mydefaultfonts; 
close all; clear all;


%name_dataset = 'MAX_Maph-1_lifeact_w2_crop-2_t=01';
name_dataset = 'MAX_Maph-1_lifeact_w2_crop-2_t=36';
%name_dataset = 'MAX_Maph-1_lifeact_w3_crop-2_t=01';
%name_dataset = 'MAX_Maph-1_lifeact_w3_crop-2_t=29';
%name_dataset = 'MAX_Maph-1_lifeact_w6_crop-2_t=18';
%name_dataset  = 'MAX_Maph-1_lifeact_w6_crop-2_t=01';

Dat = xlsread(['Data/Table_' name_dataset '.xlsx']);

if(strcmp(name_dataset,'MAX_Maph-1_lifeact_w3_crop-2_t=29')==1)
    xhole = 89; yhole = 126;
    
    radius_internal   = 15;
    radius_external   = 28;
    
    radius_external_2 = 25;
    radius_external_3 = 40;
    filter_on         = 3;
    
    coherence_threshold = 0.10;
    
elseif(strcmp(name_dataset,'MAX_Maph-1_lifeact_w3_crop-2_t=01')==1)
    xhole = 89; yhole = 126;
    
    radius_internal   = 10;
    radius_external   = 18;
    
    radius_external_2 = 25;
    radius_external_3 = 50;
    
    filter_on         = 0;
    
    coherence_threshold = 0.10;
     
elseif(strcmp(name_dataset,'MAX_Maph-1_lifeact_w6_crop-2_t=18')==1)
    xhole = 110; yhole = 122;
    
    radius_internal   = 8;
    radius_external   = 20;
    
    radius_external_2 = 25;
    radius_external_3 = 50;
    filter_on         = 0;
    
    coherence_threshold = 0.30;
    
elseif(strcmp(name_dataset,'MAX_Maph-1_lifeact_w6_crop-2_t=01')==1)
    xhole = 110; yhole = 122;
    
    radius_internal   = 8;
    radius_external   = 20;
    
    radius_external_2 = 25;
    radius_external_3 = 50;
    filter_on         = 0;
    
    coherence_threshold = 0.30;
    
elseif(strcmp(name_dataset,'MAX_Maph-1_lifeact_w2_crop-2_t=36')==1)
    xhole = 112; yhole = 93;

    radius_internal   = 15;
    radius_external   = 30;
    radius_external_2 = 40;
    radius_external_3 = 50;
    
    filter_on         = 3;
    
    coherence_threshold = 0.1;
elseif(strcmp(name_dataset,'MAX_Maph-1_lifeact_w2_crop-2_t=01')==1)
    xhole = 112; yhole = 93;

    radius_internal   = 15;
    radius_external   = 30;
    radius_external_2 = 40;
    radius_external_3 = 50;
    
    filter_on         = 0;
    
    coherence_threshold = 0;
end


fiber_orientation = atan2(Dat(:,5),Dat(:,4));
theta_orientation = atan2(Dat(:,2) - yhole,Dat(:,1) - xhole);
%diff_theta        = fiber_orientation-theta_orientation;
dot_product       = abs(Dat(:,4).*(Dat(:,1) - xhole)+Dat(:,5).*(Dat(:,2) - yhole));
nor_product       = sqrt(power(Dat(:,5),2)+power(Dat(:,4),2)).*sqrt(power(Dat(:,1) - xhole,2)+power(Dat(:,2) - yhole,2));
diff_theta        = acos(dot_product./nor_product);
proj              = @(x) x; 
%proj              = @(x) mod(x,pi./2); 


index_other = find(Dat(:,7)- coherence_threshold > 0);
if(filter_on==1)
    index_other = intersect(index_other,find(Dat(:,1)-xhole > 0));
elseif(filter_on==2)
    index_other = intersect(index_other,find(Dat(:,1)-xhole < 0));
elseif(filter_on==3)
    index_other = intersect(index_other,find(Dat(:,2)-yhole > 0));
end


% Filters all points which are closer to center of whole than threshold
distance_to_ablation_site = sqrt(power(Dat(:,1)-xhole,2)+power(Dat(:,2)-yhole,2));
index_nottoofar = find(distance_to_ablation_site < radius_external);
index_nottooclose = find(distance_to_ablation_site > radius_internal);
good_indices_1  = intersect(index_nottoofar,index_nottooclose);
good_indices_1  = intersect(index_other,good_indices_1);

index_nottoofar   = find(distance_to_ablation_site < radius_external_3);
index_nottooclose = find(distance_to_ablation_site > radius_external_2);
good_indices_2  = intersect(index_nottoofar,index_nottooclose);
good_indices_2  = intersect(index_other,good_indices_2);

good_indices_3  = find(distance_to_ablation_site > 1*radius_external_3);
good_indices_3  = intersect(index_other,good_indices_3);









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

I = imread(['Data/' name_dataset '.tif']);
h12          = figure('PaperPositionMode','auto');
set(h12, 'Visible', 'on');
hold on; hold all;
screen_dpi   = get(0, 'ScreenPixelsPerInch'); screen_display_factor = 500; 
h1           = imshow(I,[],'InitialMagnification',screen_display_factor,'Border','tight');
h1.AlphaData = 0.6;
colormap('gray');
theta = linspace(0,2*pi,50);
line(xhole + 1.*cos(theta),yhole + 1.*sin(theta),'color',[1 1 1],'LineWidth', 5);

line(xhole + radius_internal.*cos(theta),yhole + radius_internal.*sin(theta),'color',[0 0 1],'LineWidth', 1);
line(xhole + radius_external.*cos(theta),yhole + radius_external.*sin(theta),'color',[0 0 1],'LineWidth', 1);

line(xhole + radius_external_2.*cos(theta),yhole + radius_external_2.*sin(theta),'color',[1 0 0],'LineWidth', 1);
line(xhole + radius_external_3.*cos(theta),yhole + radius_external_3.*sin(theta),'color',[1 0 0],'LineWidth', 1);

for iv=1:length(good_indices_1)
    ix = good_indices_1(iv);
    line([Dat(ix,1)-5.*Dat(ix,4) Dat(ix,1)+5.*Dat(ix,4)],[Dat(ix,2)-5.*Dat(ix,5) Dat(ix,2)+5.*Dat(ix,5)],'color',[0 0 1],'LineWidth',2,'MarkerFaceColor',[0 0 1]); 
end

%remove_assholes = find(diff_theta > pi./4);
%good_indices_2 = intersect(good_indices_2,remove_assholes);
for iv=1:length(good_indices_2)
    ix = good_indices_2(iv);
    line([Dat(ix,1)-5.*Dat(ix,4) Dat(ix,1)+5.*Dat(ix,4)],[Dat(ix,2)-5.*Dat(ix,5) Dat(ix,2)+5.*Dat(ix,5)],'color',[1 0 0],'LineWidth',2,'MarkerFaceColor',[1 0 0]); 
end

for iv=1:length(good_indices_3)
    ix = good_indices_3(iv);
    line([Dat(ix,1)-5.*Dat(ix,4) Dat(ix,1)+5.*Dat(ix,4)],[Dat(ix,2)-5.*Dat(ix,5) Dat(ix,2)+5.*Dat(ix,5)],'color',[0 1 0],'LineWidth',2,'MarkerFaceColor',[0 1 0]); 
end

%for ix=1:length(Dat(:,1))
%   line([Dat(ix,1)-5.*Dat(ix,4) Dat(ix,1)+5.*Dat(ix,4)],[Dat(ix,2)-5.*Dat(ix,5) Dat(ix,2)+5.*Dat(ix,5)],'color',[0.5 0 0],'LineWidth',0.5,'MarkerFaceColor',[0.5 0 0]); 
%end

axis equal;
axis tight;
saveas(h12,['Results/' name_dataset 'rawimage.tiff'])
  








Fig1 = figure(6);
set(Fig1, 'Name', 'Histogram of Angle', 'Position', [100 500 600 400]);
%polarhistogram(pi.*vec./180,2,'FaceColor','red','FaceAlpha',.3);
polarhistogram(proj(diff_theta(good_indices_1)),5);
%rose(pi.*vec2./180,30);
set(gca, 'FontSize', 30);
ax = gca; 
ax.ThetaLim = [0 90];
saveas(Fig1, ['Results/' name_dataset 'angle.svg']);
saveas(Fig1, ['Results/' name_dataset 'angle.fig']);
saveas(Fig1, ['Results/' name_dataset 'angle.png']);



Fig1 = figure(8);
set(Fig1, 'Name', 'Histogram of Angle', 'Position', [100 500 600 400]);
%polarhistogram(pi.*vec./180,2,'FaceColor','red','FaceAlpha',.3);
polarhistogram(proj(diff_theta(good_indices_2)),10,'FaceColor','red','FaceAlpha',.3);
%rose(pi.*vec2./180,30);
set(gca, 'FontSize', 30);
ax = gca; 
ax.ThetaLim = [0 90];
saveas(Fig1, ['Results/' name_dataset 'angle_externallayer.svg']);
saveas(Fig1, ['Results/' name_dataset 'angle_externallayer.fig']);
saveas(Fig1, ['Results/' name_dataset 'angle_externallayer.png']);



Fig1 = figure(9);
set(Fig1, 'Name', 'Histogram of Angle', 'Position', [100 500 600 400]);
%polarhistogram(pi.*vec./180,2,'FaceColor','red','FaceAlpha',.3);
polarhistogram(proj(diff_theta(good_indices_3)),10,'FaceColor','green','FaceAlpha',.3);
%rose(pi.*vec2./180,30);
set(gca, 'FontSize', 30);
ax = gca; 
ax.ThetaLim = [0 90];
saveas(Fig1, ['Results/' name_dataset 'angle_control.svg']);
saveas(Fig1, ['Results/' name_dataset 'angle_control.fig']);
saveas(Fig1, ['Results/' name_dataset 'angle_control.png']);





data_1 = 90.*proj(diff_theta(good_indices_1))./(pi./2);
data_2 = 90.*proj(diff_theta(good_indices_2))./(pi./2);
data_3 = 90.*proj(diff_theta(good_indices_3))./(pi./2);

g1 = repmat({'Region 1'},length(data_1),1);
g2 = repmat({'Region 2'},length(data_2),1);
g3 = repmat({'Region 3'},length(data_3),1);
g = [g1; g2; g3];

total = [data_1',data_2' data_3'];

fig1 = figure(100);
h = boxplot(total,g,'PlotStyle','traditional','Whisker', 0);
ylabel('Angle');
ylim([0 90]);
saveas(fig1, ['Results/' name_dataset 'angle_histo.svg']);
saveas(fig1, ['Results/' name_dataset 'angle_histo.fig']);
saveas(fig1, ['Results/' name_dataset 'angle_histo.png']);


save(['Data/workspace/' name_dataset]);