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fig_3d.m
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% Reconstruction and figures for 3d exitwave. Uses output of sim_holo.
clear all;
close all;
addpath('reconstruction');
addpath('simulation');
addpath('helper');
%% settings
refError=1.0;
maskScale=1/4096; %just filter dc
sigmaMask=0;
discreteBits=0;
wienernoise=1e4;
focus_distance=-71; %distance to focus exitwave directly behind object
caption='v2';
outpath='./Tex/images';
inputfilename='.\data\sim_complexobject.mat';
%% Prepare Input
[scatterImageHolo,scatterImage,refImage,mask,softmask,outermask,inputHolo,input,settings]=prepareInput_exitwave(inputfilename,refError,maskScale,sigmaMask,discreteBits);
%move to gpu
if parallel.gpu.GPUDevice.isAvailable
gpu=gpuDevice(1);
mask=gpuArray(mask);
scatterImageHolo=gpuArray(scatterImageHolo);
scatterImage=gpuArray(scatterImage);
end
%% Reconstruction
%% use Holography and IPR
%support and start
[start,support]=holoSupport(scatterImageHolo,softmask,refImage,'threshold',1,'debug',true);
%Plan:
planHolo=recon.plan();
for n=1:50
planHolo.addStep('hio',200);
planHolo.addStep('er',1);
end
planHolo.addStep('show');
planHolo.addStep('er',100);
planHolo.addStep('show');
%Run
[resultHolo]=planHolo.run(scatterImageHolo,support,start,mask);
clear support start
%% use IPR with Shrinkwrap
%support and start
[start,support]=genericSupport(scatterImage,softmask);
%Plan
planSW=recon.plan();
for n=1:50
planSW.addStep('hio',200);
planSW.addStep('er',5);
planSW.addStep('sw',1,{10,0.05});
end
planSW.addStep('show')
for n=1:50
planSW.addStep('hio',200);
planSW.addStep('er',1);
end
planSW.addStep('er',100);
planSW.addStep('show');
%Run multiple times and average
% multi=10;
% multistart=zeros([size(start),multi]);
% for n=1:multi
% multistart(:,:,n)=gather(ift2(ft2(start).*exp(2i*pi*rand(size(start))).*softmask));
% end
% [result,images,errors]=planSW.runAvg(scatterImage,support,multistart,mask,ceil(multi/2));
[resultSW]=planSW.run(scatterImage,support,start,mask);
clear support start
%% wiener deconvolution
%get cross correlation
[~,~,cross]=holoSupport(scatterImageHolo,softmask,refImage,'threshold',1,'radDilate',50);
%and filtered (guessed) Reference
refImageFiltered=maskfilter(refImage,softmask,2.^nextpow2(size(refImage)*4));
crossPadded=pad2size(cross-cross(1),size(scatterImageHolo));
refImagePadded=pad2size(refImageFiltered-refImageFiltered(1),size(scatterImageHolo));
% deconvolution
resultDeconv=wiener(crossPadded,refImagePadded,wienernoise,true);
clear cross crossPadded refImagePadded
%% focus input
cut=@(x)x(1+end/2-end/8:end/2+end/8,1+end/2-end/8:end/2+end/8);
input=focusExitwave(input,settings.dx,settings.wavelength,true,focus_distance); %directly behind object
%% plot reconstruction results
finput=maskfilter(input,softmask);
fresultSW=maskfilter(resultSW,softmask);
fresultHolo=maskfilter(resultHolo,softmask);
fresultDeconv=maskfilter(resultDeconv,softmask);
move=@(x)moveAndMirror(finput,x);
cut=@(x)x(1+end/2-end/8:end/2+end/8,1+end/2-end/8:end/2+end/8);
norm=@(x,y)x.*(max(y(:)-y(1))./max(x(:)))+y(1);
cscale=[min(abs(input(:))),max(abs(input(:)))];
f=figure();
delim=32;
pixel=512;
scale=1/2;
f.Position=[0,0,(2*pixel+delim),(2*pixel+delim)].*scale;
ax(1)=subplot(2,2,1);
ax(1).Units='pixels';
ax(1).Position=[0,pixel+delim,pixel,pixel].*scale;
compleximagesc(norm(cut(finput),input),cscale);
axis off;
ax(1).ActivePositionProperty='position';
ax(2)=subplot(2,2,3);
ax(2).Units='pixels';
ax(2).Position=[0,0,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fresultDeconv)),input),cscale);
axis off;
ax(2).ActivePositionProperty='position';
ax(3)=subplot(2,2,2);
ax(3).Units='pixels';
ax(3).Position=[pixel+delim,pixel+delim,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fresultSW)),input),cscale);
axis off;
ax(3).ActivePositionProperty='position';
ax(4)=subplot(2,2,4);
ax(4).Units='pixels';
ax(4).Position=[pixel+delim,0,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fresultHolo)),inputHolo),cscale);
axis off;
ax(4).ActivePositionProperty='position';
f.PaperUnits='inches';
f.PaperPositionMode='manual';
f.PaperPosition=[0,0,(2*pixel+delim)/150,(2*pixel+delim)/150];
f.PaperSize=[(2*pixel+delim)/150, (2*pixel+delim)/150];
f.Resize='off';
outputfilename=sprintf('%s/recon3d-%s.png',outpath,caption);
print(outputfilename,'-dpng','-r150');
%% move results to main memory
finput=gather(finput);
fresultSW=gather(fresultSW);
fresultHolo=gather(fresultHolo);
fresultDeconv=gather(fresultDeconv);
resultSW=gather(resultSW);
resultHolo=gather(resultHolo);
resultDeconv=gather(resultDeconv);
%% plot exitwave
f=figure('visible','off');
rmin=0;
rmax = gather(max(abs(input(isfinite(input)))));
compleximagesc(input,[rmin,rmax]);
axis square
ax=gca;
ax.XTick=[];
ax.YTick=[];
subcaption='exitwave_focus';
outputfilename=sprintf('%s/fig_simholo_%s_%s.png',outpath,caption,subcaption);
save_image(outputfilename);
%% colorwheel
N=1024;
gamma=.9;
[x, y] = meshgrid(linspace(-1,1,N));
[theta, rho] = cart2pol(x, y);
h = (theta + pi) / (2 * pi);
s=ones(size(rho));
l=(rho.^gamma);
l(rho>1)=0;
rgb=hsl2rgb(cat(3,h,s,l));
%show colorwheel
f=figure('visible','off');
ax1=axes('Position',[0.2,0.2,.6,.6]);
im=imshow(rgb,'Parent', ax1);
im.AlphaData=rho<1;
%show axis
ticks=linspace(rmin,rmax,4);
ax2=polaraxes('Position',[0.2,0.2,.6,.6]);
ax2.ThetaAxisUnits = 'radians';
ax2.Color='none';
ax2.RAxis.Label.String='rel. Intensität';
ax2.RAxis.Label.Position=[2,0.7,0];
ax2.ThetaAxis.Label.Position=[0,1.15,0];
ax2.ThetaAxis.Label.String='Phase';
ax2.ThetaTick=[0:0.25:2]*pi;
ax2.RLim=[rmin,rmax];
ax2.RTick=ticks(2:end);
ax2.RAxis.TickLabelFormat='%.1g';
ax3=polaraxes('Position',[0.2,0.2,.6,.6]);
ax3.ThetaTick=[];
ax3.RLim=[rmin,rmax];
ax3.RTick=ticks(1);
ax3.RAxis.TickLabelFormat='%.1g';
ax3.Color='none';
ax3.RAxis.Color=[1,1,1];
ax2.ThetaAxis.Color=[0,0,0];
ax3.ThetaAxis.Color=[0,0,0];
f.PaperSize=[20,20];
f.PaperPosition=[-4.5,-4,28,28];
ax3.FontSize=28;
ax2.FontSize=28;
ax2.LineWidth=1;
ax2.GridAlpha=1;
ax2.GridColor=[0.3,0.3,0.3];
ax2.GridLineStyle='--';
f.Color='none';
ax1.Color='none';
subcaption='exitwave_focus_cw';
outputfilename=sprintf('%s/fig_simholo_%s_%s.png',outpath,caption,subcaption);
print(outputfilename,'-dpdf')
%% plot scatter image
f=figure('visible','off');
scatter=(abs(scatterImageHolo(1+1/4*end:3/4*end,1+1/4*end:3/4*end)));
scatter=gather(log10(scatter./max(scatter(:))));
scattermin=min(scatter(isfinite(scatter))).*.6;
im=imagesc(scatter);
colormap parula
caxis([scattermin,0]);
axis square
subcaption='scatter';
outputfilename=sprintf('%s/fig_simholo_%s_%s.png',outpath,caption,subcaption);
save_image(outputfilename);
f=figure('colormap',parula(128),'visible','off');
cb=colorbar('vert');
ax=gca;
ax.Color='none';
ax.FontSize=18;
caxis([scattermin,0]);
axis off;
cb.TickLabels=sprintfc('\\color{white} 10^{%g}',cb.Ticks);
ax.ZColor=[1,1,1];
f.PaperSize=[10,10];
f.PaperPosition=[-7.5,0,10,10];
subcaption='scatter_cb';
outputfilename=sprintf('%s/fig_simholo_%s_%s.png',outpath,caption,subcaption);
print(outputfilename,'-dpdf')
%% plot focused images
move=@(x)moveAndMirror(finput,x,true);
cut=@(x)x(1+end/2-end/8:end/2+end/8,1+end/2-end/8:end/2+end/8);
norm=@(x,y)x.*(max(y(:)-y(1))./max(x(:)))+y(1);
focusinput=gather(focusExitwave(cut(input),settings.dx,settings.wavelength,true,-50));
focusrecon=gather(focusExitwave(norm(cut(move(resultHolo)),focusinput),settings.dx,settings.wavelength,true,30));
ffocusinput=gather(maskfilter(focusinput,softmask));
ffocusrecon=gather(maskfilter(focusrecon,softmask));
cscale=[min(abs(input(:))),max(abs(input(:)))];
f=figure();
delim=32;
pixel=512;
scale=1/2;
f.Position=[0,0,(2*pixel+delim),pixel].*scale;
ax(1)=subplot(1,2,1);
ax(1).Units='pixels';
ax(1).Position=[0,0,pixel,pixel].*scale;
compleximagesc(norm(ffocusinput,input),cscale);
axis off;
ax(1).ActivePositionProperty='position';
ax(2)=subplot(1,2,2);
ax(2).Units='pixels';
ax(2).Position=[pixel+delim,0,pixel,pixel].*scale;
compleximagesc(norm(ffocusrecon,input),cscale);
axis off;
ax(2).ActivePositionProperty='position';
subcaption='focus';
outputfilename=sprintf('%s/recon3d-%s_%s.png',outpath,caption,subcaption);
print(outputfilename,'-dpng','-r150');
%% different wiener noise parameters
%prepare
[~,~,cross]=holoSupport(scatterImageHolo,softmask,refImage,'threshold',1,'radDilate',50);
refImageFiltered=maskfilter(refImage,softmask,2.^nextpow2(size(refImage)*4));
crossPadded=pad2size(cross-cross(1),size(scatterImageHolo));
refImagePadded=pad2size(refImageFiltered-refImageFiltered(1),size(scatterImageHolo));
lwienernoise=[1e2,1e4,1e6];
for n=numel(lwienernoise):-1:1
deconv{n}=gather(wiener(crossPadded,refImagePadded,lwienernoise(n),true));
fdeconv{n}=gather(maskfilter(deconv{n},softmask));
end
move=@(x)moveAndMirror(finput,x,true);
cut=@(x)x(1+end/2-end/8:end/2+end/8,1+end/2-end/8:end/2+end/8);
norm=@(x,y)x.*(max(y(:)-y(1))./max(x(:)))+y(1);
cscale=[min(abs(input(:))),max(abs(input(:)))];
f=figure();
delim=32;
pixel=512;
scale=1/2;
f.Position=[0,0,(3*pixel+2*delim),pixel].*scale;
ax(1)=subplot(1,3,1);
ax(1).Units='pixels';
ax(1).Position=[0,0,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fdeconv{1})),input),cscale);
axis off;
ax(1).ActivePositionProperty='position';
ax(2)=subplot(1,3,2);
ax(2).Units='pixels';
ax(2).Position=[pixel+delim,0,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fdeconv{2})),input),cscale);
axis off;
ax(2).ActivePositionProperty='position';
ax(3)=subplot(1,3,3);
ax(3).Units='pixels';
ax(3).Position=[2*(pixel+delim),0,pixel,pixel].*scale;
compleximagesc(norm(cut(move(fdeconv{3})),input),cscale);
axis off;
ax(2).ActivePositionProperty='position';
subcaption='wienernoise';
outputfilename=sprintf('%s/recon3d-%s_%s.png',outpath,caption,subcaption);
print(outputfilename,'-dpng','-r150');
clear cross crossPadded refImagePadded