Changeset 503

Timestamp:

04/17/13 14:39:19

Author:

cbc

Message:

Test code fo gliderOptode_Generate_L1_Data.m

Files:

• gliderproc/trunk (modified) (1 prop)
• gliderproc/trunk/extractDbd.m (modified) (1 diff)
• gliderproc/trunk/gliderOptode_Generate_L1_Data.m (modified) (1 diff)

gliderproc/trunk/extractDbd.m

@@ -6 +6 @@
-%  NOTE: At top of file, set glider index and deployment number
-%
-, seawater, 
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-%
-%

gliderproc/trunk/gliderOptode_Generate_L1_Data.m

@@ -4 +4 @@
-%  Purpose: Generate Level 1 data mat files that include optode DO data.
-%
-%  NOTE: At top of file, set glider index and deployment number
-%
-%  Requires:
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-clear all;
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-%!!!!!!  SET PRIOR TO RUNNING CODE  !!!!!!!!!!!!!!!!!!!!!!!!
-%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-%
-% SET THE GLIDER INDEX (Pelagia = 1, Ramses = 2) ...
-gliderIndex = 1;
-
-% SET THE DEPLOYMENT NUMBER (1, 2 or 3) ...
-deploymentNumber = 1;
-
-%
-%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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-% add paths for required files...
-addpath('MATLAB/util/');
-addpath('MATLAB/matutil/');
-addpath('MATLAB/seawater/');
-addpath('MATLAB/plots/');
-addpath('MATLAB/strfun/');
-addpath('MATLAB/opnml/');
-addpath('MATLAB/opnml/FEM/');
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-% glider name string...
-if (gliderIndex==1)
-    strGliderName = 'Pelagia';
-else
-    strGliderName = 'Ramses';
-end
-
-% populate arrays for the deployment start and end dates...
-% ex. strStart(2, 3) is start date for Ramses, Deployment 3
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-        end
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-        end
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-end
-%**************************************************************************
-
-
-% load glider data from existing mat file...
-strMatFilePath = strcat('GLIDER_DATA_LEVEL1/', strGliderName, '_Deployment', strDeploymentNumber, '_DataL1.mat');
-load(strMatFilePath);
-
-
-% first, apply the sort() function to ptime_oxy to make sure it increases monotonically...
-[Y,I] = sort(ptime_oxy);
-ptime_oxy = Y;
-oxy_dphase = oxy_dphase(I);
-
-
-% remove nans from EBD data...
-i = find(~isnan(oxy_dphase));
-oxy_dphase = oxy_dphase(i); ptime_oxy = ptime_oxy(i);
-
-% interpolate CTD to times of oxy_dphase 
-tempi = interp1(ptime,temp,ptime_oxy);
-salini = interp1(ptime,salinCorrected,ptime_oxy);
-depthi = interp1(ptime,depth,ptime_oxy);
-
-% first, implement temperature-dependent correction to DO concentration
-% that utilizes dphase as the input (manual page 30), coefficients from cal
-% sheets (a 5x4 matrix of values) and will be glider (and foil) dependent.
-
-% for ramses, 2 June 2010 calibration sheet
-
-C0coef=[4.53793e3 -1.62595e2 3.29574 -2.79285e-2];
-C1coef=[-2.50953e2 8.02322 -1.58398e-1 1.31141e-3];
-C2coef=[5.66417 -1.59647e-1 3.07910e-3 -2.46265e-5];
-C3coef=[-5.99449e-2 1.48326e-3 -2.82110e-5 2.15156e-7];
-C4coef=[2.43614e-4 -5.26759e-6 1.00064e-7 -7.14320e-10];
-
-C0 = C0coef(1)+C0coef(2)*tempi+C0coef(3)*tempi.^2+C0coef(4)*tempi.^3;
-C1 = C1coef(1)+C1coef(2)*tempi+C1coef(3)*tempi.^2+C1coef(4)*tempi.^3;
-C2 = C2coef(1)+C2coef(2)*tempi+C2coef(3)*tempi.^2+C2coef(4)*tempi.^3;
-C3 = C3coef(1)+C3coef(2)*tempi+C3coef(3)*tempi.^2+C3coef(4)*tempi.^3;
-C4 = C4coef(1)+C4coef(2)*tempi+C4coef(3)*tempi.^2+C4coef(4)*tempi.^3;
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-o2 = C0+C1.*oxy_dphase+C2.*oxy_dphase.^2+C3.*oxy_dphase.^3+C4.*oxy_dphase.^4;
-
-% second, implement the salinity correction to DO concentration (page 31)
-% ASSUMES DEFAULT SALINITY IN SENSOR WAS SET TO ZERO, OTHERWISE ANOHTER
-% SCALING IS REQUIRED
-
-B0=-6.24097e-3;
-B1=-6.93498e-3;
-B2=-6.90358e-3;
-B3=-4.29155e-3;
-C0=-3.11680e-7;
-
-Ts = log((298.15 - tempi) ./ (273.15 + tempi));
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-o2_salcorr = o2*exp(salini*(B0+B1*Ts+B2*Ts.*Ts+B3*Ts.*Ts.*Ts)+C0*salini.^2);
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-% third, implement the pressure correction to DO concentration (page 32)
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-o2_salprescorr = os_salcorr*(1 + 0.04*depthi/1000);
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-% use polynomial to calculate DO satuations using the measured temp and
-% sal (manual page 30)
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-A0 = 2.00856;
-A1 = 3.22400;
-A2 = 3.99063;
-A3 = 4.80299;
-A4 = 0.0978188;
-A5 = 1.71069;
-B0 = -00624097;
-B1 = -00693498;
-B2 = -00690358;
-B3 = -00429155;
-C0 = -000000311680;
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-% need interpolated temp, salinity, pressure at times of DO obs
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-rslt = A0 + A1*Ts + A2*Ts.^2 + A3*Ts.^3 + A4*Ts.^4 + A5*Ts.^5 +...
-    salini.*(B0 + B1*Ts + B2*Ts.^2 + B3*Ts.^3) + C0*salini.^2;
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-O2sol = exp(rslt);
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-o2_sat = (o2_salprescorr * 2.2414) ./ O2sol;
-
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-% convert ptime into datenum style...
-ptime_oxy_datenum = ptime_oxy/3600/24+datenum(1970, 1, 1, 0, 0, 0);
-% ptimehrly = fix(ptime_datenum*24)/24;
-% ptimedaily = fix(ptime_datenum);
-% ptimedaily2 = unique(ptimedaily);
-% ptimedaily2 = ptimedaily2(1:2:end);
-
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-lb = datenum('10-Feb-2012 12:22:00');
-ub = datenum('10-Feb-2012 12:23:00');
-%lb = datenum('22-Mar-2012 12:01:00');
-%ub = datenum('23-Mar-2012 12:02:00');
-
-% figure('Position', [500,500,1000,1000]);
-% subplot(311);
-% ind = find(ptime_oxy_datenum >= lb & ptime_oxy_datenum <= ub);
-% plot(ptime_oxy_datenum(ind), oxy_dphase(ind), 'b.');
-% datetick;
-% xlabel('time', 'fontsize', 12);
-% ylabel('DO  (dphase)', 'fontsize', 12);
-% subplot(312);
-% ind2 = find(ptime_datenum >= lb & ptime_datenum <= ub);
-% plot(ptime_datenum(ind2), temp(ind2), 'r.');
-% datetick;
-% xlabel('time', 'fontsize', 12);
-% ylabel('temp', 'fontsize', 12);
-% subplot(313);
-% ind = find(ptime_oxy_datenum >= lb & ptime_oxy_datenum <= ub);
-% ind2 = find(ptime_datenum >= lb & ptime_datenum <= ub);
-% plot(ptime_oxy_datenum(ind), ones(length(ind), 1), 'b.', ptime_datenum(ind2), ones(length(ind2), 1), 'r.');
-% datetick;
-
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-figure('Position', [500,500,1000,1000]);
-subplot(211);
-ind = find(ptime_datenum >= lb & ptime_datenum <= ub);
-plot(ptime_datenum(ind), oxy_dphase(ind), 'b.', ptime_datenum(ind), oxy_dphase_adjusted(ind), 'r.');
-datetick;
-xlabel('time', 'fontsize', 12);
-ylabel('DO  (dphase)', 'fontsize', 12);
-subplot(212);
-ind2 = find(ptime_datenum >= lb & ptime_datenum <= ub);
-plot(ptime_datenum(ind2), temp(ind2), 'r.');
-datetick;
-xlabel('time', 'fontsize', 12);
-ylabel('temp', 'fontsize', 12);
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-% interpolate DBD data to align with EBD data...
-% horizontalVelocity = interp1(ptime1_dbd, horizontalVelocity, ptime);
-% depth = interp1(ptime1_dbd, depth, ptime);
-% pitch = interp1(ptime1_dbd, pitch, ptime);
-% avgDepthRate = interp1(ptime1_dbd, avgDepthRate, ptime);
-% glideAngle = interp1(ptime1_dbd, glideAngle, ptime);
-% lat = interp1(ptime1_dbd, lat, ptime);
-% lon = interp1(ptime1_dbd, lon, ptime);
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-% create configuration struct...
-% units = struct('chlor', 'micrograms liter-1',...
-%                'dens', 'kg m-3',...
-%                'densCorrected', 'kg m-3',...
-%                'depth', 'm',...
-%                'gpsLat', 'decimal degrees',...
-%                'gpsLon', 'decimal degrees',...
-%                'pres', 'decibars',...
-%                'ptime', 'seconds since 0000-01-01T00:00',...
-%                'ptime_datenum', 'seconds since 0000-01-01T00:00',...
-%                'salin', 'psu',...
-%                'salinCorrected', 'psu',...
-%                'temp', 'deg C');
-
-% variable_description = struct('chlor', 'chlorophyll measured by glider',...
-%                               'chlorBounds', 'default chlorophyll bounds for plots',...
-%                               'dens', 'density measured by glider',...
-%                               'densBounds', 'default density bounds for plots',...
-%                               'densCorrected', 'density corrected for thermal lag',...
-%                               'depth', 'depth calculated as function of pressure and position latitude',...
-%                               'gpsLat', 'position latitude measured by glider GPS',...
-%                               'gpsLon', 'position longitude measured by glider GPS',...
-%                               'pres', 'pressure measured by glider',...
-%                               'ptime', 'time vector reported by glider',...
-%                               'ptime_datenum', 'Serial Date Number string',...
-%                               'salin', 'salinity measured by glider',...
-%                               'salinBounds', 'default salinity bounds for plots',...
-%                               'salinCorrected', 'salinity corrected for thermal lag',...
-%                               'temp', 'temperature measured by glider',...
-%                               'tempBounds', 'default temperature bounds for plots');
-
-% correction_parameters = struct('alpha_offset', correctionParams(1),...
-%                                'alpha_slope', correctionParams(2),...
-%                                'tau_offset', correctionParams(3),...
-%                                'tau_slope', correctionParams(4));
-           
-% config = struct('glider_name', strGliderName,...
-%                 'deployment_number', strDeploymentNumber,...
-%                 'start_date', strStartDate,...
-%                 'end_date', strEndDate,...
-%                 'thermal_lag_correction_parameters', correction_parameters,...
-%                 'var_descriptions', variable_description,...
-%                 'var_units', units);
-
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-% set Level 1 data mat file name...
-%strMatFileName = strcat(strGliderName, '_Deployment', strDeploymentNumber, '_WithDO_LEVEL1.mat');
-
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-% save glider/deployment data to mat file...
-% save(strMatFileName,...
-%      'config',...
-%      'chlor',...
-%      'chlorBounds',...
-%      'dens',...
-%      'densBounds',...
-%      'densCorrected',...
-%      'depth',...
-%      'gpsLat',...
-%      'gpsLon',...
-%      'pres',...
-%      'ptime',...
-%      'ptime_datenum',...
-%      'salin',...
-%      'salinBounds',...
-%      'salinCorrected',...
-%      'temp',...
-%      'tempBounds');
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