function ellipsePlot(rc_struct,sub_idx,rc_num,cond_colors,cond_labels,gca_opts,e_max,f_1,plot_ave)

l_width = 1.5;

if nargin < 9

plot_ave = true;

end

if nargin < 8

f_1 = 1;

else

end

if nargin < 7

e_max = [];

else

end

if nargin < 6

gca_opts = {'tickdir','out','box','off','fontsize',12,'fontname','Helvetica','linewidth',l_width,'Color','none'};

else

end

n_conds = size(rc_struct.data,1);

n_subs = size(rc_struct.data,2);

if nargin < 5

cond_labels = arrayfun(@(x) sprintf('cond%01d', x), 1:n_conds, 'uni', false);

end

if nargin < 4

c_brewer = load('colorBrewer_new.mat');

cond_colors = c_brewer.rgb20(1:2:end,:);

cond_colors([2,3],:) = cond_colors([3,2],:);

else

end

[raw_real,raw_imag] = getRealImag(rc_struct.data);

[comp_real,comp_imag] = getRealImag(rc_struct.comparisonData);

raw_real = cellfun(@(x,y) cat(2,x,y), raw_real,comp_real,'uni',false);

raw_imag = cellfun(@(x,y) cat(2,x,y), raw_imag,comp_imag,'uni',false);

if nargin < 3

rc_num = 1;

else

end

if plot_ave

n_bins = size(raw_real{1},1)+1;

else

n_bins = size(raw_real{1},1);

end

if nargin < 2

sub_idx = true(1,n_subs);

else

end

% loop over rc

rc_count = size(raw_real{1},2); % rc and comparison

for r = 1:rc_count

rca_real = cellfun(@(x) squeeze(nanmean(x(:,r,:),3)),raw_real,'uni',false);

rca_real = cell2mat(permute(rca_real,[3,2,1]));

rca_imag = cellfun(@(x) squeeze(nanmean(x(:,r,:),3)),raw_imag,'uni',false);

rca_imag = cell2mat(permute(rca_imag,[3,2,1]));

rca_real(end+1,:,:) = squeeze(nanmean(rca_real));

rca_imag(end+1,:,:) = squeeze(nanmean(rca_imag));

rca_real = permute(rca_real,[2,3,1]);

rca_imag = permute(rca_imag,[2,3,1]);

for b = 1:n_bins

for c = 1:n_conds

xy_vals = cat(2,rca_real(sub_idx,c,b),rca_imag(sub_idx,c,b));

nan_vals = sum(isnan(xy_vals),2)>0;

[ampDiff,phaseDiff,~,error_ellipse] = fitErrorEllipse(xy_vals(~nan_vals,:),'1STD');

ellipse_data(b,c,r).ellipse = error_ellipse;

ellipse_data(b,c,r).means = nanmean(xy_vals);

ellipse_data(b,c,r).phaseDiff = phaseDiff;

ellipse_data(b,c,r).ampDiff = ampDiff;

if b == n_bins && c == 1

[ampDiff,phaseDiff,~,error_ellipse] = fitErrorEllipse(xy_vals(~nan_vals,:),'1STD',true);

else

end

end

end

clear rca_real; clear rca_imag;

end

close all;

for r = 1:length(rc_num)

ellipse_fig = figure;

set(ellipse_fig,'units','centimeters');

fig_pos = get(gcf,'pos');

fig_pos(3) = 35;

fig_pos(4) = 20;

set(ellipse_fig,'pos',fig_pos);

bin_vals = cell2mat(cellfun(@(x) str2num(x),rc_struct.settings.binLabels,'uni',false));

if isnan(bin_vals(1))

log_step = 1;

bin_vals = (1:length(bin_vals))';

bin_text = arrayfun(@(x) num2str(x,'%.0f'),bin_vals,'uni',false);

x_min = 0.5;

if plot_ave

bin_text = [bin_text; 'ave'];

x_max = length(bin_vals)+2.5;

extra_bins = arrayfun(@(x) length(bin_vals)+x, [1,2]);

else

x_max = length(bin_vals)+.5;

extra_bins = [];

end

else

bin_text = arrayfun(@(x) num2str(x,'%.1f'),bin_vals,'uni',false);

log_step = diff(reallog(bin_vals(1:2))); % step size

x_min = reallog(bin_vals(1))-log_step*.5;

if plot_ave

bin_text = [bin_text; 'ave'];

x_max = reallog(bin_vals(end))+log_step*2.5; % add 2.5 steps

extra_bins = arrayfun(@(x) reallog(bin_vals(end))+x, [log_step,log_step*2]);

else

x_max = reallog(bin_vals(end))+log_step*.5; % add 2.5 steps

extra_bins = [];

end

bin_vals = reallog(bin_vals);

end

for b = 1:n_bins

if b == 1

e_max = 1+ceil(max(max(abs(cat(1,ellipse_data(:,:,rc_num(r)).means))))*.75);

if e_max == 0

e_max = 1;

else

end

else

end

if e_max > 1

e_units = 1;

else

e_units = .5;

end

s_h(b) = subplot(2,n_bins,n_bins+b);

hold on;

grid_h(1) = plot(zeros(1,2),[-e_max,e_max*.75],'k-','linewidth',l_width);

grid_h(2) = plot([-e_max,e_max],zeros(1,2),'k-','linewidth',l_width);

for c = 1:n_conds

cur_means = ellipse_data(b,c,rc_num(r)).means;

cur_ellipse = ellipse_data(b,c,rc_num(r)).ellipse;

temp_data = [cur_ellipse;cur_means];

temp_phase = angle(complex(temp_data(:,1),temp_data(:,2)));

temp_amp = abs(complex(temp_data(:,1),temp_data(:,2)));

cycle_len = 1000/(f_1*str2num(rc_struct.settings.freqLabels{1}(1)));

delay_ms = 180;

delay_rad = 180/cycle_len*2*pi;

plot_offset = pi/2;

temp_phase = temp_phase+delay_rad+plot_offset;

temp_complex = temp_amp.*exp(1i*temp_phase);

temp_data = [real(temp_complex),imag(temp_complex)];

cur_ellipse = temp_data(1:end-1,:);

cur_means = temp_data(end,:);

ellipse_data(b,c,rc_num(r)).means = cur_means;

ellipse_data(b,c,rc_num(r)).ellipse = cur_ellipse;

p_h(c) = plot([0 cur_means(1)],[0 cur_means(2)],'-','linewidth',l_width,'Color',cond_colors(c,:));

plot(cur_ellipse(:,1), cur_ellipse(:,2),'-','linewidth',l_width,'Color',cond_colors(c,:));

end

text(0,e_max,bin_text(b),'fontsize',12,'fontname','Helvetica','horizontalalignment','center');

xlim([-e_max,e_max]);

ylim([-e_max,e_max]);

axis square;

if b == 1

cycle_steps = linspace(0,2*pi-(pi/2),200)+plot_offset;

[cycle_x,cycle_y] = pol2cart(cycle_steps,e_max*.75);

pa_h = patch([e_max*.4,e_max*.8,e_max*.8,e_max*.4],[-e_max+.1 -e_max+.1 -.1 -.1],ones(1,3),'edgecolor','none');

uistack(pa_h,'bottom');

q_h = quiver(cycle_x(end),cycle_y(end)-e_max*.4,0,e_max*.8,50);

set(q_h,'AutoScale','off','maxheadsize',20,'color',[200,200,200]./255,'linewidth',l_width)

uistack(q_h,'bottom');

arrayfun(@(x) uistack(x,'bottom'),grid_h);

cycle_h = plot(cycle_x,cycle_y,'-','color',[200,200,200]./255,'linewidth',l_width);

uistack(cycle_h,'top');

set(gca,gca_opts{:},'ticklength',[0.03,0.03],'clipping','off','visible','on','xtick',-e_max:e_units:e_max,'ytick',-e_max:e_units:e_max);

text(-e_max*.75,-e_max*.75,num2str(cycle_len,'%d ms'));

xlabel('real','fontsize',12,'fontname','Helvetica');

ylabel('imag','fontsize',12,'fontname','Helvetica');

else

set(gca,gca_opts{:},'clipping','off','visible','off');

if b == 6

text(0,e_max*1.2,'displacement (arcmins)','fontsize',12,'fontname','Helvetica','horizontalalignment','center');

else

end

end

hold off

end

drawnow;

for b = 1:n_bins

sub_pos = get(s_h(b),'position');

sub_pos([3,4]) = sub_pos([3,4])+sub_pos(3)*1.8;

if b == 1

sub_pos(1) = sub_pos(1)-sub_pos(3)*.5;

old_pos = sub_pos;

x_plotmin = sub_pos(1);

else

sub_pos(1) = old_pos(1)+old_pos(3)/2;

old_pos = sub_pos;

if b == n_bins

x_plotmax = sub_pos(1)+sub_pos(3);

else

end

end

set(s_h(b),'position',sub_pos);

end

for z = 1:2

for c = 1:n_conds

if z == 1

% plot amplitudes

big_plot(z) = subplot(2,n_bins,1:floor(n_bins/2));

big_min = 0; big_max = 10; %ceil(max(max(squeeze(rc_struct.mean.amp_signal(:,:,rc_num(r))))));

plot_vals = rc_struct.mean.amp_signal(1:n_bins,:,rc_num(r),c)';

plot_errs = cat(1,ellipse_data(1:n_bins,c,rc_num(r)).ampDiff)';

y_text = 'amplitude (\muV)';

else

% plot phase

big_plot(z) = subplot(2,n_bins,(floor(n_bins/2)+1):n_bins);

big_min = 0; big_max = 1/f_1 * 1000;

temp_means = cat(1,ellipse_data(:,c,rc_num(r)).means);

temp_phases = angle(complex(temp_means(:,1),temp_means(:,2)))-(plot_offset);

temp_phases( temp_phases < 0 ) = 2*pi+temp_phases( temp_phases < 0 );

plot_vals = (temp_phases/(2*pi)*cycle_len)';

ph_error = cat(1,ellipse_data(1:n_bins,c,rc_num(r)).phaseDiff);

ph_error = ph_error .* pi / 180;

plot_errs = (ph_error ./(2*pi)*cycle_len)';

y_text = 'delay (ms)';

end

hold on

if c > 2

cur_x = [bin_vals', extra_bins(2)];

else

cur_x = [bin_vals', extra_bins(1)];

end

if plot_ave

if c == 1

plot(ones(1,2)*(bin_vals(end)+log_step*.5) ...

,[big_min,big_max],'k-','linewidth',l_width);

else

end

p_h(c) = plot(cur_x(1:end-1),plot_vals(1:end-1),'-o','linewidth',l_width,'Color',cond_colors(c,:),'markersize',10,'markerfacecolor','w','markeredgecolor',cond_colors(c,:));

plot(cur_x(end),plot_vals(end),'o','linewidth',l_width,'Color',cond_colors(c,:),'markersize',10,'markerfacecolor','w','markeredgecolor',cond_colors(c,:));

else

plot(cur_x,plot_vals,'-o','linewidth',l_width,'Color',cond_colors(c,:),'markersize',10,'markerfacecolor','w','markeredgecolor',cond_colors(c,:));

end

hold on

h_e(c,:) = ErrorBars(cur_x,plot_vals,plot_errs,'type','bar','color',cond_colors(c,:),'cap',false);

hold on

end

if z == 1

legend(p_h,cond_labels,'location','northwest','box','off','fontsize',12,'fontname','Helvetica');

end

cellfun(@(x) uistack(x,'bottom'),h_e,'uni',false);

xlim([x_min,x_max]);

ylim([big_min,big_max]);

if isnan(bin_vals(1))

xtick_vals = reallog([0.2,0.5,1,2,4,8,16]);

xtick_labels = arrayfun(@(x) num2str(x),([0.2,0.5,1,2,4,8,16]),'uni',false);

if plot_ave

xtick_vals = [xtick_vals,xtick_vals(end) + log_step*1.5];

xtick_labels = [xtick_labels,'ave'];

else

end

else

xtick_vals = 1:length(bin_vals)+1;

xtick_labels = bin_text;

end

set(gca,gca_opts{:},'ticklength',[0.015,0.015],'clipping','off','visible','on','xtick',xtick_vals,'xticklabels',xtick_labels);

ylabel(y_text,'fontsize',12,'fontname','Helvetica');

hold off

end

drawnow;

amp_pos = get(big_plot(1),'position');

plot_span = (x_plotmax - x_plotmin);

amp_pos(1) = x_plotmin;

amp_pos(3) = plot_span/2-plot_span/40;

set(big_plot(1),'position',amp_pos);

ph_pos = get(big_plot(2),'position');

ph_pos(3) = plot_span/2-plot_span/40;

ph_pos(1) = x_plotmax-ph_pos(3);

set(big_plot(2),'position',ph_pos);

if rc_num(r) == rc_count

export_fig(ellipse_fig,'ellipseplot_comp.pdf','-transparent','-painters');

else

export_fig(ellipse_fig,sprintf('ellipseplot_rc%d.pdf',rc_num(r)),'-transparent','-painters');

end

end