PEEM experiment cartoon matlab code

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matlab code

% Cartoon of a PEEM experimental setup with x-rays crossing over the L2 and

% L3 edges of iron from 700 to 740 eV. Experimental data ironPEEM.mp4

% courtesy Armin Kleibert, PSI.

clear; close all;

peemV = VideoReader('ironPEEM.mp4');

xanesData = importdata('FeL2L3.txt'); % Absorption data around Fe L-edge

pos1 = [0.01 0.01 0.49 0.98]; % Experiment

pos2 = [0.5 0.5 0.49 0.49]; % PEEM image

pos3 = [0.53 0.08 0.43 0.4]; % Fe L2, L3 spectrum

vid = VideoWriter('PEEMexpt.mp4','MPEG-4');

vid.Quality = 100;

vid.FrameRate = 15;

open(vid);

figure('units','pixels','position',[0 0 1920 1080]);

set(0,'defaultfigurecolor',[1 1 1]);

set(gca,'linewidth',7);

myBlue = [0.4 0.44 0.73];

myGold = [220 166 3]/255;

lp1 = [0. -0.4 0.25];

lp2 = [0. 0 -1.6];

% red - yellow - green - blue - violet custom colormap

rgb = customcolormap([0 0.25 0.5 0.75 1], {'#ff0000','#ffff00','#00ff00','#0000ff','#7f00ff'});

fliprgb = flip(rgb);

colormap(fliprgb);

Nframes = peemV.NumFrames; % Number of frames in PEEM video

frameNow = 0;

rmax = [5 4 3]; % Upper radii of three objective cones

baseHt = [0 1 2]; % Heights of bases of three objective cones

rmin = 1; % Common inner radius of three objective cones

objLensHt = [5 4.5 4]; % Axial heights of three objective cones

% Coordinates of top and bottom of lens structures

phiRange = -3*pi/4:pi/360:3*pi/4;

arcx = sin(phiRange); % Inner curved surface

arcy = cos(phiRange); % Outer curved surface

arc1x = [arcx 1.1*flip(arcx)]; % Concatenate for fill3

arc1y = [arcy 1.1*flip(arcy)]; % Concatenate for fill3

arc1z = 0.0*arc1x; % z-coordinates

for hv = 700:40/(Nframes-1):740

subplot('Position',pos1);

newplot

frameNow = frameNow+1;

% Create three cones as the curved surfaces of the objective lens of

% the PEEM electron microscope

surfRes = 360; % Fineness of cylindrical division

for cone = 1:3

r = rmin:rmax(cone);

[x1,y1,z1] = cylinder(r,surfRes);

% Delete quarter of the objective lens to see wot's goin' on, loik

for ii = rmin:rmax(cone)

for jj = 1:surfRes+1

if (y1(ii,jj) < -ii/sqrt(2)-0.001) % -0.001 needed to avoid rounding errors

x1(ii,jj) = NaN;

y1(ii,jj) = NaN;

z1(ii,jj) = NaN;

end

% Curved surface, objective 1,2,3

surf(x1,y1,z1*objLensHt(cone)+baseHt(cone),'FaceAlpha',1,...

'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

surf(1.1*x1,1.1*y1,z1*objLensHt(cone)+baseHt(cone),'FaceAlpha',1,...

'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

axis off;

axis equal;

hold on

% Top and bottom surfaces, objective lenses

fill3(rmin*arc1x,rmin*arc1y,arc1z+baseHt(cone),[0.7 0.7 0.7],...

'LineStyle','none','FaceLighting','gouraud','DiffuseStrength',1);

fill3(rmax(cone)*arc1x,rmax(cone)*arc1y,arc1z+baseHt(cone)+objLensHt(cone),...

[0.7 0.7 0.7],'LineStyle','none','FaceLighting','gouraud','DiffuseStrength',1);

% Exposed edges of cutaway, objective lenses

x1flat = -sqrt(1/2)*[rmax(cone) 1.1*rmax(cone) 1.1*rmin rmin];

y1flat = -sqrt(1/2)*[rmax(cone) 1.1*rmax(cone) 1.1*rmin rmin];

z1flat = [objLensHt(cone) objLensHt(cone) 0 0]+baseHt(cone);

fill3(x1flat,y1flat,z1flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

fill3(-x1flat,y1flat,z1flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

end

% Projector lens

% Curved surfaces

r3 = 2;

[x3,y3,z3] = cylinder(r3,surfRes);

for ii = 1:2

for jj = 1:surfRes+1

if (y3(ii,jj) < -r3/sqrt(2)-0.001)

x3(ii,jj) = NaN;

y3(ii,jj) = NaN;

z3(ii,jj) = NaN;

end

surf(x3,y3,2*z3+11,'FaceAlpha',1,'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

r4 = 4;

[x4,y4,z4] = cylinder(r4,surfRes);

for ii = 1:2

for jj = 1:surfRes+1

if (y4(ii,jj) < -r4/sqrt(2)-0.001)

x4(ii,jj) = NaN;

z4(ii,jj) = NaN;

end

surf(x4,y4,2*z4+11,'FaceAlpha',1,'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

% Top and bottom surfaces, projector lens

arc2x = [r3*arcx r4*flip(arcx)];

arc2y = [r3*arcy r4*flip(arcy)];

arc2z = 0.0*arc2x;

fill3(arc2x,arc2y,arc2z+11,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

fill3(arc2x,arc2y,arc2z+13,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

% Exposed edges of cutaway, projector lens

x2flat = -sqrt(1/2)*[r3 r4 r4 r3];

y2flat = -sqrt(1/2)*[r3 r4 r4 r3];

z2flat = [11 11 13 13];

fill3(x2flat,y2flat,z2flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

fill3(-x2flat,y2flat,z2flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

% Two shielding plates for projector lens

spHtDiff = 2.75;

for shield = 0:1

% Curved surfaces

r5 = 1.9;

[x5,y5,z5] = cylinder(r5,surfRes);

for ii = 1:2

for jj = 1:surfRes+1

if (y5(ii,jj) < -r5/sqrt(2)-0.001)

x5(ii,jj) = NaN;

y5(ii,jj) = NaN;

z5(ii,jj) = NaN;

end

surf(x5,y5,0.05*z5+10.6+(shield*spHtDiff),'FaceAlpha',1,...

'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

r6 = 5;

[x6,y6,z6] = cylinder(r6,surfRes);

for ii = 1:2

for jj = 1:surfRes+1

if (y6(ii,jj) < -r6/sqrt(2)-0.001)

x6(ii,jj) = NaN;

z6(ii,jj) = NaN;

end

surf(x6,y6,0.05*z6+10.6+(shield*spHtDiff),'FaceAlpha',1,...

'FaceColor',[0.5 0.5 0.5],'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

% Top and bottom surfaces, shielding plate 1

arc2x = [r5*arcx r6*flip(arcx)];

arc2y = [r5*arcy r6*flip(arcy)];

arc2z = 0.0*arc2x;

fill3(arc2x,arc2y,arc2z+10.6+(shield*spHtDiff),[0.4 0.4 0.4],...

'LineStyle','none','FaceLighting','gouraud','DiffuseStrength',1);

fill3(arc2x,arc2y,arc2z+10.65+(shield*spHtDiff),[0.4 0.4 0.4],...

'LineStyle','none','FaceLighting','gouraud','DiffuseStrength',1);

% Exposed edges of cutaway, projector lens

x2flat = -sqrt(1/2)*[r5 r6 r6 r5];

y2flat = -sqrt(1/2)*[r5 r6 r6 r5];

z2flat = [10.6 10.6 10.65 10.65]+(shield*spHtDiff);

fill3(x2flat,y2flat,z2flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

fill3(-x2flat,y2flat,z2flat,[0.7 0.7 0.7],'LineStyle','none',...

'FaceLighting','gouraud','DiffuseStrength',1);

end

PEEMframe = read(peemV,frameNow); % grey image but in fact RGB

XX = [1 1; -1 -1];

YY = [1 -1; 1 -1];

ZZ = [0 0; 0 0]-0.5;

surf(-5*XX,-5*YY,ZZ+20.499,PEEMframe,'FaceColor','texturemap','EdgeColor','none');

plotcube([10 10 0.7],[-5 -5 20],1,[0.5 0.5 0.5],0);

surf(XX,YY,ZZ,PEEMframe,'FaceColor','texturemap','EdgeColor','none');

plotcube([2 2 0.1],[-1 -1 -0.601],1,[0.5 0.5 0.5],0);

fill3([-7 -7 7 7],[-7 7 7 -7],[0 0 0 0]-0.6,'w','LineStyle','none',...

'FaceLighting','none','DiffuseStrength',1);

% Interpolate PEEM spectrum

xintp = 700:0.1:740; % Interpolated x-values

yintp = interp1(xanesData(:,1),xanesData(:,2),xintp,'pchip'); % Interpolated y-values

xnowIndex = 1+round(400*(hv-700)/40);

ynow = yintp(xnowIndex);

FaceAlphaPlus = ynow/200;

% Electron beam from sample to detector

surfRes2 = 90;

R = 1;

ze1 = -0.2:0.01:1;

re1 = (R^2 - ze1.^2).^0.5-0.7*R;

[xe1,ye1,ze1] = cylinder(re1,surfRes2);

for ii = 1:121

if (re1(ii) < 0)

xe1(ii,:) = NaN;

ye1(ii,:) = NaN;

ze1(ii,:) = NaN;

end

aaa = max(max(ze1));

surf(2.68*xe1,2.68*ye1,5*ze1-0.5,'FaceAlpha',0.2+1.6*FaceAlphaPlus,...

'FaceColor',myBlue,'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

aaa = 5*aaa-0.5; % Maximum height of first part of electron beam

ze1 = -1:0.01:1;

re1 = (R^2 - ze1.^2).^0.5-0.7*R;

[xe1,ye1,ze1] = cylinder(re1,surfRes2);

for ii = 1:201

if (re1(ii) < 0)

xe1(ii,:) = NaN;

ye1(ii,:) = NaN;

ze1(ii,:) = NaN;

end

bbb = min(min(ze1));

ccc = aaa+12*max(max(ze1-bbb));

surf(3.2*xe1,3.2*ye1,aaa+12*(ze1-bbb),'FaceAlpha',0.2+FaceAlphaPlus,'FaceColor',myBlue,'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

re1 = 0:1:5;

[xe1,ye1,ze1] = cylinder(re1,surfRes);

surf(xe1,ye1,ccc+8.29*(ze1),'FaceAlpha',0.2+FaceAlphaPlus,'FaceColor',myBlue,'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',1);

% Incident radiation

index = 1 + round(255*(hv-700)/40);

colNow = fliprgb(index,:);

re1 = 0.8:0.2:1.4;

[xe1,ye1,ze1] = cylinder(re1,surfRes);

xrays = surf(xe1*sind(15),ye1,14*(ze1)-1.4,'FaceAlpha',0.28,'FaceColor',colNow,'LineStyle',...

'none','FaceLighting','gouraud','DiffuseStrength',0,'AmbientStrength',1);

rotate(xrays,[0 1 0],-75,[0,0,-0.5]);

axis off;

axis equal;

xlim([-9 6])

light('Position',lp1,'Style','infinite');

light('Position',lp2,'Style','infinite');

set(gca, 'Projection','perspective');

%view(32*(frameNow/112),(112-frameNow)/3) % Use for pan version

view(20,20) % Use for static version

hold off

% -------------------------------------------------------------------

subplot('Position',pos2);

newplot

imshow(PEEMframe)

% -------------------------------------------------------------------

subplot('Position',pos3);

newplot

xintp = 700:0.1:740; % Interpolated x-values

yintp = interp1(xanesData(:,1),xanesData(:,2),xintp,'pchip'); % Interpolated y-values

hold on

plot(xintp,yintp,'Color',myBlue,'LineWidth', 3.0)

xnow = hv;

ynowIndex = 1+round(400*(hv-700)/40);

ynow = yintp(ynowIndex);

colNow = fliprgb(index,:);

plot(xnow,ynow,'o','MarkerSize',10,...

'MarkerEdgeColor','none',...

'MarkerFaceColor',colNow,'MarkerSize',14)

a = get(gca,'XTickLabel');

set(gca,'XTickLabel',a,'FontName','Helvetica','fontsize',18);

set(gca,'TickLength',[0.02, 1]);

set(gca,'linewidth',2);

xlabel('Photon energy [eV]');

ylabel('Absorption [arb. units]');

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

set(gca,'YTick',[])

xlim([700 740])

hold off

% Store the frame

frame = getframe(gcf);

writeVideo(vid,frame);

end

% Output the movie as an mpg file

close(vid)