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initial commit
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% propagate_probe.m
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% Warning: Currently working only for square pixels
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%close all % Recommended if improfile will be used (there is a bug with cursor positioning otherwise)
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import utils.*
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% Loading reconstruction
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scan = 581;
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fext = '.h5';
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filename=['*_recons' fext];
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file = dir(fullfile('~/Data10/analysis/', utils.compile_x12sa_dirname(scan), filename));
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if length(file) > 1 ; warning('Multiple files are matching'); end
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% load the last reconstruction in the provided scan number
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filename = fullfile(file(end).folder, file(end).name);
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title_str = file(end).name;
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io.load_ptycho_recons(filename);
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lambda=p.lambda; % wavelength [m]
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dis=p.z; % sample-detector distance [m]
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asize=p.asize(1);
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pixsize=p.dx_spec(1); % pixel size of final reconstruction [m]
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% Axial propagation parameters - Cut through (y,z)
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rangez = [-0.7e-3 0.7e-3]; % Range in meters, currently at zero
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step_num = 300; % Number of steps
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% Propagate to one plane
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prop_dis= 1.5e-3; % chosen propagation distance
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% Display option
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disp = 'hsv'; % Either 'hsv', 'amp', 'phase'
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x = [-asize/2 asize/2]*pixsize;
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%%%
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%%% Code starts
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%%%
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scrsz = get(0,'ScreenSize');
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mask=ones(asize,asize) - (abs(probe)==0);
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%probe_corr=rmphaseramp(probe,mask);
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probe_corr=remove_linearphase_v2(probe,mask,20);
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%probe=probe_corr;
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probe_hsv(:,:,3)=abs(probe)/max(max(abs(probe)));
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probe_hsv(:,:,2)=ones(asize,asize);
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probe_hsv(:,:,1)=angle(probe)/(2*pi)+0.5;
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figure(1);
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clf
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switch disp
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case 'hsv'
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imagesc(x*1e6,x*1e6,hsv2rgb(probe_hsv));
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case 'amp'
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imagesc(x*1e6,x*1e6,abs(probe));
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colormap bone
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case 'phase'
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imagesc(x*1e6,x*1e6,angle(probe));
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colormap bone
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end
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axis xy equal tight;
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title(['Probe ' title_str], 'interpreter', 'none');
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xlabel('x [\mum]')
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ylabel('y [\mum]')
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set(gcf,'Outerposition',[1 1 500 500])
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%
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propdists = linspace(rangez(1),rangez(2),step_num);
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back_propag_all = prop_free_nf(probe, lambda, propdists, pixsize);
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propag=squeeze(back_propag_all(asize/2,:,:));
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max_int = max(max(abs(back_propag_all).^2));
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propag_hsv=zeros(asize,step_num,3);
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propag_hsv(:,:,3)=abs(propag)/max(max(abs(propag)));
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propag_hsv(:,:,2)=ones(asize,step_num);
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propag_hsv(:,:,1)=angle(propag)/(2*pi)+0.5;
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figure(8);
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clf
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switch disp
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case 'hsv'
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imagesc(propdists*1e3,x*1e6,hsv2rgb(propag_hsv));
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case 'amp'
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imagesc(propdists*1e3,x*1e6,abs(propag));
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colormap bone
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case 'phase'
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imagesc(propdists*1e3,x*1e6,angle(propag));
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colormap bone
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end
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title(['Axial propagation ' title_str], 'interpreter', 'none');
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xlabel('z [mm]')
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ylabel('x [\mum]')
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set(gcf,'Outerposition',[1 scrsz(4)-480 1000 480])
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back = prop_free_nf(probe, lambda, prop_dis, pixsize);
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back_hsv=zeros(asize,asize,3);
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back_hsv(:,:,3)=abs(back)/max(max(abs(back)));
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back_hsv(:,:,2)=ones(asize,asize);
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back_hsv(:,:,1)=angle(back)/(2*pi)+0.5;
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figure(2);
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clf
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switch disp
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case 'hsv'
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imagesc(x*1e6,x*1e6,hsv2rgb(back_hsv));
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case 'amp'
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imagesc(x*1e6,x*1e6,abs(back));
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colormap bone
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case 'phase'
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imagesc(x*1e6,x*1e6,angle(back));
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colormap bone
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end
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axis xy equal tight;
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title(['Probe propagated to ' num2str(prop_dis*1e3) ' mm ' title_str],'interpreter', 'none');
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xlabel('x [\mum]')
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ylabel('y [\mum]')
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set(gcf,'Outerposition',[501 1 500 500])
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utils.verbose(0, '============== Focus positions: %g um =============', 1e6*propdists(math.argmax(max_int)))
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%probe=back;
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% save('probe_from_S00108_128x128_test_0_recons_00_propag_3_mm.mat','probe');
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
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% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
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% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 5. 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
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% another computing language:
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% "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
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% 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).
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% (doi: 10.1364/OE.24.029089).
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% 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
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% 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.
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% 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
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% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
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% the courts of Zürich, Switzerland.
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