% Cartoon of the experimental setup used in scanning SAXS tensor tomography
% (SSTT). Data with thanks from the group of Marianne Liebi, Swiss Light
% Source. 

clear
close all
figure('units','pixels','position',[0 0 1920 1080],'ToolBar','none');
set(0,'defaultfigurecolor',[1 1 1]);

vid = VideoWriter('ssttCartoon.mp4','MPEG-4');
vid.Quality = 100;
vid.FrameRate = 30;
open(vid);

midGrey = [0.5 0.5 0.5];
boneYellow = [224 221 214]/255;
myGold = [0.8 0.64 0];
lp = [-2 -2 1];
pos1 = [-0.1 -0.1 1.2 1.2];

% Dimensions in matlab units
incRadLength = 14; % Distance upstream to which incident radiation extends
FZPpos = -2; % Position upstream of FZP relative to focus @ (0,0,0)
samplePos = 0.0; % Position of sample downstream of focus
DetPos = 20; % Position of detector downstream
halfDetWidth = 4; % Half width of detector
sampleHt = 4.0; % Height of sample
basePlateRad = 2.8; 
imax = 10; % Determines outer radius of FZP

[x,y,z] = sphere(100);
aa = 0;
bb = 0.64;
cc = 5; 
% Add roughness to vertices of sphere vertex coordinates to render the bone
% surface to be rough - adds a touch of verisimilitude 
varx = 0.02*(rand(size(x)) - 0.5); 
vary = 0.02*(rand(size(y)) - 0.5);
varz = 0.02*(rand(size(z)) - 0.5);
x = x + varx; 
y = y + vary; 
z = z + varz; 

t = -3.5:0.1:3.5;
tt = (t.^2 + 20)/32;
[x2,y2,z2] = cylinder(tt,200);
% Add roughness to vertices of cylinder vertex coordinates to render the 
% bone surface to be rough - adds a touch of verisimilitude 
varx = 0.01*(rand(size(x2)) - 0.5); 
vary = 0.01*(rand(size(y2)) - 0.5);
varz = 0.01*(rand(size(z2)) - 0.5);
x2 = x2 + varx; 
y2 = y2 + vary; 
z2 = z2 + varz; 

[x3,y3,z3] = cylinder(1,200);

th = 0:pi/180:2*pi;
x4 = basePlateRad*sin(th);
y4 = basePlateRad*cos(th);
z4 = 0.0*x4;

% Set up range of movements of bone sample
xmovement1 = 0:0.05:1;
xmovement2 = 0.95:-0.05:-1;
xmovement3 = -0.95:0.05:0;
xrange = 0.8; 
xmovement = xrange*[xmovement1 xmovement2 xmovement3];

ymovement1 = 0:0.05:1;
ymovement2 = 0.95:-0.05:-1;
ymovement3 = -0.95:0.05:0;
yrange = 1.0; 
ymovement = yrange*[ymovement1 ymovement2 ymovement3];

thetamovement = 0:4:360;

phimax = 44;
phimovement1 = 0:1:phimax;
phimovement2 = phimax:-1:-phimax;
phimovement3 = -phimax:1:0;
phimovement = [phimovement1 phimovement2 phimovement3];

% Set up cones representing x-rays
% Incident x-rays, slightly divergent
t = 1:-0.001:0.8;
[xC1,yC1,zC1] = cylinder(t,800);
% Cone of focussed x-rays and divergent scattered x-rays
t = 0:0.001:1;
[xC2,yC2,zC2] = cylinder(t,800);

% x- and y-coordinates of FZP rings uses this range of angles 
FZPth = 0:pi/100:2*pi; 

% Import SAXS data 
data = h5read('example_dataset.h5','/data');
mask= h5read('example_dataset.h5','/mask'); 
iimax = 137; 

% Colormap for SAXS data 
myCCM = customcolormap([0 0.2 0.5 0.67 0.88 1],...
    {'#880000','#ff0000','#ffff00','#00ff00','#5555bb','#000000'});

% Determine size of SAXS images on detector 
dataXsize = size(data,1);
dataYsize = size(data,2); 
% Crop to central 50% of images from 1/4 to 3/4 in both directions 
cropXstart = round(dataXsize/4); 
cropYstart = round(dataYsize/4); 
cropXend = round(3*dataXsize/4); 
cropYend = round(3*dataYsize/4); 

subplot('position',pos1);

saxsFrame = 0; 
saxsFrameIndex1 = 1:1:136; 
saxsFrameIndex2 = 137:-1:2; 
% Frame index for SAXS images going back and forth between 1 and 137 
saxsFrameIndex = [saxsFrameIndex1 saxsFrameIndex2 saxsFrameIndex1 saxsFrameIndex2 saxsFrameIndex1 saxsFrameIndex2];
% For loop scanning x-direction
for ii = xmovement 
    hold off 
    sph1 = surf(x+aa,1.1*y+bb+ii-0.35,z+cc+0.1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    hold on
    sph2 = surf(0.8*x+aa,0.8*y-bb+ii-0.14,0.88*z+cc+1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    sph3 = surf(x+aa,y+bb+ii,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    sph4 = surf(x+aa,y-bb+ii,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    
    cyl1 = surf(0.64*x2,1.25*y2+ii,10.4*z2-5,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    
    cyl2 = surf(basePlateRad*x3,basePlateRad*y3+ii,z3-6,'FaceAlpha',1,'FaceColor',...
        midGrey,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    
    ring = fill3(x4, y4+ii, z4-5,midGrey,'LineStyle','none',...
        'FaceLighting','gouraud','DiffuseStrength',1); 
    
    % FZP
    for jj = imax:-2:1
        r1 = 0.125*(jj)^0.5;
        r2 = 0.125*(jj-1)^0.5;
        z_circle1 = r1*cos(FZPth);
        y_circle1 = r1*sin(FZPth);
        x_circle1 = 0.0*y_circle1;
        z_circle2 = r2*cos(FZPth);
        y_circle2 = r2*sin(FZPth);
        x_circle2 = 0.0*y_circle2;
        z_circle = [z_circle1 z_circle2];
        y_circle = [y_circle1 y_circle2];
        x_circle = [x_circle1 x_circle2];
        zone = fill3(x_circle+FZPpos,y_circle,z_circle,'k','LineStyle','none');
    end 
    
    % Incident, slightly divergent, radiation cone
    maxFZPrad = imax^0.5*0.125;
    incRad = surf(maxFZPrad*xC1,maxFZPrad*yC1,-FZPpos+incRadLength*zC1,...
        'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(incRad,[0 1 0],-90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(incRad,0.6*incRad.XData/halfDetWidth-2);
    
    % Focussed radiation cone after FZP
    focRad = surf(maxFZPrad*xC2,maxFZPrad*yC2,-FZPpos*zC2,...
        'FaceAlpha',0.25,'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(focRad,[0 1 0],-90,[0,0,0]);
    
    % Divergent radiation cone after focus
    maxFZPrad = imax^0.5*0.125;
    divRad = surf((1+halfDetWidth)*xC2,(1+halfDetWidth)*yC2,(DetPos)*zC2,...
        'FaceColor',myGold,'FaceAlpha',0.28,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(divRad,[0 1 0],90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(divRad,-0.5*divRad.XData/halfDetWidth-1.6);
    
    % Detector
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = 0.1*V1(:,1)+20.06; % Thin detector 
    V1(:,2) = 2.*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.1 0.1 0.1],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = V1(:,1)+20.61; % Thin detector 
    V1(:,2) = 2.1*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.1*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.25 0.25 0.25],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    
    % Dummy vertical and horizontal lines to stop image resizing
    plot3([22 22],[0 0],[-8 8],...
        'color','w', 'LineWidth', 0.1);
    plot3([22 22],[-4 4],[0 0],...
        'color','w', 'LineWidth', 0.1); 
    
    % SAXS data plotted on detector front 
    saxsFrame = saxsFrame + 1; 
    iii = saxsFrameIndex(saxsFrame); 
    imMax = double(max(max(data(:,:,iii)))); 
    imMin = double(min(min(data(:,:,iii)))); 
    imAdd = 0.0001; 
    im = double(data(cropXstart:cropXend,cropYstart:cropYend,iii)); 
    %im = double(data(:,:,iii)); 
    imNowLin = (im - imMin)./(imMax - imMin);
    %imNow = imAdd+imNowLin.*mask; 
    imNow = imAdd+imNowLin.*mask(cropXstart:cropXend,cropYstart:cropYend); 
    imNowLog = log10(imNow)+255; 
    imMin = min(min(imNowLog));

    XX = [20 20; 20 20];
    YY = [halfDetWidth -halfDetWidth; halfDetWidth -halfDetWidth];
    ZZ = [halfDetWidth halfDetWidth;-halfDetWidth -halfDetWidth]; 
    surf(XX,YY,ZZ,imNowLog,'FaceColor','texturemap','EdgeColor','none');
    colormap(myCCM)
    caxis([imMin 252])
    
    set(gca,'Projection','perspective');
    
    light('Position',lp,'Style','infinite');
    axis equal
    axis off
    frame = getframe(gcf);
    writeVideo(vid,frame);
end % For loop for x-movements


% For loop scanning y-direction
for ii = ymovement 
    hold off     
    sph1 = surf(x+aa,1.1*y+bb-0.35,z+cc+ii+0.1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    hold on
    sph2 = surf(0.8*x+aa,0.8*y-bb-0.14,0.88*z+cc+ii+1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    sph3 = surf(x+aa,y+bb,z-cc+ii,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    sph4 = surf(x+aa,y-bb,z-cc+ii,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    
    cyl1 = surf(0.64*x2,1.25*y2,10.4*z2-5+ii,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    
    cyl2 = surf(basePlateRad*x3,basePlateRad*y3,z3-6+ii,'FaceAlpha',1,'FaceColor',...
        midGrey,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    
    ring = fill3(x4, y4, z4-5+ii,midGrey,'LineStyle','none',...
        'FaceLighting','gouraud','DiffuseStrength',1); 
    
    % FZP
    for jj = imax:-2:1
        r1 = 0.125*(jj)^0.5;
        r2 = 0.125*(jj-1)^0.5;
        z_circle1 = r1*cos(FZPth);
        y_circle1 = r1*sin(FZPth);
        x_circle1 = 0.0*y_circle1;
        z_circle2 = r2*cos(FZPth);
        y_circle2 = r2*sin(FZPth);
        x_circle2 = 0.0*y_circle2;
        z_circle = [z_circle1 z_circle2];
        y_circle = [y_circle1 y_circle2];
        x_circle = [x_circle1 x_circle2];
        zone = fill3(x_circle+FZPpos,y_circle,z_circle,'k','LineStyle','none');
    end 
    
    % Incident, slightly divergent, radiation cone
    maxFZPrad = imax^0.5*0.125;
    incRad = surf(maxFZPrad*xC1,maxFZPrad*yC1,-FZPpos+incRadLength*zC1,...
        'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(incRad,[0 1 0],-90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(incRad,0.6*incRad.XData/halfDetWidth-2);
    
    % Focussed radiation cone after FZP
    focRad = surf(maxFZPrad*xC2,maxFZPrad*yC2,-FZPpos*zC2,...
        'FaceAlpha',0.25,'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(focRad,[0 1 0],-90,[0,0,0]);
    
    % Divergent radiation cone after focus
    maxFZPrad = imax^0.5*0.125;
    divRad = surf((1+halfDetWidth)*xC2,(1+halfDetWidth)*yC2,(DetPos)*zC2,...
        'FaceColor',myGold,'FaceAlpha',0.28,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(divRad,[0 1 0],90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(divRad,-0.5*divRad.XData/halfDetWidth-1.6);
    
    % Detector
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = 0.1*V1(:,1)+20.06; % Thin detector 
    V1(:,2) = 2.*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.1 0.1 0.1],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = V1(:,1)+20.61; % Thin detector 
    V1(:,2) = 2.1*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.1*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.25 0.25 0.25],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    
    % Dummy vertical and horizontal lines to stop image resizing
    plot3([22 22],[0 0],[-8 8],...
        'color','w', 'LineWidth', 0.1);
    plot3([22 22],[-4 4],[0 0],...
        'color','w', 'LineWidth', 0.1);
    
    % SAXS data plotted on detector front 
    saxsFrame = saxsFrame + 1; 
    iii = saxsFrameIndex(saxsFrame); 
    imMax = double(max(max(data(:,:,iii)))); 
    imMin = double(min(min(data(:,:,iii)))); 
    imAdd = 0.0001; 
    im = double(data(cropXstart:cropXend,cropYstart:cropYend,iii)); 
    imNowLin = (im - imMin)./(imMax - imMin);
    imNow = imAdd+imNowLin.*mask(cropXstart:cropXend,cropYstart:cropYend); 
    imNowLog = log10(imNow)+255; 
    imMin = min(min(imNowLog));

    XX = [20 20; 20 20];
    YY = [halfDetWidth -halfDetWidth; halfDetWidth -halfDetWidth];
    ZZ = [halfDetWidth halfDetWidth;-halfDetWidth -halfDetWidth]; 
    surf(XX,YY,ZZ,imNowLog,'FaceColor','texturemap','EdgeColor','none');
    colormap(myCCM)
    caxis([imMin 252])

    set(gca,'Projection','perspective');
    
    light('Position',lp,'Style','infinite');
    axis equal
    axis off
    frame = getframe(gcf);
    writeVideo(vid,frame);
end % For loop for y-movements

% For loop scanning theta rotation
for ii = thetamovement 
    hold off 
    sph1 = surf(x+aa,1.1*y+bb-0.35,z+cc+0.1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5); 
    material dull
    rotate(sph1,[0 0 1],ii,[0,0,0]);
    hold on
    sph2 = surf(0.8*x+aa,0.8*y-bb-0.14,0.88*z+cc+1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph2,[0 0 1],ii,[0,0,0]);
    sph3 = surf(x+aa,y+bb,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph3,[0 0 1],ii,[0,0,0]);
    sph4 = surf(x+aa,y-bb,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph4,[0 0 1],ii,[0,0,0]);
    
    cyl1 = surf(0.64*x2,1.25*y2,10.4*z2-5,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(cyl1,[0 0 1],ii,[0,0,0]);
    
    cyl2 = surf(basePlateRad*x3,basePlateRad*y3,z3-6,'FaceAlpha',1,'FaceColor',...
        midGrey,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    
    ring = fill3(x4, y4, z4-5,midGrey,'LineStyle','none',...
        'FaceLighting','gouraud','DiffuseStrength',1); 
    
    % FZP
    for jj = imax:-2:1
        hold on
        r1 = 0.125*(jj)^0.5;
        r2 = 0.125*(jj-1)^0.5;
        z_circle1 = r1*cos(FZPth);
        y_circle1 = r1*sin(FZPth);
        x_circle1 = 0.0*y_circle1;
        z_circle2 = r2*cos(FZPth);
        y_circle2 = r2*sin(FZPth);
        x_circle2 = 0.0*y_circle2;
        z_circle = [z_circle1 z_circle2];
        y_circle = [y_circle1 y_circle2];
        x_circle = [x_circle1 x_circle2];
        zone = fill3(x_circle+FZPpos,y_circle,z_circle,'k','LineStyle','none');
    end 
    
    % Incident, slightly divergent, radiation cone
    maxFZPrad = imax^0.5*0.125;
    incRad = surf(maxFZPrad*xC1,maxFZPrad*yC1,-FZPpos+incRadLength*zC1,...
        'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(incRad,[0 1 0],-90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(incRad,0.6*incRad.XData/halfDetWidth-2);
    
    % Focussed radiation cone after FZP
    focRad = surf(maxFZPrad*xC2,maxFZPrad*yC2,-FZPpos*zC2,...
        'FaceAlpha',0.25,'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(focRad,[0 1 0],-90,[0,0,0]);
    
    % Divergent radiation cone after focus
    maxFZPrad = imax^0.5*0.125;
    divRad = surf((1+halfDetWidth)*xC2,(1+halfDetWidth)*yC2,(DetPos)*zC2,...
        'FaceColor',myGold,'FaceAlpha',0.28,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(divRad,[0 1 0],90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(divRad,-0.5*divRad.XData/halfDetWidth-1.6);
    
    % Detector
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = 0.1*V1(:,1)+20.06; % Thin detector 
    V1(:,2) = 2.*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.1 0.1 0.1],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = V1(:,1)+20.61; % Thin detector 
    V1(:,2) = 2.1*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.1*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.25 0.25 0.25],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);

    % Dummy vertical and horizontal lines to stop image resizing
    plot3([22 22],[0 0],[-8 8],...
        'color','w', 'LineWidth', 0.1);
    plot3([22 22],[-4 4],[0 0],...
        'color','w', 'LineWidth', 0.1);
    
    % SAXS data plotted on detector front 
    saxsFrame = saxsFrame + 1; 
    iii = saxsFrameIndex(saxsFrame); 
    imMax = double(max(max(data(:,:,iii)))); 
    imMin = double(min(min(data(:,:,iii)))); 
    imAdd = 0.0001; 
    im = double(data(cropXstart:cropXend,cropYstart:cropYend,iii)); 
    imNowLin = (im - imMin)./(imMax - imMin);
    imNow = imAdd+imNowLin.*mask(cropXstart:cropXend,cropYstart:cropYend); 
    imNowLog = log10(imNow)+255; 
    imMin = min(min(imNowLog));

    XX = [20 20; 20 20];
    YY = [halfDetWidth -halfDetWidth; halfDetWidth -halfDetWidth];
    ZZ = [halfDetWidth halfDetWidth;-halfDetWidth -halfDetWidth]; 
    surf(XX,YY,ZZ,imNowLog,'FaceColor','texturemap','EdgeColor','none');
    colormap(myCCM)
    caxis([imMin 252])

    set(gca,'Projection','perspective');
    
    light('Position',lp,'Style','infinite');
    axis equal
    axis off
    frame = getframe(gcf);
    writeVideo(vid,frame);
end % For loop for theta rotations 

% For loop scanning phi rotations 
for ii = phimovement 
    hold off 
    sph1 = surf(x+aa,1.1*y+bb-0.35,z+cc+0.1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5); 
    material dull
    rotate(sph1,[0 1 0],ii,[0,0,0]);
    hold on
    sph2 = surf(0.8*x+aa,0.8*y-bb-0.14,0.88*z+cc+1,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph2,[0 1 0],ii,[0,0,0]);
    sph3 = surf(x+aa,y+bb,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph3,[0 1 0],ii,[0,0,0]);
    sph4 = surf(x+aa,y-bb,z-cc,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(sph4,[0 1 0],ii,[0,0,0]);
    
    cyl1 = surf(0.64*x2,1.25*y2,10.4*z2-5,'FaceAlpha',1,'FaceColor',...
        boneYellow,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    material dull
    rotate(cyl1,[0 1 0],ii,[0,0,0]);
    
    cyl2 = surf(basePlateRad*x3,basePlateRad*y3,z3-6,'FaceAlpha',1,'FaceColor',...
        midGrey,'LineStyle','none','FaceLighting','flat','DiffuseStrength',0.5);
    rotate(cyl2,[0 1 0],ii,[0,0,0]);
    
    ring = fill3(x4, y4, z4-5,midGrey,'LineStyle','none',...
        'FaceLighting','gouraud','DiffuseStrength',1); 
    rotate(ring,[0 1 0],ii,[0,0,0]);
    
    % FZP
    for jj = imax:-2:1
        hold on
        r1 = 0.125*(jj)^0.5;
        r2 = 0.125*(jj-1)^0.5;
        z_circle1 = r1*cos(FZPth);
        y_circle1 = r1*sin(FZPth);
        x_circle1 = 0.0*y_circle1;
        z_circle2 = r2*cos(FZPth);
        y_circle2 = r2*sin(FZPth);
        x_circle2 = 0.0*y_circle2;
        z_circle = [z_circle1 z_circle2];
        y_circle = [y_circle1 y_circle2];
        x_circle = [x_circle1 x_circle2];
        zone = fill3(x_circle+FZPpos,y_circle,z_circle,'k','LineStyle','none');
    end 
    
    % Incident, slightly divergent, radiation cone
    maxFZPrad = imax^0.5*0.125;
    incRad = surf(maxFZPrad*xC1,maxFZPrad*yC1,-FZPpos+incRadLength*zC1,...
        'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(incRad,[0 1 0],-90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(incRad,0.6*incRad.XData/halfDetWidth-2);
    
    % Focussed radiation cone after FZP
    focRad = surf(maxFZPrad*xC2,maxFZPrad*yC2,-FZPpos*zC2,...
        'FaceAlpha',0.25,'FaceColor',myGold,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(focRad,[0 1 0],-90,[0,0,0]);
    
    % Divergent radiation cone after focus
    maxFZPrad = imax^0.5*0.125;
    divRad = surf((1+halfDetWidth)*xC2,(1+halfDetWidth)*yC2,(DetPos)*zC2,...
        'FaceColor',myGold,'FaceAlpha',0.28,'LineStyle',...
        'none','FaceLighting','flat','DiffuseStrength',1);
    rotate(divRad,[0 1 0],90,[0,0,0]);
    % Vary alpha of divergent radiation in x-direction with offset so it
    % remains semitransparent for all elements of surf = divRad
    alpha(divRad,-0.5*divRad.XData/halfDetWidth-1.6);
    
    % Detector
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = 0.1*V1(:,1)+20.06; % Thin detector 
    V1(:,2) = 2.*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.1 0.1 0.1],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    [V1,F1] = platonic_solid(2,0.88); % Cube
    V1(:,1) = V1(:,1)+20.61; % Thin detector 
    V1(:,2) = 2.1*halfDetWidth*V1(:,2); % Thin detector 
    V1(:,3) = 2.1*halfDetWidth*V1(:,3); % Thin detector 
    patch('Faces',F1,'Vertices',V1,'FaceColor',[0.25 0.25 0.25],...
        'FaceAlpha',1,'EdgeColor','none','FaceLighting','flat',...
        'DiffuseStrength',1,'AmbientStrength',1,'SpecularStrength',0);
    % Dummy vertical and horizontal lines to stop image resizing
    plot3([22 22],[0 0],[-8 8],...
        'color','w', 'LineWidth', 0.1);
    plot3([22 22],[-4 4],[0 0],...
        'color','w', 'LineWidth', 0.1);  
    
    % SAXS data plotted on detector front 
    saxsFrame = saxsFrame + 1; 
    iii = saxsFrameIndex(saxsFrame); 
    imMax = double(max(max(data(:,:,iii)))); 
    imMin = double(min(min(data(:,:,iii)))); 
    imAdd = 0.0001; 
    im = double(data(cropXstart:cropXend,cropYstart:cropYend,iii)); 
    imNowLin = (im - imMin)./(imMax - imMin);
    imNow = imAdd+imNowLin.*mask(cropXstart:cropXend,cropYstart:cropYend); 
    imNowLog = log10(imNow)+255; 
    imMin = min(min(imNowLog));

    XX = [20 20; 20 20];
    YY = [halfDetWidth -halfDetWidth; halfDetWidth -halfDetWidth];
    ZZ = [halfDetWidth halfDetWidth;-halfDetWidth -halfDetWidth]; 
    surf(XX,YY,ZZ,imNowLog,'FaceColor','texturemap','EdgeColor','none');
    colormap(myCCM)
    caxis([imMin 252])

    set(gca,'Projection','perspective');
    
    light('Position',lp,'Style','infinite');
    axis equal
    axis off
    frame = getframe(gcf);
    writeVideo(vid,frame);
end % For loop for phi rotations 

close(vid);
