util/'); |
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| 21 |
|
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| 22 |
% populate arrays for the deployment start and end dates... |
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| 23 |
% ex. strStart(2, 3) is start date for Ramses, Deployment 3 |
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| 24 |
strStart = {'26-Jan-2012', '16-Feb-2012', '16-Mar-2012'; ... |
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'26-Jan-2012', '16-Feb-2012', '16-Mar-2012'}; |
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| 26 |
strEnd = {'14-Feb-2012', '08-Mar-2012', '04-Apr-2012'; ... |
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| 27 |
'14-Feb-2012', '12-Mar-2012', '03-Apr-2012'}; |
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| 28 |
|
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| 29 |
% SET THE GLIDER INDEX (Pelagia = 1, Ramses = 2) ... |
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| 30 |
for gliderIndex=1:2 |
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| 31 |
|
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| 32 |
% SET THE DEPLOYMENT NUMBER (1, 2 or 3) ... |
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| 33 |
for deploymentNumber=1:3 |
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| 34 |
|
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| 35 |
clearvars -except gliderIndex deploymentNumber strStart strEnd; |
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| 36 |
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| 37 |
% glider name string... |
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| 38 |
if (gliderIndex==1) |
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| 39 |
strGliderName = 'Pelagia'; |
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| 40 |
else |
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| 41 |
strGliderName = 'Ramses'; |
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| 42 |
end |
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| 43 |
|
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| 44 |
% deployment number string... |
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| 45 |
strDeploymentNumber = num2str(deploymentNumber); |
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| 46 |
|
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| 47 |
% deployment start date string... |
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| 48 |
strStartDate = strStart(gliderIndex, deploymentNumber); |
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| 49 |
|
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| 50 |
% deployment end date string... |
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| 51 |
strEndDate = strEnd(gliderIndex, deploymentNumber); |
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| 52 |
|
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| 53 |
% define the path to the glider ascii files... |
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| 54 |
datadir = strcat('GLIDER_DATA_LEVEL0/', strGliderName, ... |
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'_Deployment', strDeploymentNumber, '/'); |
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| 56 |
|
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| 57 |
% define optode foil calibration coefficients |
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| 58 |
% by glider and deployment |
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| 59 |
switch gliderIndex |
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| 60 |
case 1 % Pelagia |
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| 61 |
switch deploymentNumber |
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| 62 |
case {1, 2} % Deployment 1 or 2; |
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| 63 |
% before foil replacement; |
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| 64 |
% 21 June 2004 calibration date; |
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| 65 |
% batch 2204 |
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| 66 |
C0coef=[3.12899E+03,-1.05764E+02,2.06640E+00,-1.68983E-02]; |
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| 67 |
C1coef=[-1.67671E+02,4.80582E+00,-8.73323E-02,6.61507E-04]; |
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| 68 |
C2coef=[3.73685E+00,-8.78300E-02,1.47560E-03,-9.96701E-06]; |
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| 69 |
C3coef=[-3.96052E-02,7.46930E-04,-1,17804E-05,6.677619E-08]; |
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| 70 |
C4coef=[1.61999E-04,-2.37870E-06,3.63223E-08,-1.62194E-10]; |
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| 71 |
case 3 % Deployment 3; |
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| 72 |
% replaced foil on 12 March 2012; |
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| 73 |
% 18 August 2010 calibration date; |
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% batch 1023 |
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| 75 |
C0coef=[4.27019336E+03,-1.32723585E+02,2.15629751E+00,-1.40275831E-02]; |
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| 76 |
C1coef=[-2.29729690E+02,5.74242078E+00,-6.85357898E-02,1.88612346E-04]; |
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C2coef=[5.06401550E+00,-9.62084932E-02,5.22180779E-04,7.70889717E-06]; |
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C3coef=[-5.26332308E-02,7.15467419E-04,3.31185072E-06,-1.86124024E-07]; |
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| 79 |
C4coef=[2.10916841E-04,-1.84087896E-06,-4.28645540E-08,1.11120317E-09]; |
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| 80 |
end |
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| 81 |
case 2 % Ramses all deployments; |
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| 82 |
% 2 June 2010 calibration date; |
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% batch 5009 |
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| 84 |
C0coef=[4.53793e3 -1.62595e2 3.29574 -2.79285e-2]; |
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| 85 |
C1coef=[-2.50953e2 8.02322 -1.58398e-1 1.31141e-3]; |
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| 86 |
C2coef=[5.66417 -1.59647e-1 3.07910e-3 -2.46265e-5]; |
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C3coef=[-5.99449e-2 1.48326e-3 -2.82110e-5 2.15156e-7]; |
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C4coef=[2.43614e-4 -5.26759e-6 1.00064e-7 -7.14320e-10]; |
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| 89 |
end |
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| 90 |
|
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| 91 |
%*** READ IN EBD DATA **** |
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| 92 |
% declare arrays for accumulating data |
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| 93 |
oxyw_oxygen = []; |
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| 94 |
oxyw_saturation = []; |
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| 95 |
oxyw_temp = []; |
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| 96 |
oxyw_dphase = []; |
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| 97 |
% oxyw_bphase = []; |
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| 98 |
% oxyw_rphase = []; |
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% oxyw_bamp = []; |
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% oxyw_bpot = []; |
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| 101 |
% oxyw_ramp = []; |
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% oxyw_rawtemp = []; |
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| 103 |
% oxyw_time = []; |
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| 104 |
% oxyw_installed = []; |
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| 105 |
ptime_ebd = []; |
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| 106 |
|
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| 107 |
% try to load all *.ebdasc files at once... |
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| 108 |
[files, Dstruct] = wilddir(datadir, '.ebdasc'); |
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| 109 |
nfile = size(files, 1); |
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| 110 |
|
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| 111 |
for i=1:nfile-1 |
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| 112 |
% protect against empty ebd file |
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| 113 |
if(Dstruct(i).bytes>0) |
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| 114 |
data = read_gliderasc2([datadir, files(i,:)]); |
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| 115 |
|
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| 116 |
% if the number of values (in data.data) is less than the number |
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| 117 |
% of vars (in data.vars), this means that the data were not |
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| 118 |
% completely read in. To correct this, pad data.data with NaNs |
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| 119 |
% until its length equals that of data.vars... |
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| 120 |
if (length(data.data) < length(data.vars)) |
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| 121 |
data.data = padarray(data.data, ... |
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| 122 |
[0 length(data.vars)-length(data.data)], ... |
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| 123 |
NaN, 'post'); |
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| 124 |
end |
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| 125 |
|
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| 126 |
% concatenate variables with data... |
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| 127 |
if(~isempty(data.data)) |
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| 128 |
oxyw_oxygen = [oxyw_oxygen; ... |
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| 129 |
data.data(:,strmatch('sci_oxy3835_wphase_oxygen',... |
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| 130 |
data.vars, 'exact'))]; |
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| 131 |
oxyw_saturation = [oxyw_saturation; ... |
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| 132 |
data.data(:,strmatch('sci_oxy3835_wphase_saturation',... |
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| 133 |
data.vars, 'exact'))]; |
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| 134 |
oxyw_temp = [oxyw_temp; ... |
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| 135 |
data.data(:,strmatch('sci_oxy3835_wphase_temp',... |
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| 136 |
data.vars, 'exact'))]; |
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| 137 |
oxyw_dphase = [oxyw_dphase; ... |
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| 138 |
data.data(:,strmatch('sci_oxy3835_wphase_dphase',... |
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| 139 |
data.vars, 'exact'))]; |
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| 140 |
% oxyw_bphase = [oxyw_bphase; ... |
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| 141 |
% data.data(:,strmatch('sci_oxy3835_wphase_bphase',... |
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| 142 |
% data.vars, 'exact'))]; |
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| 143 |
% oxyw_rphase = [oxyw_rphase; ... |
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| 144 |
% data.data(:,strmatch('sci_oxy3835_wphase_rphase',... |
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| 145 |
% data.vars, 'exact'))]; |
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| 146 |
% oxyw_bamp = [oxyw_bamp; ... |
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| 147 |
% data.data(:,strmatch('sci_oxy3835_wphase_bamp',... |
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| 148 |
% data.vars, 'exact'))]; |
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| 149 |
% oxyw_bpot = [oxyw_bpot; ... |
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| 150 |
% data.data(:,strmatch('sci_oxy3835_wphase_bpot',... |
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| 151 |
% data.vars, 'exact'))]; |
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| 152 |
% oxyw_ramp = [oxyw_ramp; ... |
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| 153 |
% data.data(:,strmatch('sci_oxy3835_wphase_ramp',... |
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| 154 |
% data.vars, 'exact'))]; |
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| 155 |
% oxyw_rawtemp = [oxyw_rawtemp; ... |
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| 156 |
% data.data(:,strmatch('sci_oxy3835_wphase_rawtemp',... |
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| 157 |
% data.vars, 'exact'))]; |
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| 158 |
% oxyw_time = [oxyw_time; ... |
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| 159 |
% data.data(:,strmatch('sci_oxy3835_wphase_timestamp',... |
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| 160 |
% data.vars, 'exact'))]; |
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% oxyw_installed = [oxyw_installed; ... |
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| 162 |
% data.data(:,strmatch('sci_oxy3835_wphase_is_installed',... |
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| 163 |
% data.vars, 'exact'))]; |
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| 164 |
ptime_ebd = [ptime_ebd; ... |
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| 165 |
data.data(:,strmatch('sci_m_present_time',... |
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| 166 |
data.vars, 'exact'))]; |
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| 167 |
end |
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| 168 |
|
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data = []; |
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| 170 |
end |
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| 171 |
end |
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| 172 |
%*** END READ IN EBD DATA **** |
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| 173 |
|
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| 174 |
% remove nans from EBD data... |
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| 175 |
i = find(~isnan(oxyw_dphase)); |
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| 176 |
oxyw_dphase = oxyw_dphase(i); |
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| 177 |
ptime_ebd = ptime_ebd(i); |
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| 178 |
oxyw_oxygen = oxyw_oxygen(i); |
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| 179 |
oxyw_saturation = oxyw_saturation(i); |
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| 180 |
oxyw_temp = oxyw_temp(i); |
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| 181 |
% oxyw_bphase = oxyw_bphase(i); |
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| 182 |
% oxyw_rphase = oxyw_rphase(i); |
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| 183 |
% oxyw_bamp = oxyw_bamp(i); |
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| 184 |
% oxyw_bpot = oxyw_bpot(i); |
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| 185 |
% oxyw_ramp = oxyw_ramp(i); |
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| 186 |
% oxyw_rawtemp = oxyw_rawtemp(i); |
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| 187 |
% oxyw_time = oxyw_time(i); |
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| 188 |
% oxyw_installed = oxyw_installed(i); |
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| 189 |
|
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| 190 |
% apply the sort() function to ptime_oxy |
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| 191 |
% to make sure it increases monotonically... |
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| 192 |
[Y,I] = sort(ptime_ebd); |
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| 193 |
ptime_ebd = Y; |
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| 194 |
oxyw_oxygen = oxyw_oxygen(I); |
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oxyw_saturation = oxyw_saturation(I); |
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| 196 |
oxyw_temp = oxyw_temp(I); |
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| 197 |
oxyw_dphase = oxyw_dphase(I); |
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| 198 |
% oxyw_bphase = oxyw_bphase(I); |
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| 199 |
% oxyw_rphase = oxyw_rphase(I); |
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| 200 |
% oxyw_bamp = oxyw_bamp(I); |
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| 201 |
% oxyw_bpot = oxyw_bpot(I); |
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| 202 |
% oxyw_ramp = oxyw_ramp(I); |
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| 203 |
% oxyw_rawtemp = oxyw_rawtemp(I); |
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| 204 |
% oxyw_time = oxyw_time(I); |
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| 205 |
% oxyw_installed = oxyw_installed(I); |
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| 206 |
|
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| 207 |
% load CTD data from existing mat file... |
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| 208 |
strMatFilePath = strcat('GLIDER_DATA_LEVEL1/', strGliderName, ... |
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| 209 |
'_Deployment', strDeploymentNumber, '_CTD_L1.mat'); |
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| 210 |
load(strMatFilePath); |
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| 211 |
|
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| 212 |
% interpolate CTD to times of oxyw_dphase |
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| 213 |
tempi = interp1(ptime,temp,ptime_ebd); |
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| 214 |
salini = interp1(ptime,salinCorrected,ptime_ebd); |
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| 215 |
depthi = interp1(ptime,depth,ptime_ebd); |
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| 216 |
|
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| 217 |
% first, implement temperature-dependent correction to DO concentration |
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| 218 |
% that utilizes dphase as the input (manual page 30), coefficients from cal |
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| 219 |
% sheets (a 5x4 matrix of values) and will be glider (and foil) dependent. |
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| 220 |
C0 = C0coef(1) + (C0coef(2) .* tempi) + ... |
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| 221 |
(C0coef(3) .* (tempi.^2)) + (C0coef(4) .* (tempi.^3)); |
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| 222 |
C1 = C1coef(1) + (C1coef(2) .* tempi) + ... |
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| 223 |
(C1coef(3) .* (tempi.^2)) + (C1coef(4) .* (tempi.^3)); |
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| 224 |
C2 = C2coef(1) + (C2coef(2) .* tempi) + ... |
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| 225 |
(C2coef(3) .* (tempi.^2)) + (C2coef(4) .* (tempi.^3)); |
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| 226 |
C3 = C3coef(1) + (C3coef(2) .* tempi) + ... |
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| 227 |
(C3coef(3) .* (tempi.^2)) + (C3coef(4) .* (tempi.^3)); |
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| 228 |
C4 = C4coef(1) + (C4coef(2) .* tempi) + ... |
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| 229 |
(C4coef(3) .* (tempi.^2)) + (C4coef(4) .* (tempi.^3)); |
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| 230 |
|
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| 231 |
o2_tcorr = C0 + (C1 .* oxyw_dphase) + (C2 .* (oxyw_dphase.^2)) + ... |
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| 232 |
(C3 .* (oxyw_dphase.^3)) + (C4 .* (oxyw_dphase.^4)); |
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| 233 |
|
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| 234 |
% second, implement the salinity correction to DO concentration (page 31) |
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| 235 |
% ASSUMES DEFAULT SALINITY IN SENSOR WAS SET TO ZERO, OTHERWISE ANOHTER |
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| 236 |
% SCALING IS REQUIRED |
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| 237 |
B0=-6.24097e-3; |
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| 238 |
B1=-6.93498e-3; |
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| 239 |
B2=-6.90358e-3; |
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| 240 |
B3=-4.29155e-3; |
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| 241 |
C0=-3.11680e-7; |
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| 242 |
|
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| 243 |
Ts = log((298.15 - tempi) ./ (273.15 + tempi)); |
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| 244 |
|
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| 245 |
o2_tscorr = o2_tcorr .* ... |
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| 246 |
exp((salini .* (B0 + (B1 .* Ts) + (B2 .* (Ts.^2)) + ... |
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| 247 |
(B3 .* (Ts.^3)))) + ... |
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| 248 |
(C0 .* (salini.^2))); |
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| 249 |
|
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| 250 |
% third, implement the pressure correction to DO concentration (page 32) |
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| 251 |
o2_tspcorr = o2_tscorr .* (1 + (0.04 .* depthi ./ 1000)); |
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| 252 |
|
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| 253 |
% use polynomial to calculate DO satuations using the measured temp and |
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| 254 |
% sal (manual page 30) |
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| 255 |
A0 = 2.00856; |
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| 256 |
A1 = 3.22400; |
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| 257 |
A2 = 3.99063; |
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| 258 |
A3 = 4.80299; |
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| 259 |
A4 = 9.78188e-1; |
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| 260 |
A5 = 1.71069; |
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| 261 |
B0 = -6.24097e-3; |
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| 262 |
B1 = -6.93498e-3; |
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| 263 |
B2 = -6.90358e-3; |
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| 264 |
B3 = -4.29155e-3; |
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| 265 |
C0 = -3.11680e-7; |
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| 266 |
|
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| 267 |
% need interpolated temp, salinity, pressure at times of DO obs |
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| 268 |
rslt = (A0 + (A1 .* Ts) + (A2 .* (Ts.^2)) + (A3 .* (Ts.^3)) + ... |
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| 269 |
(A4 .* (Ts.^4)) + (A5 .* (Ts.^5))) + ... |
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| 270 |
(salini .* (B0 + (B1 .* Ts) + (B2 .* (Ts.^2)) + (B3 .*(Ts.^3)))) + ... |
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| 271 |
(C0 .* (salini.^2)); |
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| 272 |
|
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| 273 |
o2_sol = exp(rslt); |
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| 274 |
|
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| 275 |
o2_sat = (o2_tspcorr .* 2.2414) ./ o2_sol; |
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| 276 |
|
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| 277 |
% convert ptime into datenum style... |
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| 278 |
ptime_ebd_datenum = (ptime_ebd/3600/24) + datenum(1970, 1, 1, 0, 0, 0); |
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| 279 |
|
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| 280 |
% create configuration struct... |
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| 281 |
units = struct( ... |
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| 282 |
'oxyw_oxygen', '10e-6 mol/dm3', ... |
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| 283 |
'oxyw_saturation', 'percent', ... |
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| 284 |
'oxyw_temp', 'degrees C', ... |
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| 285 |
'oxyw_dphase', 'degrees', ... |
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| 286 |
... % 'oxyw_bphase', 'degrees', ... |
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| 287 |
... % 'oxyw_rphase', 'degrees', ... |
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| 288 |
... % 'oxyw_bamp', 'mA', ... |
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| 289 |
... % 'oxyw_bpot', 'mV', ... |
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| 290 |
... % 'oxyw_ramp', 'mA', ... |
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| 291 |
... % 'oxyw_rawtemp', 'degrees C', ... |
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| 292 |
... % 'oxyw_time', 'timestamp', ... |
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| 293 |
... % 'oxyw_installed', 'bool', ... |
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| 294 |
'ptime_ebd', 'seconds since 0000-01-01T00:00', ... |
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| 295 |
'ptime_ebd_datenum', 'days since 1970-01-01T00:00', ... |
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| 296 |
'tempi', 'degrees C', ... |
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| 297 |
'salini', 'psu', ... |
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| 298 |
'depthi', 'meters', ... |
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| 299 |
'o2_tcorr', '10e-6 mol/dm3', ... |
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| 300 |
'o2_tscorr', '10e-6 mol/dm3', ... |
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| 301 |
'o2_tspcorr', '10e-6 mol/dm3', ... |
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| 302 |
'o2_sol', 'cm3/liter at 1031 hPa', ... |
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| 303 |
'o2_sat', 'percent'); |
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| 304 |
|
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| 305 |
variable_description = struct( ... |
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| 306 |
'oxyw_oxygen', 'dissolved oxygen', ... |
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| 307 |
'oxyw_saturation', 'dissolved oxygen saturation', ... |
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| 308 |
'oxyw_temp', 'water temperature', ... |
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| 309 |
'oxyw_dphase', 'phase difference', ... |
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| 310 |
... % 'oxyw_bphase', 'blue phase', ... |
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| 311 |
... % 'oxyw_rphase', 'red phase', ... |
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| 312 |
... % 'oxyw_bamp', 'blue current bias', ... |
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| 313 |
... % 'oxyw_bpot', 'blue voltage bias', ... |
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| 314 |
... % 'oxyw_ramp', 'red current bias', ... |
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| 315 |
... % 'oxyw_rawtemp', 'raw water temperature', ... |
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| 316 |
... % 'oxyw_time', 'optode timestampe', ... |
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| 317 |
... % 'oxyw_installed', 'bool', ... |
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| 318 |
'ptime_ebd', 'science computer time', ... |
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| 319 |
'ptime_ebd_datenum', 'science computer date', ... |
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| 320 |
'tempi', 'interpolated CTD water temperature', ... |
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| 321 |
'salini', 'interpoloted CTD salinity', ... |
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| 322 |
'depthi', 'interpolated CTD depth', ... |
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| 323 |
'o2_tcorr', 'temperature corrected dissolved oxygen', ... |
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| 324 |
'o2_tscorr', 'temperature and salinity corrected dissolved oxygen', ... |
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| 325 |
'o2_tspcorr', 'temperature, salinity, and pressure corrected dissolved oxygen', ... |
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| 326 |
'o2_sol', 'corrected oxygen solubility', ... |
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| 327 |
'o2_sat', 'corrected oxygen saturation'); |
|---|
| 328 |
|
|---|
| 329 |
correction_coefficients = struct('C0coef', C0coef, ... |
|---|
| 330 |
'C1coef', C1coef, ... |
|---|
| 331 |
'C2coef', C2coef, ... |
|---|
| 332 |
'C3coef', C3coef, ... |
|---|
| 333 |
'C4coef', C4coef); |
|---|
| 334 |
|
|---|
| 335 |
config = struct('glider_name', strGliderName,... |
|---|
| 336 |
'deployment_number', strDeploymentNumber,... |
|---|
| 337 |
'start_date', strStartDate,... |
|---|
| 338 |
'end_date', strEndDate,... |
|---|
| 339 |
'correction_coefficients', correction_coefficients,... |
|---|
| 340 |
'var_descriptions', variable_description,... |
|---|
| 341 |
'var_units', units); |
|---|
| 342 |
|
|---|
| 343 |
% set Level 1 data mat file name... |
|---|
| 344 |
strMatFileName = strcat(strGliderName, '_Deployment', strDeploymentNumber, '_DO_L1.mat'); |
|---|
| 345 |
|
|---|
| 346 |
% save flight data to mat file... |
|---|
| 347 |
save(strMatFileName,... |
|---|
| 348 |
'config', ... |
|---|
| 349 |
'oxyw_oxygen', ... |
|---|
| 350 |
'oxyw_saturation', ... |
|---|
| 351 |
'oxyw_temp', ... |
|---|
| 352 |
'oxyw_dphase', ... |
|---|
| 353 |
... % 'oxyw_bphase', ... |
|---|
| 354 |
... % 'oxyw_rphase', ... |
|---|
| 355 |
... % 'oxyw_bamp', ... |
|---|
| 356 |
... % 'oxyw_bpot', ... |
|---|
| 357 |
... % 'oxyw_ramp', ... |
|---|
| 358 |
... % 'oxyw_rawtemp', ... |
|---|
| 359 |
... % 'oxyw_time', ... |
|---|
| 360 |
... % 'oxyw_installed', ... |
|---|
| 361 |
'ptime_ebd', ... |
|---|
| 362 |
'ptime_ebd_datenum', ... |
|---|
| 363 |
'tempi', ... |
|---|
| 364 |
'salini', ... |
|---|
| 365 |
'depthi', ... |
|---|
| 366 |
'o2_tcorr', ... |
|---|
| 367 |
'o2_tscorr', ... |
|---|
| 368 |
'o2_tspcorr', ... |
|---|
| 369 |
'o2_sol', ... |
|---|
| 370 |
'o2_sat'); |
|---|
| 371 |
|
|---|
| 372 |
end |
|---|
| 373 |
end |
|---|
