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%

%   TopoSurfArea differences for juw_el_table // All participants

%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Topography analysis

% Author: Julius Welzel // University of Oldenburg, 2019

% Version: 1.0 // 28.02.2019 // Initial setup

% define paths

PATHIN_ERD =  [MAIN '04_Data\ana04_erd\'];

PATHIN_RT = [MAIN '04_Data\'];

PATHIN_EMG = [MAIN '04_Data\ana03_emg\'];

PATHOUT_TOPODIFF = [MAIN '04_Data\ana07_TOPOdiff\'];

setGlobal(PATHOUT_TOPODIFF);

if ~exist(PATHOUT_TOPODIFF)

  mkdir(PATHOUT_TOPODIFF);

end 

list = dir(fullfile([PATHIN_RT 'ana02_clean\*clean*.set']));

SUBJ = extractBefore({list.name},'_');

load([PATHIN_ERD 'ERD_mue.mat']);

load([PATHIN_ERD 'cfg_mue.mat']);

load([PATHIN_EMG 'emg_all.mat']);

% define trails of interest

ME_trials = [cfg.blck_idx{[1 4],1}];

MI_trials = [cfg.blck_idx{[2 3],1}];

SUBJ = str2double(SUBJ);

old = (SUBJ>=80);

young = (SUBJ<80);

%% Zscore data over all participants only for MI trials

z_top = zscore(nanmean(m_rERD_trial,3),[],1);

top_old = mean(z_top(old,:));

top_young = mean(z_top(young,:));

%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%

%                   Extract surface area

%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%

p_interp = 100; % points to interpolate

% get cartesian coordinates by MIKE X COHEN :D and grid data

[elocsX,elocsY] = pol2cart(pi/180*[cfg.chanlocs.theta],[cfg.chanlocs.radius]);

elocsX = elocsX*-1; %swap left/ right

xlin = linspace(min(elocsX),max(elocsX),p_interp);

ylin = linspace(min(elocsY),max(elocsY),p_interp);

[Xgrid, Ygrid] = meshgrid(xlin,ylin);

%% calculate surface area  of topoplot for each trial

%{

surf_old = {};

surf_young = {};

for s = find(young)

    disp(['SUBJ: ' num2str(SUBJ(s))])

   for t = MI_trials

       topo = zscore((m_rERD_trial(s,:,t)));

       surf_st = griddata(elocsX,elocsY,topo,Xgrid,Ygrid,'cubic');

       top_thresh = min(min(topo))*0.5;

       surf_st(surf_st>top_thresh) = NaN;

       surf_young{end+1} = SurfArea(surf_st,Xgrid,Ygrid);

   end

end

for s = find(old)

    disp(['SUBJ: ' num2str(SUBJ(s))])

   for t = MI_trials

       topo = zscore((m_rERD_trial(s,:,t)));

       surf_st = griddata(elocsX,elocsY,topo,Xgrid,Ygrid,'cubic');

       top_thresh = min(min(topo))*0.5;

       surf_st(surf_st>top_thresh) = NaN;

       surf_old{end+1} = SurfArea(surf_st,Xgrid,Ygrid);

   end

end

%}

%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%

%                   3D topographies of ERD maps

%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Plot topographie interpolated with surface area scatter

figure

ax1 = subplot(2,4,[1 2]);

Z_young = griddata(elocsX,elocsY,top_young,Xgrid,Ygrid,'cubic');

mesh(Xgrid,Ygrid,Z_young) % interpolate

colormap(ax1,c_young_map)

axis tight;hold on;

plot3(elocsX,elocsY,top_young,'.k','MarkerSize',15)

title 'Interpolated Topoplot Young'

hold on

surf(Xgrid,Ygrid,min(min(Z_young))*0.5*ones(size(Z_young)),'FaceAlpha',0.5,'EdgeColor','none')

stlwrite('mod_young3D.stl',Xgrid,Ygrid,Z_young*0.2,'FaceColor',c_young) 

ax2 = subplot(2,4,[5 6]);

Z_old = griddata(elocsX,elocsY,top_old,Xgrid,Ygrid,'cubic');

mesh(Xgrid,Ygrid,Z_old) % interpolate

colormap(ax2,c_old_map)

axis tight;hold on;

plot3(elocsX,elocsY,top_old,'.k','MarkerSize',15)

title 'Interpolated Topoplot Old'

hold on

surf(Xgrid,Ygrid,min(min(Z_old))*0.5*ones(size(Z_old)),'FaceAlpha',0.5,'EdgeColor','none')

stlwrite('mod_old3D.stl',Xgrid,Ygrid,Z_old*0.2,'FaceColor',c_old*255) 

x_values = linspace(0,3,length(surf_old));

subplot(2,4,[3 4 7 8])

pd = fitdist([surf_old{:}]','normal');

y = pdf(pd,x_values);

p1 = plot(x_values,y,'Color',c_old,'LineWidth',2);

hold on

scatter([surf_old{:}],x_values,2,c_old)

hold on

pd = fitdist([surf_young{:}]','normal');

y = pdf(pd,x_values);

p2 = plot(x_values,y,'Color',c_young,'LineWidth',2);

hold on

scatter([surf_young{:}],x_values,2,c_young)

legend([p1 p2],{'OLD','YOUNG'})

title ({'Surface Area of highest 50% ERD','All trials each group'})

% save_fig(gcf,PATHOUT_TOPODIFF,'surf_area_ERD_st','fontsize',15,'figsize',[0 0 35 25]);

%% only 3D topoplots over both groups with topoplot

c_lines = 10;

figure;

ax1 = subplot(1,2,1);

Z_young = griddata(elocsX,elocsY,mean(z_top(young,:)),Xgrid,Ygrid,'cubic');

mesh(Xgrid,Ygrid,Z_young) % interpolate

colormap(ax1,c_map)

axis tight;hold on;    

plot3(elocsX,elocsY,mean(z_top(young,:)),'.k','MarkerSize',15) %plot electrodes

title '3D Topoplot Young'

zlabel 'z-Score'

set(gca,'YTickLabel',[]);

set(gca,'XTickLabel',[]);

hold on

%intersect lines

surf(Xgrid,Ygrid,0*ones(size(Z_young)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')

%topoplot

[~,h] = contourf(Xgrid,Ygrid,Z_young,c_lines);       %# get handle to contourgroup object

colormap (ax1,c_map)

%# change the ZData property of the inner patches

h.ContourZLevel = 1.1*min(min(Z_young));

% OLD 3D PLOT

ax2 = subplot(1,2,2);

Z_old = griddata(elocsX,elocsY,mean(z_top(old,:)),Xgrid,Ygrid,'cubic');

mesh(Xgrid,Ygrid,Z_old) % interpolate

colormap(ax2,c_map)

axis tight;hold on;

plot3(elocsX,elocsY,mean(z_top(old,:)),'.k','MarkerSize',15)

title '3D Topolot Old'

zlabel 'z-Score'

set(gca,'YTickLabel',[]);

set(gca,'XTickLabel',[]);

hold on

%intetsect planes

surf(Xgrid,Ygrid,0*ones(size(Z_old)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')

hold on

%topoplot

[~,h] = contourf(Xgrid,Ygrid,Z_old,c_lines);       %# get handle to contourgroup object

colormap (ax1,c_map)

%# change the ZData property of the inner patches

h.ContourZLevel = 1.1*min(min(Z_old));

% save_fig(gcf,PATHOUT_TOPODIFF,'3D_tops','figtype','.fig')

%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%

%                  Calculate area of intersection

%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%{

gd(1).Z= griddata(elocsX,elocsY,mean(z_top(young,:)),Xgrid,Ygrid,'cubic'); %young

gd(2).Z = griddata(elocsX,elocsY,mean(z_top(old,:)),Xgrid,Ygrid,'cubic'); %old

group = {'Young','Old'};

plane_sect = linspace(0,-1.2,6);

for g = 1:length(gd)

    figure

    for i = 1:length(plane_sect)

        subplot(2,3,i)

        mesh(Xgrid,Ygrid,gd(g).Z) % interpolate

        hold on

        surf(Xgrid,Ygrid,plane_sect(i)*ones(size(gd(g).Z)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')

        hold on

        % Take the difference between the two surface heights and find the contour

        % where that surface is zero.

        zdiff = gd(g).Z - (plane_sect(i)*ones(size(gd(g).Z)));

        C = contour(Xgrid, Ygrid, zdiff,[0,0]);

        [a, ca] = cont_area(C,Xgrid,Ygrid,gd(g).Z);

        % Visualize the line.

        cl = line(ca.xL, ca.yL, ca.zL, 'Color', 'k', 'LineWidth', 3);

        title(['Area : ' num2str(a) ' at z = ' num2str(plane_sect(i))])

    end

    sgtitle ([group{g} ' participants'])

    save_fig(gcf,PATHOUT_TOPODIFF,['SurfArea_' group{g}],'figtype','.fig')

end

%}

maps_st = zscore(nanmean(m_rERD_trial,3),[],1);

for s = 1:length(SUBJ)

    if SUBJ(s)<50;c_map = c_y_map;else;c_map = c_o_map;end;

    area_z_t_avg(s,:) = inter_area(cfg.chanlocs,maps_st(s,:),24,SUBJ(s),PATHOUT_TOPODIFF,c_map);

end

[m_a_old se_a_old] = mean_SEM(area_z_t_avg(old,:)');

[m_a_young se_a_young] = mean_SEM(area_z_t_avg(young,:)');

AO = shadedErrorBar(1:24,m_a_old,se_a_old,'lineprops',{'-','Color',c_old,'LineWidth',2})

hold on

AY = shadedErrorBar(1:24,m_a_young,se_a_young,'lineprops',{'-','Color',c_young,'LineWidth',2})