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Copy pathdiurnal_figures.m
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diurnal_figures.m
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% Making figures of diurnal patterns of
% SIF
% GPP
load('SIF760daily.mat','halfhourly_result','raw_final_result');
load('HF_2013_GPP.mat');
% load('SIF760_result.mat');
load('hf_barn_2013_env.mat','apar','fapar','par');
% mkdir('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\','sif_gpp\');
% mkdir('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\','sif_gpp_linear\');
% mkdir('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\','sifyield\');
% mkdir('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\','sif_gpp_mm\');
% mkdir('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\','sifyield_linear\');
%SIF-GPP linear
rsq_total = nan(numel(gpp_doy),1);
p_total = nan(numel(gpp_doy),1);
rmse_total = nan(numel(gpp_doy),1);
%SIF-GPP Michaelis-Menten
rsq1_total = nan(numel(gpp_doy),1);
p1_total = nan(numel(gpp_doy),1);
rmse1_total = nan(numel(gpp_doy),1);
%SIFyield-GPP linear
rsq2_total = nan(numel(gpp_doy),1);
p2_total = nan(numel(gpp_doy),1);
rmse2_total = nan(numel(gpp_doy),1);
for doy_i=81:81 %1:numel(gpp_doy)
lb = double(gpp_doy(doy_i))+0.;
ub = double(gpp_doy(doy_i))+1.;
temp_time = 24.0*(doy(doy>= lb & doy <ub) - gpp_doy(doy_i));
temp_sif = halfhourly_result(halfhourly_result(:,1)>= lb & halfhourly_result(:,1)<ub,2);
temp_gpp = gpp_raw(doy>= lb & doy <ub);
temp_apar = apar(doy>= lb & doy <ub);
temp_par = par(doy>= lb & doy <ub);
temp_yield = temp_sif./temp_apar;
temp_lue = temp_gpp./temp_apar;
temp_time_1 = 24.0*(raw_final_result(raw_final_result(:,1) >= lb & raw_final_result(:,1) < ub & raw_final_result(:,3) >=0.99, 1) - gpp_doy(doy_i));
temp_array_1 = raw_final_result(raw_final_result(:,1) >= lb & raw_final_result(:,1) < ub & raw_final_result(:,3) >=0.99, 2);
gpp_pos_sub = temp_gpp>0;
temp_gpp = temp_gpp(gpp_pos_sub);
temp_sif = temp_sif(gpp_pos_sub);
temp_time= temp_time(gpp_pos_sub);
temp_yield = temp_yield(gpp_pos_sub);
temp_apar = temp_apar(gpp_pos_sub);
%Figure 1
fig = figure;
set(gcf,'PaperUnits','inches','PaperPosition',[0.25 0.25 10 6]);
set(fig,'Visible','off');
[AX,H1,H2] = plotyy(temp_time,temp_sif,temp_time,temp_gpp);
set(H1,'marker','O');
set(H2,'marker','O');
set(AX,'xlim',[0,24]);
set(AX(1),'box','off'); % Primary Y axis ticks only show on one side
set(get(AX(1),'Ylabel'),'String','SIF(mw/m2/sr/nm)','FontSize',15,'FontName','Whitney-Book');
set(get(AX(2),'Ylabel'),'String','GPP(umol/m2/second)','FontSize',15,'FontName','Whitney-Book');
set(AX(1),'YLim',[0 3],'FontSize',12,'FontName','Whitney-Book');
set(AX(2),'YLim',[0 50],'FontSize',12,'FontName','Whitney-Book');
xlabel('Hours','FontSize',16,'FontName','Whitney-Book');
xlim_fig = xlim;
ylim_fig = ylim;
wdth = xlim_fig(2)-xlim_fig(1);
ht = ylim_fig(2)-ylim_fig(1);
pos = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.05*ht];
text(pos(1),pos(2),num2str(gpp_doy(doy_i)),'FontSize',20,'FontName','Whitney-Book');
%=================
%Figure 2
pp = polyfit(temp_sif(temp_sif>0),temp_gpp(temp_sif>0),1);
fitresult = linearfit(polyval(pp,temp_sif(temp_sif>0)),temp_gpp(temp_sif>0));
rsq = fitresult(6);
pvalue = fitresult(7);
slope = fitresult(1);
intercept = fitresult(3);
rmse = fitresult(5);
rsq_total(doy_i) = rsq;
p_total(doy_i) = pvalue;
rmse_total(doy_i) = rmse;
fig2 = figure;
set(gcf,'PaperUnits','inches','PaperPosition',[0.25 0.25 10 6]);
set(fig2,'Visible','off');
start = min(temp_sif(temp_sif>0));
stop = max(temp_sif(temp_sif>0))+0.1*max(temp_sif(temp_sif>0)); %pad 10%
plot(temp_sif(temp_sif>0),temp_gpp(temp_sif>0),'ro',...
start:0.1:stop,polyval(pp,start:0.1:stop),'r-');
axis([0 3 0 50]);
xlabel('SIF(mw/sr/m2/nm)','FontSize',15,'FontName','Whitney-Book');
ylabel('GPP(umol/m2/second)','FontSize',15,'FontName','Whitney-Book');
xlim_fig = xlim;
ylim_fig = ylim;
wdth = xlim_fig(2)-xlim_fig(1);
ht = ylim_fig(2)-ylim_fig(1);
pos = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.05*ht];
info = [num2str(gpp_doy(doy_i),'%d'),' ','R2=',num2str(rsq,' %4.2f'),' ','RMSE=',num2str(rmse,' %4.2f')];
text(pos(1),pos(2),info,'FontSize',20,'FontName','Whitney-Book');
pos2 = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.15*ht];
eq = ['GPP=' num2str(pp(2),'%6.4f') '+' num2str(pp(1),'%6.4f') '*SIF ' 'p=' num2str(pvalue,'%6.4f') ];
text(pos2(1),pos2(2),eq ,'FontSize',15,'FontName','Whitney-Book');
%=================
%Figure 3
fig3 = figure;
set(gcf,'PaperUnits','inches','PaperPosition',[0.25 0.25 10 6]);
set(fig3,'Visible','Off');
[AX,H1,H2] = plotyy(temp_time,temp_yield,temp_time,temp_gpp);
set(H1,'marker','O');
set(H2,'marker','O');
set(AX,'xlim',[0,24]);
set(AX(1),'box','off'); % Primary Y axis ticks only show on one side
set(get(AX(1),'Ylabel'),'String','SIFyield','FontSize',15,'FontName','Whitney-Book');
set(get(AX(2),'Ylabel'),'String','GPP(umol/m2/second)','FontSize',15,'FontName','Whitney-Book');
set(AX(1),'YLim',[0 0.001],'FontSize',12,'FontName','Whitney-Book');
set(AX(2),'YLim',[0 50],'FontSize',12,'FontName','Whitney-Book');
xlabel('Hours','FontSize',16,'FontName','Whitney-Book');
xlim_fig = xlim;
ylim_fig = ylim;
wdth = xlim_fig(2)-xlim_fig(1);
ht = ylim_fig(2)-ylim_fig(1);
pos = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.05*ht];
text(pos(1),pos(2),num2str(gpp_doy(doy_i)),'FontSize',20,'FontName','Whitney-Book');
%=================
%Figure 4
x0 = [20 1];
lb_mm = [-inf,-inf];
ub_mm = [inf,inf];
options = optimset('TolX',1e-10,'TolFun',1e-10,'Display','off');
[x,SSresid] = lsqcurvefit(@michaelis_menten,x0,temp_sif(temp_sif>0),temp_gpp(temp_sif>0),lb_mm,ub_mm,options);
SStotal = (length(temp_gpp(temp_sif>0))-1) * var(temp_gpp(temp_sif>0));
rsq1_total(doy_i) = 1 - SSresid/SStotal;
rmse1_total(doy_i) = (SSresid/(length(temp_gpp(temp_sif>0))))^(0.5);
fig4 = figure;
set(gcf,'PaperUnits','inches','PaperPosition',[0.25 0.25 10 6]);
set(fig4,'Visible','off');
start = min(temp_sif(temp_sif>0));
stop = max(temp_sif(temp_sif>0))+0.1*max(temp_sif(temp_sif>0)); %pad 10%
plot(temp_sif(temp_sif>0),temp_gpp(temp_sif>0),'ro',...
start:0.1:stop,michaelis_menten(x,transpose(start:0.1:stop)),'r-');
axis([0 3 0 50]);
xlabel('SIF(mw/sr/m2/nm)','FontSize',15,'FontName','Whitney-Book');
ylabel('GPP(umol/m2/second)','FontSize',15,'FontName','Whitney-Book');
xlim_fig = xlim;
ylim_fig = ylim;
wdth = xlim_fig(2)-xlim_fig(1);
ht = ylim_fig(2)-ylim_fig(1);
pos = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.05*ht];
info = [num2str(gpp_doy(doy_i),'%d'),' ','R2=',num2str(rsq1_total(doy_i),' %4.2f'),' ','RMSE=',num2str(rmse1_total(doy_i),' %4.2f')];
text(pos(1),pos(2),info,'FontSize',20,'FontName','Whitney-Book');
pos2 = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.15*ht];
eq = ['GPP=' num2str(x(1),'%6.4f') '*SIF/(' num2str(x(2),'%6.4f') '+SIF)'];
text(pos2(1),pos2(2),eq ,'FontSize',15,'FontName','Whitney-Book');
%==========================
%Figure 5
pp5 = polyfit(temp_yield(temp_sif>0),temp_gpp(temp_sif>0),1);
fitresult = linearfit(polyval(pp5,temp_yield(temp_sif>0)),temp_gpp(temp_sif>0));
rsq2 = fitresult(6);
pvalue2 = fitresult(7);
slope2 = fitresult(1);
intercept2 = fitresult(3);
rmse2 = fitresult(5);
rsq2_total(doy_i) = rsq2;
p2_total(doy_i) = pvalue2;
rmse2_total(doy_i) = rmse2;
fig5 = figure;
set(gcf,'PaperUnits','inches','PaperPosition',[0.25 0.25 10 6]);
set(fig5,'Visible','off');
start = min(temp_yield(temp_sif>0));
stop = max(temp_yield(temp_sif>0))+0.1*max(temp_yield(temp_sif>0));
plot(temp_yield(temp_sif>0),temp_gpp(temp_sif>0),'ro',...
start:0.0001:stop,polyval(pp5,start:0.0001:stop),'r-');
axis([0 0.001 0 50]);
xlabel('SIFyield','FontSize',15,'FontName','Whitney-Book');
ylabel('GPP(umol/m2/second)','FontSize',15,'FontName','Whitney-Book');
xlim_fig = xlim;
ylim_fig = ylim;
wdth = xlim_fig(2)-xlim_fig(1);
ht = ylim_fig(2)-ylim_fig(1);
pos = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.05*ht];
info = [num2str(gpp_doy(doy_i),'%d'),' ','R2=',num2str(rsq2,' %4.2f'),' ','RMSE=',num2str(rmse2,' %4.2f')];
text(pos(1),pos(2),info,'FontSize',20,'FontName','Whitney-Book');
pos2 = [xlim_fig(1)+0.02*wdth ylim_fig(2)-0.15*ht];
eq = ['GPP=' num2str(pp5(2),'%6.4f') '+' num2str(pp5(1),'%6.4f') '*SIFyield ' 'p=' num2str(pvalue2,'%6.4f') ];
text(pos2(1),pos2(2),eq ,'FontSize',15,'FontName','Whitney-Book');
%=================
fig_fp = fullfile(strcat('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\sif_gpp\',num2str(gpp_doy(doy_i)),'_f760_comp.jpg'));
fig2_fp = fullfile(strcat('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\sif_gpp_linear\',num2str(gpp_doy(doy_i)),'_f760_linear.jpg'));
fig3_fp = fullfile(strcat('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\sifyield\',num2str(gpp_doy(doy_i)),'_f760_yield.jpg'));
fig4_fp = fullfile(strcat('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\sif_gpp_mm\',num2str(gpp_doy(doy_i)),'_f760_mm.jpg'));
fig5_fp = fullfile(strcat('F:\01.ResearchProject\9.Fluorescence\4.JPG\gpp_0328\sifyield_linear\',num2str(gpp_doy(doy_i)),'_f760_yield_linear.jpg'));
saveas(fig,fig_fp);
close(fig);
saveas(fig2,fig2_fp);
close(fig2);
saveas(fig3,fig3_fp);
close(fig3);
saveas(fig4,fig4_fp);
close(fig4);
saveas(fig5,fig5_fp);
close(fig5);
end
[nelements,centers] = hist(rsq_total(~isnan(rsq_total)),10);
save('diurnal_figures.mat');
clearvars