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% gliderEcopuck_Generate_L1_Data.m |
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% |
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% Purpose: Generate Level 1 data mat files for Ecopuck data. |
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% |
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% Requires: |
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% MATLAB folder - contains util |
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% |
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% Authors: Chris Calloway |
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% Marine Sciences Department |
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% UNC-Chapel Hill |
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% |
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% Created: January 2014 |
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% |
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%////////////////////////////////////////////////////////////////////////// |
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clear all; |
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|
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% add paths for required files... |
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addpath('MATLAB/util/'); |
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|
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% populate arrays for the deployment start and end dates... |
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% ex. strStart(2, 3) is start date for Ramses, Deployment 3 |
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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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strEnd = {'14-Feb-2012', '08-Mar-2012', '04-Apr-2012'; ... |
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'14-Feb-2012', '12-Mar-2012', '03-Apr-2012'}; |
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|
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% SET THE GLIDER INDEX (Pelagia = 1, Ramses = 2) ... |
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for gliderIndex=1:2 |
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|
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% SET THE DEPLOYMENT NUMBER (1, 2 or 3) ... |
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for deploymentNumber=1:3 |
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|
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clearvars -except gliderIndex deploymentNumber strStart strEnd; |
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|
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% glider name string... |
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if (gliderIndex==1) |
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strGliderName = 'Pelagia'; |
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else |
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strGliderName = 'Ramses'; |
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end |
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|
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% deployment number string... |
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strDeploymentNumber = num2str(deploymentNumber); |
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|
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% deployment start date string... |
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strStartDate = strStart(gliderIndex, deploymentNumber); |
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|
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% deployment end date string... |
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strEndDate = strEnd(gliderIndex, deploymentNumber); |
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|
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% define the path to the glider ascii files... |
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datadir = strcat('GLIDER_DATA_LEVEL0/', strGliderName, ... |
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'_Deployment', strDeploymentNumber, '/'); |
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|
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disp(['Processing Ecopuck data for ', strGliderName, ' Deployment ', strDeploymentNumber]); |
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|
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%*** READ IN EBD DATA **** |
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% declare arrays for accumulating data |
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chlor = []; |
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cdom = []; |
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scatter = []; |
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chlor_sig = []; |
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cdom_sig = []; |
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scatter_sig = []; |
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chlor_ref = []; |
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cdom_ref = []; |
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scatter_ref = []; |
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ptime_ebd = []; |
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|
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% different var names per glider |
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switch gliderIndex |
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case 1 % Pelagia |
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chlor_name = 'sci_bbfl2s_chlor_scaled'; |
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cdom_name = 'sci_bbfl2s_cdom_scaled'; |
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scatter_name = 'sci_bbfl2s_bb_scaled'; |
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chlor_sig_name = 'sci_bbfl2s_chlor_sig'; |
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cdom_sig_name = 'sci_bbfl2s_cdom_sig'; |
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scatter_sig_name = 'sci_bbfl2s_bb_sig'; |
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chlor_ref_name = 'sci_bbfl2s_chlor_ref'; |
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cdom_ref_name = 'sci_bbfl2s_cdom_ref'; |
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scatter_ref_name = 'sci_bbfl2s_bb_ref'; |
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case 2 % Ramses |
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chlor_name = 'sci_flbbcd_chlor_units'; |
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cdom_name = 'sci_flbbcd_cdom_units'; |
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scatter_name = 'sci_flbbcd_bb_units'; |
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chlor_sig_name = 'sci_flbbcd_chlor_sig'; |
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cdom_sig_name = 'sci_flbbcd_cdom_sig'; |
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scatter_sig_name = 'sci_flbbcd_bb_sig'; |
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chlor_ref_name = 'sci_flbbcd_chlor_ref'; |
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cdom_ref_name = 'sci_flbbcd_cdom_ref'; |
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scatter_ref_name = 'sci_flbbcd_bb_ref'; |
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end |
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|
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% try to load all *.ebdasc files at once... |
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[files, Dstruct] = wilddir(datadir, '.ebdasc'); |
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nfile = size(files, 1); |
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for i=1:nfile-1 |
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% protect against empty ebd file |
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if(Dstruct(i).bytes>0) |
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data = read_gliderasc2([datadir, files(i,:)]); |
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|
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% if the number of values (in data.data) is less than the number |
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% of vars (in data.vars), this means that the data were not |
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% completely read in. To correct this, pad data.data with NaNs |
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% until its length equals that of data.vars... |
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if (length(data.data) < length(data.vars)) |
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data.data = padarray(data.data, ... |
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[0 length(data.vars)-length(data.data)], ... |
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NaN, 'post'); |
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end |
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|
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% concatenate variables with data... |
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if(~isempty(data.data)) |
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chlor = [chlor; ... |
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data.data(:,strmatch(chlor_name,... |
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data.vars, 'exact'))]; |
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cdom = [cdom; ... |
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data.data(:,strmatch(cdom_name,... |
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data.vars, 'exact'))]; |
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scatter = [scatter; ... |
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data.data(:,strmatch(scatter_name,... |
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data.vars, 'exact'))]; |
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chlor_sig = [chlor_sig; ... |
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data.data(:,strmatch(chlor_sig_name,... |
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data.vars, 'exact'))]; |
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cdom_sig = [cdom_sig; ... |
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data.data(:,strmatch(cdom_sig_name,... |
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data.vars, 'exact'))]; |
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scatter_sig = [scatter_sig; ... |
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data.data(:,strmatch(scatter_sig_name,... |
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data.vars, 'exact'))]; |
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chlor_ref = [chlor_ref; ... |
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data.data(:,strmatch(chlor_ref_name,... |
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data.vars, 'exact'))]; |
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cdom_ref = [cdom_ref; ... |
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data.data(:,strmatch(cdom_ref_name,... |
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data.vars, 'exact'))]; |
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scatter_ref = [scatter_ref; ... |
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data.data(:,strmatch(scatter_ref_name,... |
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data.vars, 'exact'))]; |
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ptime_ebd = [ptime_ebd; ... |
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data.data(:,strmatch('sci_m_present_time',... |
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data.vars, 'exact'))]; |
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end |
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data = []; |
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end |
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end |
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%*** END READ IN EBD DATA **** |
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|
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% remove nans from EBD data... |
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i = find(~isnan(chlor)); |
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chlor = chlor(i); |
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cdom = cdom(i); |
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scatter = scatter(i); |
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chlor_sig = chlor_sig(i); |
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cdom_sig = cdom_sig(i); |
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scatter_sig = scatter_sig(i); |
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chlor_ref = chlor_ref(i); |
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cdom_ref = cdom_ref(i); |
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scatter_ref = scatter_ref(i); |
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ptime_ebd = ptime_ebd(i); |
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% apply the sort() function to ptime_oxy |
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% to make sure it increases monotonically... |
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[Y,I] = sort(ptime_ebd); |
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ptime_ebd = Y; |
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chlor = chlor(I); |
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cdom = cdom(I); |
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scatter = scatter(I); |
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chlor_sig = chlor_sig(I); |
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cdom_sig = cdom_sig(I); |
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scatter_sig = scatter_sig(I); |
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chlor_ref = chlor_ref(I); |
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cdom_ref = cdom_ref(I); |
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scatter_ref = scatter_ref(I); |
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% convert ptime into datenum style... |
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ptime_ebd_datenum = (ptime_ebd/3600/24) + datenum(1970, 1, 1, 0, 0, 0); |
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|
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% create configuration struct... |
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units = struct( ... |
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'chlor', '10e-6 g/l', ... |
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'cdom', 'ppb', ... |
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'scatter', '1/mm', ... |
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'chlor_sig', 'count', ... |
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'cdom_sig', 'count', ... |
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'scatter_sig', 'count', ... |
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'chlor_ref', 'count', ... |
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'cdom_ref', 'count', ... |
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'scatter_ref', 'count', ... |
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'ptime_ebd', 'seconds since 0000-01-01T00:00', ... |
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'ptime_ebd_datenum', 'days since 1970-01-01T00:00'); |
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|
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variable_description = struct( ... |
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'chlor', 'chlorophyll', ... |
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'cdom', 'chromophoric dissolved organic matter', ... |
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'scatter', 'backscatter', ... |
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'chlor_sig', 'chlorophyll raw count', ... |
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'cdom_sig', 'chromophoric dissolved organic matter raw count', ... |
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'scatter_sig', 'backscatter raw count', ... |
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'chlor_ref', 'chlorophyll reference count', ... |
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'cdom_ref', 'chromophoric dissolved organic matter reference count', ... |
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'scatter_ref', 'backscatter reference count', ... |
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'ptime_ebd', 'science computer time', ... |
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'ptime_ebd_datenum', 'science computer date'); |
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|
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config = struct('glider_name', strGliderName,... |
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'deployment_number', strDeploymentNumber,... |
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'start_date', strStartDate,... |
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'end_date', strEndDate,... |
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'var_descriptions', variable_description,... |
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'var_units', units); |
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|
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% set Level 1 data mat file name... |
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strMatFileName = strcat(strGliderName, '_Deployment', strDeploymentNumber, '_ECO_L1.mat'); |
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|
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% save flight data to mat file... |
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save(strMatFileName,... |
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'config', ... |
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'chlor', ... |
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'cdom', ... |
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'scatter', ... |
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'chlor_sig', ... |
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'cdom_sig', ... |
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'scatter_sig', ... |
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'chlor_ref', ... |
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'cdom_ref', ... |
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'scatter_ref', ... |
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'ptime_ebd', ... |
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'ptime_ebd_datenum'); |
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end |
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end |
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