% propagate_probe.m % Warning: Currently working only for square pixels %close all % Recommended if improfile will be used (there is a bug with cursor positioning otherwise) import utils.* % Loading reconstruction scan = 581; fext = '.h5'; filename=['*_recons' fext]; file = dir(fullfile('~/Data10/analysis/', utils.compile_x12sa_dirname(scan), filename)); if length(file) > 1 ; warning('Multiple files are matching'); end % load the last reconstruction in the provided scan number filename = fullfile(file(end).folder, file(end).name); title_str = file(end).name; io.load_ptycho_recons(filename); lambda=p.lambda; % wavelength [m] dis=p.z; % sample-detector distance [m] asize=p.asize(1); pixsize=p.dx_spec(1); % pixel size of final reconstruction [m] % Axial propagation parameters - Cut through (y,z) rangez = [-0.7e-3 0.7e-3]; % Range in meters, currently at zero step_num = 300; % Number of steps % Propagate to one plane prop_dis= 1.5e-3; % chosen propagation distance % Display option disp = 'hsv'; % Either 'hsv', 'amp', 'phase' x = [-asize/2 asize/2]*pixsize; %%% %%% Code starts %%% scrsz = get(0,'ScreenSize'); mask=ones(asize,asize) - (abs(probe)==0); %probe_corr=rmphaseramp(probe,mask); probe_corr=remove_linearphase_v2(probe,mask,20); %probe=probe_corr; probe_hsv(:,:,3)=abs(probe)/max(max(abs(probe))); probe_hsv(:,:,2)=ones(asize,asize); probe_hsv(:,:,1)=angle(probe)/(2*pi)+0.5; figure(1); clf switch disp case 'hsv' imagesc(x*1e6,x*1e6,hsv2rgb(probe_hsv)); case 'amp' imagesc(x*1e6,x*1e6,abs(probe)); colormap bone case 'phase' imagesc(x*1e6,x*1e6,angle(probe)); colormap bone end axis xy equal tight; title(['Probe ' title_str], 'interpreter', 'none'); xlabel('x [\mum]') ylabel('y [\mum]') set(gcf,'Outerposition',[1 1 500 500]) % propdists = linspace(rangez(1),rangez(2),step_num); back_propag_all = prop_free_nf(probe, lambda, propdists, pixsize); propag=squeeze(back_propag_all(asize/2,:,:)); max_int = max(max(abs(back_propag_all).^2)); propag_hsv=zeros(asize,step_num,3); propag_hsv(:,:,3)=abs(propag)/max(max(abs(propag))); propag_hsv(:,:,2)=ones(asize,step_num); propag_hsv(:,:,1)=angle(propag)/(2*pi)+0.5; figure(8); clf switch disp case 'hsv' imagesc(propdists*1e3,x*1e6,hsv2rgb(propag_hsv)); case 'amp' imagesc(propdists*1e3,x*1e6,abs(propag)); colormap bone case 'phase' imagesc(propdists*1e3,x*1e6,angle(propag)); colormap bone end title(['Axial propagation ' title_str], 'interpreter', 'none'); xlabel('z [mm]') ylabel('x [\mum]') set(gcf,'Outerposition',[1 scrsz(4)-480 1000 480]) back = prop_free_nf(probe, lambda, prop_dis, pixsize); back_hsv=zeros(asize,asize,3); back_hsv(:,:,3)=abs(back)/max(max(abs(back))); back_hsv(:,:,2)=ones(asize,asize); back_hsv(:,:,1)=angle(back)/(2*pi)+0.5; figure(2); clf switch disp case 'hsv' imagesc(x*1e6,x*1e6,hsv2rgb(back_hsv)); case 'amp' imagesc(x*1e6,x*1e6,abs(back)); colormap bone case 'phase' imagesc(x*1e6,x*1e6,angle(back)); colormap bone end axis xy equal tight; title(['Probe propagated to ' num2str(prop_dis*1e3) ' mm ' title_str],'interpreter', 'none'); xlabel('x [\mum]') ylabel('y [\mum]') set(gcf,'Outerposition',[501 1 500 500]) utils.verbose(0, '============== Focus positions: %g um =============', 1e6*propdists(math.argmax(max_int))) %probe=back; % save('probe_from_S00108_128x128_test_0_recons_00_propag_3_mm.mat','probe'); % Academic License Agreement % % Source Code % % Introduction % • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR") % will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS % ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM"). % % Terms and Conditions of the LICENSE % 1. 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LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into % another computing language: % "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul % Scherrer Institut, Switzerland." % % Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map: % P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008). % (doi: 10.1126/science.1158573), % for maximum likelihood: % P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012). % (doi: 10.1088/1367-2630/14/6/063004), % for mixed coherent modes: % P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806), % and/or for multislice: % E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016). % (doi: 10.1364/OE.24.029089). % 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the % names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case. % 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE % agrees to preserve same. 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