https://wiki-pnb.eri.ucsb.edu/index.php?action=history&feed=atom&title=Plot_bbp_final 2026-04-06T15:09:06Z Revision history for this page on the wiki MediaWiki 1.34.0 https://wiki-pnb.eri.ucsb.edu/index.php?title=Plot_bbp_final&diff=862&oldid=prev 2015-10-29T23:26:45Z

<p>Created page with &quot;&lt;pre&gt; function [eta, etaf] = plot_bbp_final(cruise) [filename,path] = uigetfile([&#039;home/data65/pb/HYDROSCAT/&#039;,cruise,&#039;/final/&#039;],&#039;Choose HS-6 file to plot&#039;); fid = fopen([path...&quot;</p> <p><b>New page</b></p><div>&lt;pre&gt;<br /> function [eta, etaf] = plot_bbp_final(cruise)<br /> <br /> [filename,path] = uigetfile(['home/data65/pb/HYDROSCAT/',cruise,'/final/'],'Choose HS-6 file to plot');<br /> <br /> fid = fopen([path filename],'r');<br /> C = textscan(fid,'%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f','delimiter',',','HeaderLines',120);<br /> % C = textscan(fid,'%s%s%s%s%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f','delimiter',',');<br /> fclose(fid);<br /> <br /> %lambda = [ 442 470 510 589 671];<br /> %newlambda = [420 442 470 510 589 700] as of 4/2010<br /> lambda = [420 442 470 510 589 700];<br /> % lambda = [420 700 442 510 470 589];<br /> bbs = [C{69} C{70} C{71} C{72} C{73} C{74}]; <br /> %%bbs = [C{69} C{71} C{73} C{72} C{74} C{70}];%re-arrange to match uncorrected 3/7/2011<br /> bbz = [C{75} C{76} C{77} C{78} C{79} C{80}]; <br /> %%bbz = [C{75} C{77} C{79} C{78} C{80} C{76}];%re-arrange to match uncorrected 3/7/2011<br /> bbs(bbs==-9.9e+35) = NaN;<br /> bbz(bbz==-9.9e+35) = NaN;<br /> <br /> <br /> %after Mobley 3.31<br /> bbw_525 = (16.06/2)*1.46e-4;<br /> bbw = bbw_525*((525./lambda).^4.32);<br /> <br /> bbps = bbs - repmat(bbw,size(bbs,1),1);<br /> %plot(1:length(bbps),bbps);<br /> depths = C{81};<br /> <br /> % s = input('Choose which scattering correction to apply, method 1, 2, or 3; Enter 0 for none?');<br /> %<br /> % switch s<br /> % case 0<br /> % q = ac9.out.a_corr;<br /> % case 1<br /> % q = ac9.out.a_scorr1;<br /> % case 2<br /> % q = ac9.out.a_scorr2;<br /> % case 3<br /> % q = ac9.out.a_scorr3;<br /> % otherwise<br /> % end<br /> <br /> %<br /> % qc = ac9.out.c_corr;<br /> % qc(qc==-9.9e+35) = NaN;<br /> % b = qc-q;<br /> <br /> plot_spectrum(bbps,'b_b_p',depths,filename,bbw);<br /> plot_spectrum(bbz,'b_b\_Zhang',depths,filename,bbw);<br /> %plot_spectrum(b,'b',filename);<br /> <br /> function S = plot_spectrum(q,type,d,filename,bbw)<br /> %wl = [ 442 470 510 589 671];<br /> wl = [420 442 470 510 589 700];<br /> % wl = [420 700 442 510 470 589];<br /> % d = 1:220';<br /> % d = d';<br /> <br /> %Plot all spectra at once<br /> %%q = q(:,[1 6 2 4 3 5]);<br /> qd = denan(q);<br /> <br /> c = jet(size(qd,1));<br /> <br /> <br /> %%%Calculate eta, using 442, 510 and 589 nm wavelengths<br /> eta = [];<br /> opts = optimset('fminsearch');<br /> opts = optimset('MaxFunEvals', 5000,'MaxIter',5000, 'TolFun',1e-6,'TolX',1e-4);<br /> <br /> lambda_for_eta = wl([1 3 4]);<br /> %%%%%lambda_for_eta = wl([1 5 4]);<br /> lambda_for_eta = lambda_for_eta';<br /> <br /> for i = 1:size(q,1)<br /> bbp = q(i,[1 3 4])';<br /> %%%% bbp = q(i,[1 5 4])';<br /> temp = ([[ 1 1 1]',log(lambda_for_eta)])\log(bbp); %this regression allows for an intercept -<br /> eta(i) = -temp(2);<br /> <br /> r = corrcoef(bbp,bbp(1)*((lambda_for_eta/lambda_for_eta(1)).^(temp(2))));<br /> eta_R2(i) = r(1,2)^2;<br /> <br /> if ~any(isnan(q(i,:)))<br /> [X,cost] = fminsearch(@cost_eta,[1 0.005],opts,q(i,:),wl);<br /> else<br /> X = [NaN NaN];<br /> end<br /> etaf(i) = X(1);<br /> end<br /> <br /> figure<br /> plot(eta,-d,'rx-')<br /> hold on<br /> plot(eta_R2, -d, 'ko-');<br /> legend({'\eta fit linearly, using 442, 510 , 589 nm channels','R^2 of \eta fit'});<br /> ylabel('Depth, m');<br /> hold on<br /> %plot([0.009 0.009],[0 -220], 'k-.');<br /> %plot([0.025 0.025],[0 -220], 'k-.');<br /> title(filename)<br /> <br /> <br /> %%%%%%%%%%%%End of fitting for eta<br /> <br /> figure<br /> hold on<br /> set(gca, 'ColorOrder',c)<br /> plot(wl,q,'o-')<br /> plot(wl,mean(qd),'ko-', 'LineWidth',3)<br /> plot(wl, bbw, 'bo-', 'LineWidth', 3)<br /> zeroline<br /> xlabel('Wavelength, nm')<br /> ylabel(type)<br /> title('Mean spectrum in black, Morel saltwater bb in blue')<br /> %title(filename)<br /> <br /> %Plot the profiles<br /> c = jet(6);<br /> <br /> figure<br /> subplot(131)<br /> plot(q(:,1),-d,'Color',c(1,:))<br /> hold on<br /> plot(q(:,2),-d,'Color',c(2,:))<br /> zeroline_horizontal<br /> axis([-Inf Inf -220 0])<br /> legend({[type,'442'],[type,'470']},'Location','SouthOutside');<br /> legend boxoff<br /> <br /> subplot(132)<br /> plot(q(:,3),-d,'Color',c(3,:))<br /> hold on<br /> plot(q(:,4),-d,'Color',c(4,:))<br /> zeroline_horizontal<br /> axis([-Inf Inf -220 0])<br /> legend({[type,'510'],[type,'589']},'Location','SouthOutside');<br /> legend boxoff<br /> title(filename)<br /> <br /> subplot(133)<br /> %plot(q(:,5),-d,'Color',c(5,:))<br /> plot(q(:,5),-d,'k');<br /> hold on<br /> % plot(q(:,6),-d,'Color',c(6,:))<br /> plot(q(:,6),-d,'b');<br /> zeroline_horizontal<br /> axis([-Inf Inf -220 0])<br /> legend({[type,'671']},'Location','SouthOutside');<br /> legend boxoff<br /> &lt;/pre&gt;</div>

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