run_MC_uncertainty_analysis.m

% function run_MC_uncertainty_analysis
clear;
%flags
printfig=0;
runCS=1;
runIM=1;
runMC=1;
savemat=0;
loadmat=1;
savematplot=0;
runplotMC=1;

if ispc
addpath Z:\Planar_Uncertainty_work\codes\export_fig_new\altmany-export_fig-5be2ca4\;
addpath Z:\Planar_Uncertainty_work\codes\color_code\;
else
addpath /home/shannon/a/bhattac3/Planar_Uncertainty_work/codes/export_fig_new/;
addpath /home/shannon/a/bhattac3/Planar_Uncertainty_work/codes/color_code/;
end

if ispc
    basedirname='Z:\Planar_Uncertainty_work\';
else
    basedirname='/home/shannon/a/bhattac3/Planar_Uncertainty_work/';
end

%cases
casename_org={'PivChal03B','PivChal05B','stagnation_flow','Vortex_Ring','Jetdata'};
% casename={'PivChal03B','','','',''};

% casename={'','PivChal05B','','',''};

% casename={'','','stagnation_flow','',''};

% casename={'','','','Vortex_Ring',''};

% casename={'','','','','Jetdata'};

% runname='10_14_2015_deform_whittaker_blackman';
% runname='10_22_2015_different_processing_windows';
% runname='03_09_2017/WS32';
% runname='03_09_2017\WS32';

% runname=['03_21_2017',filesep,'WS32'];
% % runname=['03_21_2017',filesep,'WS64'];

% runname=['07_31_2018',filesep,'WS64'];
runname=['07_31_2018',filesep,'WS32'];

%%
%Get directories
% [inputdir,outputdir]=in_out_directory_set(basedirname,runname);
% [inputdir,outputdir]=in_out_directory_set_10_22_2015(basedirname,runname);

% [inputdir,outputdir]=in_out_directory_set_03_09_2017(basedirname,runname);
% [inputdir,outputdir]=in_out_directory_set_03_09_2017_ws64(basedirname,runname);

% [inputdir,outputdir]=in_out_directory_set_07_30_2018_ws1(basedirname,runname);
[inputdir,outputdir]=in_out_directory_set_07_30_2018_ws2(basedirname,runname);
%%
casename1={'PivChal03B','PivChal05B','stagnation_flow','Vortex_Ring','Jetdata'};
% casename1={'','','','','Jetdata'};

% Compute error and uncertainty estimates for each case
% compute_error_uncertainty(casename1,inputdir,outputdir,savemat);

% keyboard;
%%
if runplotMC==1
casename={'PivChal03B','','','',''};
if loadmat==1
A1=load(fullfile(outputdir{1},'PivChal03B.mat'));
end
[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD]=plot_MC_uncertainty(A1,casename,outputdir,savematplot,printfig,runCS,runIM,runMC);
covg1=[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD];

casename={'','PivChal05B','','',''};
if loadmat==1
A2=load(fullfile(outputdir{1},'PivChal05B.mat'));
end
[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD]=plot_MC_uncertainty(A2,casename,outputdir,savematplot,printfig,runCS,runIM,runMC);
covg2=[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD];

casename={'','','stagnation_flow','',''};
if loadmat==1
A3=load(fullfile(outputdir{1},'stagnation_flow.mat'));
end
[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD]=plot_MC_uncertainty(A3,casename,outputdir,savematplot,printfig,runCS,runIM,runMC);
covg3=[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD];

casename={'','','','Vortex_Ring',''};
if loadmat==1
A4=load(fullfile(outputdir{1},'Vortex_Ring.mat'));
end
[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD]=plot_MC_uncertainty(A4,casename,outputdir,savematplot,printfig,runCS,runIM,runMC);
covg4=[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD];
% 
casename={'','','','','Jetdata'};
if loadmat==1
A5=load(fullfile(outputdir{1},'Jetdata.mat'));
end
[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD]=plot_MC_uncertainty(A5,casename,outputdir,savematplot,printfig,runCS,runIM,runMC);
covg5=[covxMC,covyMC,covxIM,covyIM,covxCS,covyCS,covP,covD];

close all;
end
% keyboard;
%%
% save([outputdir{1},filesep,'Coverage_03_18_2018_lowcutoff.mat'],'covg1','covg2','covg3','covg4','covg5');
% save([outputdir{1},filesep,'Coverage_07_30_2018_lowcutoff.mat'],'covg1','covg2','covg3','covg4','covg5');
%% Gradient analysis
% % clc;
% % outputdir1=fullfile(basedirname,'Results','final_plots',runname,'SOC_gradient','matfiles');
% % outputdir2=fullfile(basedirname,'Results','final_plots',runname,'New_gradient','matfiles');
% % % casename={'PivChal03B','','','',''};
% % for i=1:5
% % casename=casename_org{i};
% % if loadmat==1
% % A1=load(fullfile(outputdir1,[casename,'.mat']));
% % B1=load(fullfile(outputdir2,[casename,'.mat']));
% % end
% % 
% % diffx=A1.UMCx(:)-B1.UMCx(:);
% % diffy=A1.UMCy(:)-B1.UMCy(:);
% % lnx=find(abs(diffx)>=0.01);
% % lny=find(abs(diffy)>=0.01);
% % 
% % fprintf([casename,' \n ']);
% % fprintf('Difference in UMCx UMCy between SOCdiff and Richdiff: \n %d %d \n',[length(lnx),length(lny)]);
% % fprintf('Percent Difference in UMCx UMCy between SOCdiff and Richdiff: \n %f %f \n',[100*length(lnx)/length(diffx) 100*length(lny)/length(diffx)]);
% % [mean(diffx(lnx)) mean(diffy(lny))]
% % length(diffx)
% % 
% % Udiff1=A1.Udiff;
% % Vdiff1=A1.Vdiff;
% % L11=[length(find(abs(Udiff1)>0.05)) length(find(abs(Vdiff1)>0.05))];
% % Udiff2=B1.Udiff;
% % Vdiff2=B1.Vdiff;
% % L22=[length(find(abs(Udiff2)>0.05)) length(find(abs(Vdiff2)>0.05))];
% % 
% % fprintf('Udiff and Vdiff >0.05 SOCdiff: \n %d %d \n',L11);
% % fprintf('Udiff and Vdiff >0.05 Richdiff: \n %d %d \n',L22);
% % 
% % end
%%
%{
% printfig=1;
addpath Z:\Planar_Uncertainty_work\Results\final_plots\applyhatch_pluscolor_bundle\;
set(0,'DefaultAxesFontName', 'Times New Roman');
crimson=rgb('crimson');
dblue=rgb('deepskyblue');
blueviolet=rgb('blueviolet');
lw=1.5;fs=20;lw2=2.5;
% Plot uncertainty histograms
figure;hold on;
set(gcf,'DefaultLineLineWidth',lw);set(gca,'FontSize',fs);
bh=bar([covg1; covg2; covg3; covg4; covg5]);
set(bh(1),'Facecolor',crimson,'Edgecolor','k','LineWidth',lw2);set(bh(2),'Facecolor',crimson,'Edgecolor','k','LineStyle','--','LineWidth',lw2);
set(bh(3),'Facecolor',dblue,'Edgecolor','k','LineWidth',lw2);set(bh(4),'Facecolor',dblue,'Edgecolor','k','LineStyle','--','LineWidth',lw2);
set(bh(5),'Facecolor',blueviolet,'Edgecolor','k','LineWidth',lw2);set(bh(6),'Facecolor',blueviolet,'Edgecolor','k','LineStyle','--','LineWidth',lw2);
xl=xlim(gca);
plot(linspace(xl(1),xl(2),5),68.5.*ones(5,1),'k--');
hold off;
set(gca,'XTick',[1 2 3 4 5])
set(gca,'XTickLabel',casename_org);
box on;
set(gcf,'color','white');
set(gcf,'units','normalized','outerposition',[0 0 0.8 0.8]);
ylabel('Coverage (%)');
title('Standard Uncertainty Coverage');
legend('MC_x','MC_y','PD_x','PD_y','CS_x','CS_y','orientation','horizontal');
% applyhatch_pluscolor(gcf,'./././././././././././././././',1,360);
if printfig==1
    export_fig(gcf,fullfile(outputdir{2},'coverage_plot.png'),'-painters','-r360');
end

% Plot the uncertainty histograms
% plot_MC_uncertainty(A,casename,outputdir,printfig,runCS,runIM,runMC);
%}

%Spatial uncertainties


%Uncertainty Timeseries




% end