mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 19:39:08 +09:00
110 lines
3.5 KiB
Matlab
110 lines
3.5 KiB
Matlab
%view_probe_variation.m
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close all
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clear
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addpath(strcat(pwd,'/utils/'))
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% load a .mat reconstruction file w. probe variation correction
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%% calculate probes at each scan positions
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Np_p = [size(probe,1),size(probe,2)];
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probes = reshape(probe(:,:,1,:),prod(Np_p),[]);
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probes = reshape(probes * outputs.probe_evolution', Np_p(1), Np_p(2), []);
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%% generate a movie to show scan positions and probes
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disp('Generating movie frames')
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figure1 = figure('Color',[1 1 1],'OuterPosition',[100 100 1800 600]);
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clear M
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object_roi = object(p.object_ROI{:},:);
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N_sample = 1;
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N_frames = 120;
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%N_frames = floor(size(outputs.probe_positions(:,1),1)/N_sample);
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%scale = p.dx_spec*1e6; % x-ray
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%unit_label = '\mum'; % x-ray
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scale = p.dx_spec; % electron
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unit_label = 'A';
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for i=1:N_frames
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clf()
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subplot(1,2,1)
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aobject = angle(object);
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range = sp_quantile(angle(object_roi), [1e-3, 1-1e-3],10);
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aobject = (aobject - range(1)) / (range(2) - range(1));
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Np_o = size(object);
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grids = {(-ceil(Np_o(2)/2):ceil(Np_o(2)/2)-1)*scale(2), ...
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(-ceil(Np_o(1)/2):ceil(Np_o(1)/2)-1)*scale(1)};
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imagesc(grids{:}, aobject, [-2, 1]); % reduce contrast
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colormap bone
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axis xy
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hold on
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pos = outputs.probe_positions;
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pos_0 = outputs.probe_positions_0;
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pos_scales = pos .* scale([2,1]);
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pos_scales_0 = pos_0 .* scale([2,1]);
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scatter( pos_scales(:,1), pos_scales(:,2),'.r')
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scatter( pos_scales_0(:,1), pos_scales_0(:,2),10, '.','MarkerEdgeColor','b')
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scatter( pos_scales(1+(i-1)*N_sample,1), pos_scales(1+(i-1)*N_sample,2),50,'ok','filled')
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axis equal xy tight
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range = [min(pos_scales(:,1)), max(pos_scales(:,1)), min(pos_scales(:,2)), max(pos_scales(:,2))];
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axis(range)
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title(['\fontsize{12}{\color{blue}initial positions, '...
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'\color{red}refined positions, \color{black}current probe position}'])
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ylabel(['Position [', unit_label, ']'])
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subplot(1,2,2)
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imagesc_hsv(probes(:,:,1+(i-1)*N_sample),'stabilize_phase',false)
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axis off
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title('primary probe mode')
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drawnow;
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M(i) = getframe(gcf);
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end
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disp('Done')
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%% save movie
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disp('Saving movie...')
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movieName = strcat('probes_selected.avi');
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v= VideoWriter(movieName);
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v.FrameRate= 5;
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open(v)
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writeVideo(v,M);
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close(v)
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disp('Done')
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%% plot OPR modes (U)
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N_vp = size(probe,4)-1;
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figure
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ax(1)=subplot(2,1+N_vp,1);
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imagesc_hsv(probe(:,:,1,1),'stabilize_phase',false)
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axis xy off
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title('Constant mode')
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for ii = 2:N_vp+1
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ax(ii)=subplot(2,1+N_vp,ii);
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imagesc_hsv(probe(:,:,1,ii),'stabilize_phase',false)
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axis xy off
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title(sprintf('Variable mode %i', ii-1))
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end
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for ii = 1:N_vp+1
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ax(ii+1+N_vp)=subplot(2,1+N_vp,1+N_vp+ii);
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scatter(outputs.probe_positions(:,1)*p.dx_spec(1),outputs.probe_positions(:,2)*p.dx_spec(1),[],outputs.probe_evolution(:,ii));
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%axis xy off
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title(strcat('Average weights:', num2str(mean(outputs.probe_evolution(:,ii)))))
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%title(strcat(num2str(mean(outputs.probe_evolution(:,ii)))))
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end
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%% save probes as a tiff stack
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Np_p = [size(probe,1),size(probe,2)];
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probes = reshape(probe(:,:,1,:),prod(Np_p),[]);
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probes = reshape(probes * outputs.probe_evolution', Np_p(1), Np_p(2), []);
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resampleFactor = round(size(probes,3)/200); %only save ~100 images
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probes_temp = probes(:,:,1:resampleFactor:end);
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saveName = strcat(reconDir,'probes_Niter',num2str(Niter),'.tiff');
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imwrite(convert_to_rgb(probes_temp(:,:,1)), saveName,'tiff')
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for i=2:size(probes_temp,3)
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imwrite(convert_to_rgb(probes_temp(:,:,i)), saveName,'tiff', 'WriteMode','append')
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end
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