Cartoon of scanning-SAXS tensor tomography experimental setup
Matlab code
% 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);