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ptycho/+core/+FPM/FP_prealign.m
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%% FP_PREALIGN prealign Fourier ptychographic data
% [p] = FP_prealign(p)
% FP_prealign is an alignment routine for Fourier ptychographic
% measurements. Due to the changes in frequency content, a global
% registration is not sufficient. We therefore sort the frames such that
% images with similar frequency content can be aligned.
%
% ** p p structure
%
% *taken from p.prealign:*
% ** ctr_sh shift the center before cropping the final dataset to asize
% ** crop_dft crop the images by crop_dft before calculating the dftregistration
% ** axis start the alignment procedure along specified axis or rotation (1 or 2)
% ** numiter number of iterations
% ** rad_filt_min discard positions below rad_filt_min
% ** rad_filt_max discard positions beyond rad_filt_max
% ** mfiles discard specific data points
% ** flat_corr apply a flat-field correction
% ** filt_align remove interpolation artifacts
% ** save_alignment save final shifts / alignment
% ** load_alignment overwrite alignment with previous alignment
% ** alignment_file specify path+file
% ** plot alignment turn on/off plotting during the alignment
%
% returns:
% ++ p p structure
%
% see also: <base> utils.dftregistration
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p] = FP_prealign(p)
import utils.*
%% initial checks
par = p.prealign;
% parse inputs
check_input = @(x) islogical(x) || isnumeric(x);
parse_par = inputParser;
parse_par.KeepUnmatched = true;
parse_par.addParameter('ctr_sh', [0 0], @isnumeric)
parse_par.addParameter('crop_dft', 1, @isnumeric)
parse_par.addParameter('axis', 1, @isnumeric)
parse_par.addParameter('numiter', 3, @isnumeric)
parse_par.addParameter('rad_filt_min', 0, @isnumeric)
parse_par.addParameter('rad_filt_max',Inf, @isnumeric)
parse_par.addParameter('mfiles', [], @isnumeric)
parse_par.addParameter('save_alignment', false, check_input)
parse_par.addParameter('load_alignment', false, check_input)
parse_par.addParameter('plot_alignment', false, check_input)
parse_par.addParameter('sort_pos_radii', false, check_input)
parse_par.addParameter('mag_est', [], @isnumeric)
parse_par.parse(par);
par = utils.update_param(par, parse_par.Results);
if isempty(par.mag_est)
warning('The magnification was not specified. I will assume mag_est=100.')
par.mag_est = 100;
end
%% load data and optimize position arangement
detStorage = p.detectors(p.scanID).detStorage;
detParams = p.detectors(p.scanID).params;
if p.scanID==1
if ~isfield(detParams, 'detposmotor')
error('Please specify the detector motor (det.detposmotor) in your detector template.')
end
p.positions_real = p.positions_orig;
p.det_pos = p.positions_real(p.scanidxs{p.scanID},:);
if (~isempty(p.spec.motor.coarse_motors))
% adjust the positions in case of coarse stage movements
coarse_pos = [];
for ii = 1:length(p.scan_number)
coarse_pos = [coarse_pos; [p.meta{ii}.spec.(p.spec.motor.coarse_motors{2}).*1e-3 p.meta{ii}.spec.(p.spec.motor.coarse_motors{1}).*1e-3]];
end
coarse_cen = [(max(coarse_pos(:,1)) - min(coarse_pos(:,1)))./2 (max(coarse_pos(:,2))-min(coarse_pos(:,2)))./2];
for ii = 1:length(p.scan_number)
p.positions_real(p.scanidxs{ii},1) = p.positions_real(p.scanidxs{ii},1)+p.meta{ii}.spec.(p.coarsey)*1e-3-min(coarse_pos(:,1))-coarse_cen(1);
p.positions_real(p.scanidxs{ii},2) = p.positions_real(p.scanidxs{ii},2)+p.meta{ii}.spec.(p.coarsex)*1e-3-min(coarse_pos(:,2))-coarse_cen(2);
p.det_pos(p.scanidxs{ii},1) = p.meta{ii}.spec.hy;
p.det_pos(p.scanidxs{ii},2) = p.meta{ii}.spec.hx;
end
p.coarsex = [];
p.coarsey = [];
else
% load the detector positions
for ii=1:length(p.scan_number)
p.det_pos(p.scanidxs{ii},1) = p.meta{ii}.spec.(detParams.detposmotor{1});
p.det_pos(p.scanidxs{ii},2) = p.meta{ii}.spec.(detParams.detposmotor{2});
end
end
end
par.det_pos = p.det_pos(p.scanidxs{p.scanID},:);
pos = p.positions_real(p.scanidxs{p.scanID},:);
data = detStorage.data;
% remove unwanted files
if ~isempty(par.mfiles)
pos(par.mfiles,:) = [];
data(:,:,par.mfiles) = [];
end
% remove files out of range
indx = [];
for ii=1:size(pos,1)
if sqrt(pos(ii,1)^2 + pos(ii,2)^2)<par.rad_filt_min || sqrt(pos(ii,1)^2 + pos(ii,2)^2)>par.rad_filt_max %|| pos(ii,2)>35e-6
indx = [indx ii];
end
end
pos(indx,:) = [];
par.det_pos(indx,:) = [];
data(:,:,indx) = [];
% if p.scanID>1
% p.positions_real(indx+sum(p.numpts(1:tmp.ii-1)),:) = [];
% end
par.pos = pos;
par.pos_orig = pos;
%%% update p values with new positions %%%
tmp_append_pos = p.positions_real([p.scanidxs{min(p.scanID+1, length(p.numpts)+1):end}],:);
tmp_append_det = p.det_pos([p.scanidxs{min(p.scanID+1, length(p.numpts)+1):end}],:);
p.numpts(p.scanID) = size(par.pos,1);
scanfirstindex = [1 cumsum(p.numpts)+1]; % First index for scan number
for ii = 1:p.numscans
p.scanindexrange(ii,:) = [scanfirstindex(ii) scanfirstindex(ii+1)-1];
end
for ii = 1:p.numscans
p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,2);
end
% adjust positions container
p.positions_real([p.scanidxs{p.scanID:end}],:) = [];
p.positions_real(p.scanidxs{p.scanID},:) = par.pos;
p.positions_real = [p.positions_real; tmp_append_pos];
p.det_pos([p.scanidxs{p.scanID:end}],:) = [];
p.det_pos(p.scanidxs{p.scanID},:) = par.det_pos;
p.det_pos = [p.det_pos; tmp_append_det];
par.data = data;
par.sz = size(par.data);
fft_mask = ones(par.asize);
fft_mask(round(par.asize(1)/4)-5:round(par.asize(1)/4)+5,:) = 0;
fft_mask(:,round(par.asize(2)/4)-5:round(par.asize(2)/4)+5) = 0;
fft_mask(:,round(par.asize(2)*3/4)-5:round(par.asize(2)*3/4)+5) = 0;
fft_mask(round(par.asize(1)*3/4)-5:round(par.asize(1)*3/4)+5,:) = 0;
if ~isempty(detParams.mask_saturated_value)
par.data = (abs(ifft2(fftshift(fft_mask).*fft2(par.data.*(par.data<detParams.mask_saturated_value)))));
else
par.data = (abs(ifft2(fftshift(fft_mask).*fft2(par.data))));
end
clear data;
par.orig_data = (abs(ifft2(fftshift(fft_mask).*fft2(par.data))));%par.data;
if par.prealign_data
par.sum_shift_total = zeros(par.sz(3), 2);
for ii=1:par.numiter*length(par.type)
par.iterii = ii;
verbose(2, 'Iteration %d/%d', ii, par.numiter*length(par.type))
% sort positions
verbose(3, 'Sorting positions.')
sort_type = par.type{mod(ii+1,length(par.type))+1};
par = core.FPM.sort_pos(par, sort_type);
verbose(4, 'Aligning data along sorted positions.')
% align along sorted positions
par = core.FPM.align_data(par);
fig30 = plotting.smart_figure(30);
clf;
set(groot,'CurrentFigure',fig30);
imagesc(mean(par.data,3));
colormap(bone(256))
title(sprintf('Alignment after %d iteration(s)', ii))
drawnow()
if ~mod(ii,length(par.type))
if par.axis==1
par.axis = 2;
else
par.axis = 1;
end
end
end
end
if par.sort_pos_radii
par = core.FPM.sort_pos_radii(par);
end
% use distortion matrix or load alignment from disk
if par.save_alignment
sum_shift_total = par.sum_shift_total;
save(sprintf('alignment_S%05d.mat', p.scan_number(p.scanID)), 'sum_shift_total');
end
if par.use_distortion_corr && isempty(par.distortion_corr)
par.distortion_corr = core.FPM.distortion_matrix(p, par.sum_shift_total, par.det_pos, par.mag_est);
elseif ischar(par.distortion_corr)
f = io.load_ptycho_recons(par.distorion_corr);
par.distortion_corr = f.p.prealign.distortion_corr;
end
if par.use_distortion_corr
p.prealign.distortion_corr = par.distortion_corr;
pos = core.FPM.get_positions(par.distortion_corr, par.pos.*1e3);
sum_shift_total = (pos - par.det_pos)./p.ds./1e3;
elseif par.load_alignment
if isempty(par.alignment_file) || ~exist(par.alignment_file, 'file')
error('Could not load specified alignment file.')
end
f = load(par.alignment_file);
sum_shift_total = f.sum_shift_total;
else
sum_shift_total = par.sum_shift_total;
end
%%%%%%%%%%%%%%%%
% apply shifts %
%%%%%%%%%%%%%%%%
mask = zeros([size(detStorage.mask) p.numpts(p.scanID)]);
utils.verbose(2, 'Applying shifts to image stack and mask.');
for ii=1:p.numpts(p.scanID)
data(:,:,ii) = ifftshift(utils.crop_pad(abs(utils.shiftpp2(par.orig_data(:,:,ii), sum_shift_total(ii,1), sum_shift_total(ii,2))), p.asize));
mask(:,:,ii) = abs(utils.shiftpp2(detStorage.mask, round(sum_shift_total(ii,1)), round(sum_shift_total(ii,2))));
end
if utils.verbose > 2
fig30 = plotting.smart_figure(30);
clf;
set(groot,'CurrentFigure',fig30);
imagesc(fftshift(mean(data,3)));
colormap(bone(256))
title('Alignment')
drawnow()
end
detStorage.data = data;
detStorage.mask = round(mask);
% if par.prealign_data
p.positions_real(p.scanidxs{p.scanID},1) = p.positions_real(p.scanidxs{p.scanID},1);
p.positions_real(p.scanidxs{p.scanID},2) = p.positions_real(p.scanidxs{p.scanID},2);
% end
if p.scanID==length(p.numpts)
p = core.ptycho_adjust_positions(p);
p = core.prepare_initial_guess(p);
end
end
ptycho/+core/+FPM/align_data.m
+141
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%ALIGN_DATA align data along given path
% par = align_data(par, varargin)
%
% align_data is a helper function of FP_prealign
% It uses utils.dftregistration to achieve a subpixel alignment
%
% ** par FP_prealign structure
%
% returns:
% ++ par updated FP_prealign structure
%
%
% see also: core.FPM.FP_prealign
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function par = align_data(par, varargin)
%% start optimization
crop_fct = 4;
import utils.dftregistration
import utils.shiftpp2
import utils.progressbar
align_tic = tic;
for ii=1:length(par.align_section)
N = size(par.align_section{ii},1);
par.shift_cal = zeros(N,2);
par.shift_sum = zeros(N,2);
if par.plot_alignment
fig2 = plotting.smart_figure(2);
clf;
end
crop = par.crop_dft;
data = par.data;
alid = par.alid{ii};
iterii = par.iterii;
data_fft = fft2(data(crop:end-crop,crop:end-crop,:));
for jj = 1:size(alid,2)-1
reg = dftregistration(data_fft(:,:,alid(jj)), data_fft(:,:,alid(jj+1)), 100*iterii);
if abs(reg(3))>25 || abs(reg(4))>25
fprintf('%d cropped registration %d and %d\n', jj, alid(jj), alid(jj+1))
for rep_ii=1:20
sh = [round(rand()*crop*crop_fct) round(rand()*crop*crop_fct)];
reg = dftregistration(fft2(data(crop*crop_fct+sh(1):end-crop*crop_fct+sh(1),crop*crop_fct+sh(2):end-crop*crop_fct+sh(2),alid(jj))), fft2(data(crop*crop_fct+sh(1):end-crop*crop_fct+sh(1),crop*crop_fct+sh(2):end-crop*crop_fct+sh(2),alid(jj+1))), 100*iterii);
if abs(reg(3))<20 && abs(reg(4))<20
break;
end
reg = [0 0 0 0];
end
end
% plot alignment
par.shift_cal(jj,:) = [reg(3) reg(4)];
if par.plot_alignment
shift = sum(par.shift_cal(par.align_section{ii}(1):jj,:),1);
temp = par.data(crop:end-crop,crop:end-crop,par.alid{ii}(jj+1));
set(groot,'CurrentFigure',fig2);
imagesc(abs(shiftpp2(temp, -shift(1),-shift(2))));
title(sprintf('Aligned frame %d', par.alid{ii}(jj)));
% fprintf('shift: %f, %f\n', -shift(1),-shift(2))
drawnow()
end
if utils.verbose >= 2
progressbar(jj,N-1)
end
end
utils.verbose(2, 'Mean shift: %0.3f px', mean(sqrt(sum(abs(par.shift_cal).^2,2))))
utils.verbose(2, 'Max shift: %0.3f px', max(sqrt(sum(abs(par.shift_cal).^2,2))))
for jj = 1:size(par.alid{ii},2)-1
shift = sum(par.shift_cal(par.align_section{ii}(1):jj,:),1);
par.sum_shift_total(par.alid{ii}(jj+1),:) = par.sum_shift_total(par.alid{ii}(jj+1),:) - shift;
par.data(:,:,par.alid{ii}(jj+1)) = abs(shiftpp2(par.data(:,:,par.alid{ii}(jj+1)), -shift(1), -shift(2)));
% par.raw_data(:,:,par.alid{ii}(jj+1)) = abs(shiftpp2(par.raw_data(:,:,par.alid{ii}(jj+1)), -shift(1), -shift(2)));
end
end
align_time = toc(align_tic);
utils.verbose(3, 'Elapsed time for alignment: %0.3f s.', align_time);
end
ptycho/+core/+FPM/distortion_matrix.m
+107
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%DISTORTION_MATRIX
% C = distortion_matrix(p, shift, det_pos, mag_est, varargin)
% calculate the coefficients of distortion matrix of a Fourier
% ptychographic setup
%
% ** p p structure
% ** shift estimated shift
% ** det_pos detector position
% ** mag_est estimation of the magnification
%
% returns:
% ++ C distortion matrix coefficients
%
% see also: core.FPM.FP_prealign
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function C = distortion_matrix(p, shift, det_pos, mag_est, varargin)
import utils.verbose
pos = p.positions_real(p.scanidxs{p.scanID},:);
det_pos_aligned = det_pos + shift.*p.ds.*1e3;
pos = pos.*1e3;
C0(8) = 0;
C0(1) = mag_est;
err_fun = @(C)( mean( sqrt(abs(nansum(abs(det_pos_aligned - core.FPM.get_positions(C, pos)).^2,2)))));
opt.MaxFunEvals = 500000;
if utils.verbose > 3
opt.Display = 'final';
end
[C, fval] = fminsearch( err_fun, C0, opt);
utils.verbose(2, ['Calc. correction: ', repmat('%3.5g ', 1,length(C))], C)
utils.verbose(2, 'Mean error: %d', fval)
if utils.verbose > 2
pos_ret = core.FPM.get_positions(C, pos);
plotting.smart_figure(20)
clf
hold on
plot(pos_ret(:,1), pos_ret(:,2), 'rx')
plot(det_pos_aligned(:,1), det_pos_aligned(:,2), 'bx')
axis equal tight
hold off
end
end
ptycho/+core/+FPM/get_positions.m
+73
View File
@@ -0,0 +1,73 @@
%GET_POSITIONS
% new_pos = get_positions(C, pos)
% helper function for core.FPM.FP_prealign and core.FPM.distortion_matrix
%
% ** C distortion matrix coeffs
% ** pos positions vector
%
% returns:
% new_pos updated positions vector
%
% see also: core.FPM.distortion_matrix
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function new_pos = get_positions(C, pos)
new_pos = (((C(1))*[1-C(4), (-C(2))/180*pi;(C(2)+C(3))/180*pi,1]*(pos' + (C([7,8]))*fliplr(pos)'))' + C([5,6]));
end
ptycho/+core/+FPM/sort_pos.m
+301
View File
@@ -0,0 +1,301 @@
%SORT_POS sort positions
% par = sort_pos(par, varargin)
%
% sort_pos is a helper function of FP_prealign
% it minimizes the path length, similar to the travelling salesman problem,
% albeit optimized for the peculiarities of a Fourier ptychographic scan
%
% ** par FP_prealign structure
%
% *optional*
% ** sort_type 'raster', 'round' or 'raster_lim'
%
% returns:
% ++ par updated FP_prealign structure
%
%
% see also: core.FPM.FP_prealign
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function par = sort_pos(par, varargin)
pos = par.pos;
sel_axis = par.axis;
if nargin > 1
sort_type = varargin{1};
else
sort_type = 'raster';
end
if strcmp(sort_type, 'raster')
% first find highest and lowest measurements
pos_min = min(pos(:,1));
pos_max = max(pos(:,1));
offset = 2e-6;
stepsz = 10e-6;
% now select rows of with width of stepsz
stpindx = 0;
offset = offset + stepsz;
row = {};
while true
lb = pos_min-offset + stpindx*stepsz;
tb = pos_min-offset + (stpindx+1)*stepsz;
if pos_max-tb<stepsz
tb = tb + stepsz;
end
if lb >= pos_max
break;
end
row{stpindx+1} = [];
for i=1:size(pos,1)
if (pos(i,sel_axis)>=lb) && (pos(i,sel_axis)<tb)
row{stpindx+1} = [row{stpindx+1} i];
end
end
stpindx = stpindx + 1;
end
% get pos in correct order for alignment
ascend=true;
alid = [];
if sel_axis==1
axsort = 2;
else
axsort=1;
end
for i=1:size(row,2)
if isempty(row{i})
continue
else
if ascend
direction = 'ascend';
else
direction = 'descend';
end
[~,I] = sort(pos(row{i}, axsort), direction);
row_sel = row{i};
alid = [alid row_sel(I)];
ascend = ~ascend;
end
end
elseif strcmp(sort_type, 'round')
clear alid;
alid{1} = [];
if sel_axis==1
ascend = true;
else
ascend = false;
end
dr = 10e-6;
radii = sqrt(par.pos(:,1).^2 + par.pos(:,2).^2);
rad_max = max(radii);
rad_min = min(radii);
stepindx = 0;
shell = {};
last_run = false;
% find positions in shell
while true
lb = rad_min + stepindx*dr;
tb = rad_min + (stepindx+1)*dr;
if rad_max-tb<dr
tb = tb + dr;
last_run = true;
end
shell{stepindx+1} = [];
for ii=1:size(par.pos,1)
if radii(ii)>=lb && radii(ii)<tb
shell{stepindx+1} = [shell{stepindx+1} ii];
end
end
stepindx = stepindx + 1;
if last_run
break;
end
end
% get pos in correct order for alignment
for shindx=1:size(shell,2)
if isempty(shell{shindx})
fprintf('Warning: Empty shell in path optimization!')
continue
else
if ascend
direction = 'ascend';
else
direction = 'descend';
end
[~,I] = sort(atan2(par.pos(shell{shindx},1),par.pos(shell{shindx},2)), direction);
shell_sel = shell{shindx};
alid{1} = [alid{1} shell_sel(I)];
ascend = ~ascend;
end
end
par.align_section = [];
par.align_section{1} = 1:par.sz(3)-1;
par.align_section{1} = par.align_section{1}';
elseif strcmp(sort_type, 'raster_lim')
clear alid;
alid{1} = [];
% split positions into 4 subsections
par.align_section{1} = find(par.pos(:,mod(sel_axis,2)+1)<-par.rad_filt_min);
par.align_section{2} = find(par.pos(:,mod(sel_axis,2)+1)>par.rad_filt_min);
par.align_section{3} = find(par.pos(:,mod(sel_axis+1,2)+1)<-par.rad_filt_min);
par.align_section{4} = find(par.pos(:,mod(sel_axis+1,2)+1)>par.rad_filt_min);
offset = 2e-6;
stepsz = 10e-6;
% now select rows of with width of stepsz
for jj=1:length(par.align_section)
% first find highest and lowest measurements
pos_min = min(pos(par.align_section{jj},sel_axis));
pos_max = max(pos(par.align_section{jj},sel_axis));
stpindx = 0;
offset = offset + stepsz;
row = {};
last_run = false;
while true
lb = pos_min-offset + stpindx*stepsz;
tb = pos_min-offset + (stpindx+1)*stepsz;
if pos_max-tb<stepsz
tb = tb + stepsz;
last_run = true;
end
row{stpindx+1} = [];
for ii=par.align_section{jj}'
if (pos(ii,sel_axis)>=lb) && (pos(ii,sel_axis)<tb)
row{stpindx+1} = [row{stpindx+1} ii];
end
end
stpindx = stpindx + 1;
if last_run
break;
end
end
% get pos in correct order for alignment
ascend=true;
alid{jj} = [];
if sel_axis==1
axsort = 2;
else
axsort=1;
end
for ii=1:size(row,2)
if isempty(row{ii})
continue
else
if ascend
direction = 'ascend';
else
direction = 'descend';
end
[~,I] = sort(pos(row{ii}, axsort), direction);
row_sel = row{ii};
alid{jj} = [alid{jj} row_sel(I)];
ascend = ~ascend;
end
end
end
end
if par.plot_alignment
fig1 = plotting.smart_figure(1);
clf;
hold on
plot(pos(:,1), pos(:,2))
title('Alignment')
colors = jet(length(par.align_section));
for jj=1:length(par.align_section)
for ii=1:size(alid{jj},2)-1
set(groot,'CurrentFigure',fig1);
plot(pos(alid{jj}(ii),1), pos(alid{jj}(ii),2), 'Color', colors(jj,:), 'Marker', 'x')
pause(0.01)
end
end
hold off
end
par.alid = [];
par.alid = alid;
end
ptycho/+core/+FPM/sort_pos_radii.m
+87
View File
@@ -0,0 +1,87 @@
%SORT_POS_RADII sort positions along their radial distance
% par = sort_pos_radii(par, varargin)
%
% sort_pos_radii is a helper function of FP_prealign
%
% ** par final structure of FP_prealign
%
% returns:
% ++ par updated FP_prealign structure
%
% see also: core.FPM.FP_prealign
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function par = sort_pos_radii(par, varargin)
pos = par.pos;
radii = sqrt(pos(:,1).^2 + pos(:,2).^2);
[~, I] = sort(radii);
orig_data_temp = par.orig_data;
pos_temp = pos;
shift_temp = par.sum_shift_total;
det_pos_temp = par.det_pos;
for ii=1:size(pos,1)
orig_data_temp(:,:,ii) = par.orig_data(:,:,I(ii));
pos_temp(ii,:) = pos(I(ii),:);
shift_temp(ii,:) = par.sum_shift_total(I(ii),:);
det_pos_temp(ii,:) = par.det_pos(I(ii),:);
end
par.pos = pos_temp;
par.sum_shift_total = shift_temp;
par.orig_data = orig_data_temp;
par.det_pos = det_pos_temp;
end
ptycho/+core/+analysis/aligned_FSC_template.m
+204
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@@ -0,0 +1,204 @@
%ALIGNED_FSC_TEMPLATE
% Script to align images and compute FSC
%
% References relevant to this code:
% For using this FSC code with ptychography: J. Vila-Comamala, et al., "Characterization of high-resolution diffractive X-ray optics by ptychographic coherent diffractive imaging," Opt. Express 19, 21333-21344 (2011).
% For subpixel alignment: M. Guizar-Sicairos, et al., "Efficient subpixel image registration algorithms," Opt. Lett. 33, 156 (2008).
% For matching of phase ramp by approximate least squared error: M. Guizar-Sicairos, et al., "Phase tomography from x-ray coherent diffractive imaging projections," Opt. Express 19, 21345-21357 (2011).
%
addpath ../base/
% clear;
% close all;
params = struct;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Reconstruction files %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
openwithGUI = 1; % Use GUI for choosing files, otherwise specify parameters below
scan1 = [89]; % Scan number of first image
scan2 = [90]; % Scan number of second image
sample_name = ''; % File prefix
suffix = 'test_1_recons.h5'; % File suffix
analysis_folder = '../../analysis/'; % /mnt/das-gpfs/work/p12345/analysis/ % /sls/X12SA/Data10/e12345/analysis/
filenamewithpath1 = ['image1.tif']; % Give the full filename and path - Overrides the parameters above; Can be in .mat or any format supported by 'imread'
filenamewithpath2 = ['image2.tif']; % Give the full filename and path - Overrides the parameters above; Can be in .mat or any format supported by 'imread'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Alignment parameters %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
params.verbose_level = 3; % adjust output level
params.plotting = 2; % (3) show everything, (2) show aligned images + FSC, (1) show FSC, (0) none
params.remove_ramp = 1; % Try to remove ramp from whole image before initial alignment
params.image_prop = 'phasor'; % = 'complex' or = 'phasor' (phase with unit amplitude) or = 'phase' (Note: phase should not be used if there is phase wrapping)
params.crop = 'manual';
% '' for using the default half size of the probe
% 'manual' for using GUI to select region. This will display the range, e.g. {600:800, 600:800}
% {600:800, 600:800} for custom vertical and horizontal cropping, respectively
params.flipped_images = 0; % If images are taken with a horizontal flip, e.g. 0 & 180 for tomography
params.GUIguess = 0; % To click for an initial alignment guess, ignores the values below
params.guessx = []; % Some initial guess for x alignment
params.guessy = [];
%%%%%%%%%%%%%%%%%%%%%%
%%% FSC parameters %%%
%%%%%%%%%%%%%%%%%%%%%%
params.taper = 20; % Pixels of image tapering (smoothing at edges) - Increase until the FSC does not change anymore
params.SNRt = 0.5; % SNRt = 0.2071 for 1/2 bit threshold for resolution of the average of the 2 images
% SNRt = 0.5 for 1 bit threshold for resolution of each individual image
params.thickring = 10; % Thickness of Fourier domain ring for FSC in pixels
params.freq_thr = 0.05; % (default 0.05) To ignore the crossings before freq_thr for determining resolution
%%%%%%%%%%%%
%%% misc %%%
%%%%%%%%%%%%
params.prop_obj = false; % propagation distance at the sample plane; leave empty to use the value from the reconstruction p structure; set to "false" for no propagation
params.apod = []; % if true, applies an apodization before propagating by params.prop_obj, the apodization border is around the valid reconstruction region; leave empty to use the value from the reconstruction p structure
params.lambda = []; % wavelength; needed for propagating the object; leave empty to use the value from the reconstruction p structure
params.pixel_size = []; % pixel size at the object plane; leave empty to use the value from the reconstruction p structure
%%%%%%%%%%%%%%%%%%%%
%%% FP parameter %%%
%%%%%%%%%%%%%%%%%%%%
%%% the following parameters are ignored, unless p.fourier_ptycho==true %%%
params.filter_FFT = true; % apply a circular mask to the reconstructed spectrum (needs p.plot_maskdim)
params.crop_factor = 0.9; % crop final image by the given factor
params.crop_asize = [800 800]; % crop object before applying the FFT
params.z_lens = 49.456e-3; % FZP focal distance
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Do not modify below %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
caller = dbstack;
if length(caller)==1
addpath('utils')
scanfolder1 = utils.compile_x12sa_dirname(scan1(1)); % Looks for the file in this folder, I leave a variable so that the folder can be overriden
scanfolder2 = utils.compile_x12sa_dirname(scan2(1));
%%% Opening file %%%
if openwithGUI
disp('Using GUI open mode')
if exist([analysis_folder scanfolder1],'dir')
uipath1 = [analysis_folder scanfolder1];
else
uipath1 = [];
end
if exist([analysis_folder scanfolder2],'dir')
uipath2 = [analysis_folder scanfolder2];
else
uipath2 = [];
end
filetypes = {'*.h5;*.mat','Reconstruction files (*.h5,*.mat)'; '*.*', 'All Files (*.*)'};
[filename, pathname] = uigetfile(filetypes,'Open first reconstruction', uipath1);
file{1} = fullfile(pathname,filename);
[filename, pathname] = uigetfile(filetypes,'Open second reconstruction', uipath2);
file{2} = fullfile(pathname,filename);
else
% Checking recons 1 %
if ~isempty(filenamewithpath1)
file{1} = filenamewithpath1;
else
file{1} = fullfile(analysis_folder,scanfolder1,[sample_name '*' suffix]);
D = dir(file{1});
if numel(D) == 0
error(['I did not find any file: ' file{1}])
elseif numel(D) > 1
warning(['I found many files with the mask: ' file{1}]);
warning(['I selected ' D(1).name]);
end
file{1} = fullfile(analysis_folder,scanfolder1,D(1).name);
end
% Checking recons 2 %
if ~isempty(filenamewithpath2)
file{2} = filenamewithpath2;
else
file{2} = fullfile(analysis_folder,scanfolder2,[sample_name '*' suffix]);
D = dir(file{2});
if numel(D) == 0
error(['I did not find any file: ' file{2}])
elseif numel(D) > 1
warning(['I found many files with the mask: ' file{2}]);
warning(['I selected ' D(1).name]);
end
file{2} = fullfile(analysis_folder,scanfolder2,D(1).name);
end
end
% Making a JPEG of FSC
[~,filename] = fileparts(file{1});
params.out_fn = sprintf('%sonline/ptycho/%s_FSC.jpg', analysis_folder, filename);
[resolution] = aligned_FSC(file{1}, file{2}, params);
end
% 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 PtychoShelves
% computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
%
% Terms and Conditions of the LICENSE
% 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
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% another computing language:
% "Data processing was carried out using the PtychoShelves 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
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
% and 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 LSQ-ML:
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
% (doi: 10.1364/OE.26.003108),
% 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),
% and/or for OPRP:
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, Ptychographic coherent diffractive imaging with orthogonal probe relaxation.
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
ptycho/+core/+analysis/calc_FSC.m
+121
View File
@@ -0,0 +1,121 @@
%CALC_FSC calculate the FRC for the reconstructed scans
% ** p p structure
%
% returns:
% ++ p updated p structure
% ++ resolution FSC resolution
%
% see also: aligned_FSC
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p, resolution] = calc_FSC(p)
% get parameters from template
run('aligned_FSC_template')
crop = round(p.object_size(1,:)*0.1);
ob_good_range = {p.asize(1)/2+crop(1):p.object_size(1,1)-p.asize(1)/2-crop(1), p.asize(2)/2+crop(2):p.object_size(1,2)-p.asize(2)/2-crop(2)};
% store verbose level
verbose_lvl = utils.verbose;
% adjust structure
params.plotting = (p.plot.show_FSC+max(utils.verbose-2, 0))*p.use_display;
params.crop = ob_good_range;
params.pixel_size = p.dx_spec;
params.asize = p.asize;
params.apod = p.plot.obj_apod;
params.thickring = ceil(min(min(p.object_size-p.asize))/100); % 100 rings should be enough
params.show_summary = utils.verbose > 2;
params.image_prop = 'variation'; %% seems to provide better alignement stability then the original phasor option
utils.verbose(struct('prefix', {'analysis'}))
utils.verbose(0, 'Calculating FSC ...')
% if the original object is available, use it for comparison
if isfield(p, 'simulation') && isfield(p.simulation, 'obj')
params.fname{1} = 'Reconstruction';
params.fname{2} = 'Model';
obj{1} = prod(p.object{1}(:,:,1,:),4);
obj{2} = prod(p.simulation.obj{1}(:,:,1,:),4);
else
params.fname{1} = sprintf('S%05u', p.scan_number(1));
params.fname{2} = sprintf('S%05u', p.scan_number(2));
for ii=1:p.numobjs
obj{ii} = prod(p.object{ii}(:,:,1,:),4);
end
end
if verbose_lvl < 3
params.verbose_level = 1;
end
% update params if needed
if isfield(p, 'FSC')
params = utils.update_param(params, p.FSC);
end
resolution = aligned_FSC(obj{1}, obj{2}, params);
% restore verbose level
utils.verbose(verbose_lvl);
utils.verbose(struct('prefix', {'saving'}))
p.FSC.resolution = resolution;
p.FSC.params = params;
end
ptycho/+core/+analysis/plot_error_metric.m
+184
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@@ -0,0 +1,184 @@
%PLOT_ERROR_METRIC plot evolution of the provided error metric
% ** p p structure
% ** final bool - indicates if it is final plot
% ** use_display if false, do not open figures to plot the results
%
% *returns*
% ++fig - image handle
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function fig4 = plot_error_metric(p, final, use_display)
if ~use_display
fig4 = plotting.smart_figure('Visible', 'off');
else
if p.plot.windowautopos && ~ishandle(4) && isfield(p.plot, 'scrsz') % position it only if the window does not exist
fig4 = plotting.smart_figure(4);
set(gcf,'Outerposition',[1 1 ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig4 = plotting.smart_figure(4);
end
end
% if p.numobjs==1; clf; end
Neng = length(p.engines);
Nrows = 1+p.plot.positions;
if final
eng_id = 0;
err_final = [];
for ieng=1:Neng
eng = p.engines{ieng};
if ~isfield(eng, 'error_metric_final'); continue; end
iieng = 1;
if ~iscell(eng.error_metric_final)
err_final(eng_id+1).iteration = eng.error_metric_final.iteration;
err_final(eng_id+1).value = eng.error_metric_final.value;
err_final(eng_id+1).method = eng.error_metric_final.method;
err_final(eng_id+1).err_metric = eng.error_metric_final.err_metric;
else
for iieng=1:length(eng.error_metric_final)
err_final(eng_id+iieng).iteration = eng.error_metric_final{iieng}.iteration;
err_final(eng_id+iieng).value = eng.error_metric_final{iieng}.value;
err_final(eng_id+iieng).method = eng.error_metric_final{iieng}.method;
err_final(eng_id+iieng).err_metric = eng.error_metric_final{iieng}.err_metric;
end
end
eng_id = eng_id + iieng;
end
for ieng = 1:length(err_final)
subplot(Nrows,length(err_final),ieng);
cla()
plot(err_final(ieng).iteration,err_final(ieng).value);
if ~isvector(err_final(ieng).value) % error values for each position -> plot also average
hold on
plot(err_final(ieng).iteration, mean(err_final(ieng).value,2), '-k', 'LineWidth',2)
hold off
end
title(err_final(ieng).method,'interpreter','none');
legend(err_final(ieng).err_metric)
grid on
axis tight
xlabel('Iteration')
if p.plot.log_scale(1)
set(gca, 'xscale', 'log')
end
if p.plot.log_scale(2)
if all(err_final(ieng).value > 0); set(gca, 'yscale', 'log'); end
end
if ~isempty(err_final(ieng).iteration)
xlim([0, err_final(ieng).iteration(end)])
end
end
plotting.suptitle(replace(sprintf('error: %s %s', p.plot.errtitlestring, p.plot.extratitlestring),'_', '-'), ...
'Interpreter', 'none');
elseif isfield(p, 'error_metric') && ~isempty(p.error_metric)
err = p.error_metric;
if p.plot.positions
subplot(2,1,1);
end
cla()
if iscell(err)
err = cell2mat(err);
end
if ~isempty(err(1).iteration)&&size(err,1)==2
try
subplot(2,2,1);
plot(err(1).iteration, err(1).value); grid on; title(sprintf('error\n'),'interpreter','none');
if p.plot.log_scale(1)
set(gca, 'xscale', 'log')
end
if p.plot.log_scale(2)
if all(err > 0); set(gca, 'yscale', 'log'); end
end
subplot(2,2,2);
plot(err(1).iteration(end)+err(2).iteration, log10(err(2).value),'r'); grid on
if p.plot.log_scale(1)
set(gca, 'xscale', 'log')
end
if p.plot.log_scale(2)
if all(err > 0); set(gca, 'yscale', 'log'); end
end
catch
end
else
subplot(2,2,[1 2]);
plot(err(1).iteration,err(1).value,'r'); grid on
if p.plot.log_scale(1)
set(gca, 'xscale', 'log')
end
if p.plot.log_scale(2)
if all(err(1).value > 0); set(gca, 'yscale', 'log'); end
end
axis tight
end
plotting.suptitle(sprintf('error: %s %s\n', p.plot.errtitlestring, p.plot.extratitlestring), 'Interpreter', 'none');
end
end
ptycho/+core/+analysis/plot_object_spectrum.m
+127
View File
@@ -0,0 +1,127 @@
%PLOT_OBJECT_SPECTRUM
% plot fourier transformation of the reconstructed object
%
% ** p p structure
% ** use_display if false, dont plot results on screen
%
% *returns*
% ++fig - image handle
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function fig6 = plot_object_spectrum(p, use_display)
count_plotobj = 1;
[objpix] = get_object_pixel_size(p);
for obnum = 1:p.numobjs
for obmode = 1:p.object_modes
ob_plot = p.object{obnum}(:,:,obmode,:);
ob_plot = prod(ob_plot,4); % make one eDoF image
if ~p.fourier_ptycho
ob_plot = fftshift(fft2(ob_plot));
end
absob = abs(ob_plot);
if ~use_display && count_plotobj == 1
fig6 = plotting.smart_figure('Visible', 'off');
else
if count_plotobj == 1
if p.plot.windowautopos && ~ishandle(6) % position it only if the window does not exist
fig6 = plotting.smart_figure(6);
set(gcf,'Outerposition',[ceil(p.plot.scrsz(4)*2/p.plot.horz_fact)+1 ceil(p.plot.scrsz(4)/2) ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig6 = plotting.smart_figure(6);
end
else
set(groot,'CurrentFigure',fig6);
end
end
ax_abs(count_plotobj)=subplot(p.plot.subplwinobj(1),p.plot.subplwinobj(2),count_plotobj);
good_fov(1) = (p.object_size(obnum,1)/2 - p.asize(1)/2) .*p.dx_spec(1)*1e6;
good_fov(2) = (p.object_size(obnum,2)/2 - p.asize(2)/2) .*p.dx_spec(2)*1e6;
if ~p.plot.realaxes
imagesc(log10(absob));
else
obj_ax = {([1 p.object_size(obnum,2)]-floor(p.object_size(obnum,2)/2)+1)*objpix(2)*1e6,([1 p.object_size(obnum,1)]-floor(p.object_size(obnum,1)/2)+1)*objpix(1)*1e6};
imagesc(obj_ax{:},log10(absob));
xlabel('\mum')
ylabel('\mum')
end
colorbar
axis image xy tight
if p.share_object
title(sprintf('log10 object spectrum: %s %s', p.plot.obtitlestring, p.plot.extratitlestring),'interpreter','none');
else
title(sprintf('log10 object spectrum: %s %s', p.scan_str{obnum}, p.plot.extratitlestring),'interpreter','none');
end
count_plotobj = count_plotobj + 1;
end
end
end
ptycho/+core/+analysis/plot_objects.m
+350
View File
@@ -0,0 +1,350 @@
%PLOT_OBJECTS plot reconstructed objects and layers
% ** p p structure
% ** use_display if false, dont plot results on screen
% *returns*
% ++fig - image handle
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [fig1, fig2] = plot_objects(p, use_display)
import math.*
import utils.*
% prepare quadratic phase for FP backpropagation and calculate the pixel
% size
[objpix, FP_pre_phase_factor] = get_object_pixel_size(p);
% mask for backpropagation (FP only)
if p.fourier_ptycho && p.plot.filt
for ii=1:p.numobjs
ob_mask{ii} = ifftshift(filt2d_pad(p.object_size(ii,:), round(p.plot.FP_maskdim/p.dx_spec(1)*1.2), round(p.plot.FP_maskdim/p.dx_spec(1)), 'circ'));
end
end
if length(unique(p.share_object_ID)) ~= length(p.object)
% the GPU engine allows to modify the sharing within the engine and it
% can cause inconsitencies during plotting
utils.verbose(0,'Number of object does not correspond to the number of share_object_ID, resetting ... ')
if length(p.object) == 1
% assume shared scans
p.share_object_ID(:) = 1;
elseif length(p.object) == length(p.share_object_ID)
% assume unshared scans
p.share_object_ID(:) = 1:length(p.object);
else
error('Correct settings of the shared objects could not be determined')
end
end
count_plotobj = 1;
%modified by YJ for electron pty
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
unitFactor = 0.1;
unitLabel = 'nm';
else %X-ray
unitFactor = 1e6;
unitLabel = '\mum';
end
for obmode = 1:p.object_modes
for obnum = 1:p.numobjs
% number of layers for multilayer object reconstruction
Nlayers = size(p.object{obnum},4);
% get the new object - 2D or 3D array
ob_plot = p.object{obnum}(:,:,obmode,:);
% enforce update of the object_size
object_size(obnum,:) = [size(ob_plot,1), size(ob_plot,2)];
% get the actual reconstructed area and calculate the corresponding
% mask
ob_good_range = {p.asize(1)/2:object_size(obnum,1)-p.asize(1)/2, p.asize(2)/2:object_size(obnum,2)-p.asize(2)/2};
plot_mask = false(object_size(obnum,:));
plot_mask(ob_good_range{:},:) = true;
% remove phase offset and phase ramp (if requested)
ob_plot = utils.stabilize_phase(ob_plot, 'weight', plot_mask, ...
'remove_ramp', p.plot.remove_phase_ramp);
if p.fourier_ptycho
% propagate from lens plane to object plane
ob_plot = ifft2(ifftshift(ob_plot.*ob_mask{obnum}))*p.object_size(obnum,1).*ifftshift(FP_pre_phase_factor{obnum});
else
if p.plot.show_layers
if ~p.plot.show_layers_stack
% plot multiple layers next to each other
ob_plot = reshape(ob_plot,object_size(obnum,1), object_size(obnum,2)* Nlayers);
object_size(obnum,:) = size(ob_plot);
plot_mask = repmat(plot_mask,1,Nlayers);
else
% 3D object for imagesc3D
ob_plot = squeeze(ob_plot);
end
else
% plot single eDOF image
ob_plot = prod(ob_plot,4); % show extended depth of focus images
end
end
% apply apodization
if p.plot.obj_apod
try
filt_size = [size(ob_good_range{1},2) size(ob_good_range{2},2)];
ob_plot_size = [size(ob_plot,1),size(ob_plot,2)];
ob_plot = ob_plot.*fftshift(utils.filt2d_pad(ob_plot_size, max(1,filt_size), max(1,filt_size-min(floor(filt_size.*0.05)))));
catch
utils.verbose(2, 'Failed to apply apodization.')
end
end
% propagate object
if p.plot.prop_obj ~= 0
ob_plot = utils.prop_free_nf(ob_plot, p.lambda, p.plot.prop_obj, objpix);
end
% get complex conjugate
if p.plot.conjugate
ob_plot = conj(ob_plot);
end
% precalculate absorption and phase
absob = abs(ob_plot);
phob = angle(ob_plot);
%%%%%%%%%%%%%%%%%
%%% AMPLITUDE %%%
%%%%%%%%%%%%%%%%%
% prepare figure handle for absorption images
if ~use_display && count_plotobj == 1
fig1 = plotting.smart_figure('Visible', 'off');
else
if count_plotobj == 1
if p.plot.windowautopos && ~ishandle(1) % position it only if the window does not exist
fig1 = plotting.smart_figure(1);
set(gcf,'Outerposition',[ceil(p.plot.scrsz(4)/p.plot.horz_fact)+1 ceil(p.plot.scrsz(4)/2) ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig1 = plotting.smart_figure(1);
end
clf;
else
set(groot,'CurrentFigure',fig1);
end
end
ax_abs(count_plotobj)=subplot(p.plot.subplwinobj(1),p.plot.subplwinobj(2),count_plotobj);
range = [min(p.positions([p.scanidxs{p.share_object_ID == obnum}],:)), ...
max(p.positions([p.scanidxs{p.share_object_ID == obnum}],:))];
% FOV [xmin, ymin, xmax, ymax]
good_fov(1) = -(p.object_size(obnum,1)/2 - p.asize(1)/2-range(1));
good_fov(2) = -(p.object_size(obnum,2)/2 - p.asize(2)/2-range(2));
good_fov(3) = good_fov(1) + range(3)-range(1);
good_fov(4) = good_fov(2) + range(4)-range(2);
good_fov = good_fov.*p.dx_spec([1,2,1,2])*unitFactor;
fov_box = [good_fov(2),good_fov(1),good_fov(4)-good_fov(2), good_fov(3)-good_fov(1)]; % [xmin, ymin, W, H] coordinates of the FOV box
% plot the absorption
if ~p.plot.realaxes
plotting.imagesc3D(absob);
if p.plot.fov_box && ~(p.plot.show_layers && ~p.plot.show_layers_stack && Nlayers > 1)
rectangle('Position',[p.asize([2,1])/2 , p.object_size([2,1]) - p.asize([2,1])], 'EdgeColor', p.plot.fov_box_color)
end
else
obj_ax = {([1 object_size(obnum,2)]-floor(object_size(obnum,2)/2)+1)*objpix(2)*unitFactor,([1 object_size(obnum,1)]-floor(object_size(obnum,1)/2)+1)*objpix(1)*unitFactor};
plotting.imagesc3D(obj_ax{:},absob);
xlabel(unitLabel)
ylabel(unitLabel)
if p.plot.fov_box && p.plot.show_layers && ~p.plot.show_layers_stack && Nlayers > 1
% plot bar around each layer
for layer = 1:Nlayers
rectangle('Position', [good_fov(2) + (layer-(Nlayers+1)/2)*p.object_size(obnum,2).*p.dx_spec(1)*unitFactor ,good_fov(1), good_fov(4)-good_fov(2),good_fov(3)-good_fov(1)], 'EdgeColor', p.plot.fov_box_color)
end
elseif p.plot.fov_box
rectangle('Position',fov_box, 'EdgeColor', p.plot.fov_box_color)
end
end
% calculate a proper colorbar range
try
amp_range = sp_quantile(absob(plot_mask),[1e-4,1-1e-4], 10);
catch
keyboard
end
if amp_range(1) < amp_range(2)
caxis(amp_range);
end
colormap(bone(256)); colorbar
axis image xy tight
if check_option(p, 'show_only_FOV') && p.plot.realaxes
axis([good_fov(2) good_fov(4) good_fov(1) good_fov(3)])
elseif check_option(p, 'show_only_FOV') && ~p.plot.realaxes
axis([p.asize(2)/2, object_size(obnum,2) - p.asize(2)/2, p.asize(1)/2, object_size(obnum,1) - p.asize(1)/2, ])
end
% prepare title strings
if p.share_object
title(sprintf('amplitude: %s %s', p.plot.obtitlestring, p.plot.extratitlestring),'interpreter','none');
else
title(sprintf('amplitude: %s %s', p.scan_str{obnum}, p.plot.extratitlestring),'interpreter','none');
end
%%%%%%%%%%%%%%%%%%%
%%%%%% PHASE %%%%%%
%%%%%%%%%%%%%%%%%%%
% prepare figure handle for phase images
if ~use_display && count_plotobj == 1
fig2 = plotting.smart_figure('Visible', 'off');
else
if count_plotobj == 1
if p.plot.windowautopos && ~ishandle(2) % position it only if the window does not exist
fig2 = plotting.smart_figure(2);
set(gcf,'Outerposition',[1 ceil(p.plot.scrsz(4)/2) ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig2 = plotting.smart_figure(2);
end
clf;
else
set(groot,'CurrentFigure',fig2);
end
end
if check_option(p.plot, 'residua') && ~check_option(p, 'fourier_ptycho')
% find residua to plot and avoid plotting residua in not illuminated regions
residues = plot_mask(2:end, 2:end) & (abs(utils.findresidues(ob_plot)) > 0.1);
[residues_ind{1}, residues_ind{2}] = find(residues);
end
ax_phase(count_plotobj)=subplot(p.plot.subplwinobj(1),p.plot.subplwinobj(2),count_plotobj);
% plot the phase
if ~p.plot.realaxes
plotting.imagesc3D(phob);
if p.plot.fov_box && ~(p.plot.show_layers && ~p.plot.show_layers_stack && Nlayers > 1)
rectangle('Position',[p.asize([2,1])/2 , p.object_size([2,1]) - p.asize([2,1])], 'EdgeColor', p.plot.fov_box_color)
end
if check_option(p.plot, 'residua')
hold all
plot(residues_ind{[2,1]},'or')
hold off
end
else
plotting.imagesc3D(obj_ax{:},phob);
xlabel(unitLabel)
ylabel(unitLabel)
if p.plot.fov_box && p.plot.show_layers && ~p.plot.show_layers_stack && Nlayers > 1
% plot bar around each layer
for layer = 1:Nlayers
rectangle('Position', [good_fov(2) + (layer-(Nlayers+1)/2)*p.object_size(obnum,2).*p.dx_spec(1)*unitFactor ,good_fov(1), good_fov(4)-good_fov(2),good_fov(3)-good_fov(1)], 'EdgeColor', p.plot.fov_box_color)
end
elseif p.plot.fov_box
rectangle('Position',fov_box, 'EdgeColor', p.plot.fov_box_color)
end
if check_option(p.plot, 'residua')
hold all
plot((residues_ind{2}-size(ob_plot,2)/2)*objpix(2)*unitFactor,(residues_ind{1}-size(ob_plot,1)/2)*objpix(1)*unitFactor,'or')
hold off
end
end
p_range = sp_quantile(phob(plot_mask),[1e-4,1-1e-4], 10);
if p_range(1) < p_range(2)
caxis(p_range);
end
colormap(bone(256));colorbar
if p.share_object
title(sprintf('phase: %s %s', p.plot.obtitlestring, p.plot.extratitlestring),'interpreter','none');
else
title(sprintf('phase: %s %s', p.scan_str{obnum}, p.plot.extratitlestring),'interpreter','none');
end
axis image xy tight
if check_option(p, 'show_only_FOV') && p.plot.realaxes
axis([-good_fov(2) good_fov(2) -good_fov(1) good_fov(1)])
elseif check_option(p, 'show_only_FOV') && ~p.plot.realaxes
axis([p.asize(2)/2, object_size(obnum,2) - p.asize(2)/2, p.asize(1)/2, object_size(obnum,1) - p.asize(1)/2, ])
end
count_plotobj = count_plotobj + 1;
end
if use_display
% link axes in case of zooming
try linkaxes([ax_abs, ax_phase], 'xy'); end
end
end
end
ptycho/+core/+analysis/plot_positions.m
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% PLOT_POSITIONS
% plot positions of the illumination with respect to the object
%
% ** p p structure
%
%
%
%
function plot_positions(p)
%modified by YJ for electron pty
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
unitFactor = 0.1;
unitLabel = 'nm';
else %X-ray
unitFactor = 1e6;
unitLabel = '\mum';
end
% NOTE: the positions are appended to fig 4 (cf. plot_error_metric)
numscans = length(p.scan_number);
scanfirstindex = [1 cumsum(p.numpts)+1]; % First index for scan number
for ii = 1:numscans
p.scanidxs{ii} = scanfirstindex(ii):(scanfirstindex(ii+1)-1);
end
subplot(2,2,[3 4]);
for ii = 1:numscans
idx = min(ii,p.numobjs);
positions_centered(p.scanidxs{ii},:) = p.positions(p.scanidxs{ii},:) - p.object_size(idx,:)/2 + p.asize/2;
end
cla()
if p.plot.realaxes
scale = p.dx_spec*unitFactor;
else
% plot positions in pixels, useful for grazing incidence ptycho
scale = [1,1];
end
hold all
for ii = 1:numscans
plot(positions_centered(p.scanidxs{ii},2).*scale(2), ...
positions_centered(p.scanidxs{ii},1).*scale(1),...
'x:','markersize',4);
end
grid on;
if numscans==1
title('positions','interpreter','none');
else
title('positions (red 1st, blue 2nd)','interpreter','none');
end
if p.plot.realaxes
xlabel(unitLabel);
ylabel(unitLabel);
else
xlabel('pixels');
ylabel('pixels');
end
axis tight equal;
end
ptycho/+core/+analysis/plot_probes.m
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%PLOT_PROBES plot reconstructed probes
% ** p p structure
% ** use_display if false, dont plot results on screen
%
% *returns*
% fig - image handle
function fig3 = plot_probes(p, use_display)
import utils.rmphaseramp
import plotting.c2image
%modified by YJ for electron pty
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
unitFactor = 0.1;
unitLabel = 'nm';
else %X-ray
unitFactor = 1e6;
unitLabel = '\mum';
end
count_plotprb = 1;
for prmode = 1:p.probe_modes
for prnum = 1:p.numprobs
aux = p.probes(:,:,prnum,:);
E = sum(abs(aux(:)).^2);
if ~use_display && count_plotprb == 1
fig3 = plotting.smart_figure('Visible', 'off');
else
if count_plotprb == 1
if p.plot.windowautopos && ~ishandle(3) % position it only if the window does not exist
fig3 = plotting.smart_figure(3);
set(gcf,'Outerposition',[ceil(p.plot.scrsz(4)/p.plot.horz_fact) 1 ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig3 = plotting.smart_figure(3);
end
clf;
else
set(groot,'CurrentFigure',fig3);
end
end
probe = p.probes(:,:,prnum,prmode);
if p.plot.remove_phase_ramp
probe = rmphaseramp(rmphaseramp(probe,'abs'),'abs');
end
subplot(p.plot.subplwinprob(1),p.plot.subplwinprob(2),count_plotprb)
if ~p.plot.realaxes
imagesc(c2image(probe));
else
iaxis{1} = ([1 p.asize(2)]-floor(p.asize(2)/2)+1)*p.dx_spec(2)*unitFactor;
iaxis{2} = ([1 p.asize(1)]-floor(p.asize(1)/2)+1)*p.dx_spec(1)*unitFactor;
imagesc(iaxis{:},c2image(probe));
xlabel(unitLabel)
ylabel(unitLabel)
end
if p.share_probe
titlestring = sprintf('probe: %s %s', p.plot.prtitlestring, p.plot.extratitlestring);
else
titlestring = sprintf('probe: %s %s',p.scan_str{prnum}, p.plot.extratitlestring);
end
if p.probe_modes > 1
Ethis = sum(sum(abs(p.probes(:,:,prnum,prmode)).^2));
Ethis = Ethis/E;
titlestring = [titlestring sprintf(' %.1f%%',Ethis*100)];
end
title(titlestring,'interpreter','none');
axis image xy tight
count_plotprb = count_plotprb + 1;
end
end
end
ptycho/+core/+analysis/plot_probes_at_detector.m
+66
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% PLOT_PROBES_AT_DETECTOR
% plot reconstructed probes propagated to the detector
%
% ** p p structure
% ** use_display if false, do now show plots
%
% *returns*
% ++fig - image handle
%
%
function fig5 = plot_probes_at_detector(p, use_display)
count_plotprb = 1;
for prmode = 1:p.probe_modes
for prnum = 1:p.numprobs
aux = p.probes(:,:,prnum,:);
E = sum(abs(aux(:)).^2);
if ~use_display && count_plotprb == 1
fig5 = plotting.smart_figure('Visible', 'off');
else
if count_plotprb == 1
if p.plot.windowautopos && ~ishandle(5) % position it only if the window does not exist
fig5 = plotting.smart_figure(5);
set(gcf,'Outerposition',[ceil(p.plot.scrsz(4)*2/p.plot.horz_fact) 1 ceil(p.plot.scrsz(4)/p.plot.horz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
else
fig5 = plotting.smart_figure(5);
end
clf;
else
set(groot,'CurrentFigure',fig5);
end
end
subplot(p.plot.subplwinprob(1),p.plot.subplwinprob(2),count_plotprb)
af_probe = abs(fftshift(fft2(p.probes(:,:,prnum,prmode)))).^2;
max_af_probe = max(af_probe(:));
if isfield(p, 'renorm')
af_probe = af_probe / single(p.renorm).^2;
end
if ~p.plot.realaxes
imagesc(log10(1e-2*max_af_probe+af_probe));
else
imagesc(([1 p.asize(2)]-floor(p.asize(2)/2)+1)*p.ds*1e3,([1 p.asize(1)]-floor(p.asize(1)/2)+1)*p.ds*1e3,log10(1e-2*max_af_probe+af_probe));
xlabel('mm')
ylabel('mm')
end
if p.share_probe
titlestring = sprintf('log10 FFT probe: %s %s', p.plot.prtitlestring, p.plot.extratitlestring);
else
titlestring = sprintf('log10 FFT probe: %s %s',p.scan_str{prnum}, p.plot.extratitlestring);
end
if p.probe_modes > 1
Ethis = sum(sum(abs(p.probes(:,:,prnum,prmode)).^2));
Ethis = Ethis/E;
titlestring = [titlestring sprintf(' %.1f%%',Ethis*100)];
end
title(titlestring,'interpreter','none');
axis image xy tight
colormap(plotting.franzmap)
colorbar
count_plotprb = count_plotprb + 1;
end
end
end
ptycho/+core/+analysis/plot_raw_data.m
+60
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%PLOT_RAW_DATA Simple plotting routine for masked raw data
%
% ** p p structure
%
% see also: core.initialize_ptycho
function plot_raw_data(p)
import utils.verbose
magnitude = p.fmag .* p.fmask;
max_intensity = (max(max(magnitude))/p.renorm).^2;
verbose(1, 'Plotting prepared data.')
kk = 1;
title_list = cell(1,size(p.fmag,3));
for jj=1:p.numscans
for ii = p.scanidxs{jj}
title_list{kk} = sprintf('Scan S%0.5d - Point (%d) maximal intensity:%.4g',p.scan_number(jj), ii, max_intensity(kk));
kk = kk +1 ;
end
end
% really enforce popup of this figure, it gets very annoying when running somewhere in background
if ishandle(10)
close(10);
end
fig = figure(10);
if ~p.fourier_ptycho
plt_fnct = @(x)(log10(0.1+math.fftshift_2D(x / p.renorm).^2));
else
plt_fnct = @(x)((x / p.renorm).^2);
end
plotting.imagesc3D(magnitude, 'title_list', title_list, 'fnct', plt_fnct);
if ~p.fourier_ptycho
caxis([-1, log10(max(max_intensity))])
else
caxis(math.sp_quantile((magnitude/p.renorm).^2, [1e-6 1-1e-6], 10))
end
c = colorbar;
ylabel(c, 'log10 counts')
ax = fig.CurrentAxes;
axis(ax, 'xy', 'equal', 'image')
colormap(ax, 'plotting.franzmap')
if p.plot.windowautopos
horiz_fact = 2.5;
if check_option(p.plot, 'object_spectrum')
pos = 3;
else
pos = 2;
end
set(gcf,'Outerposition',[ceil(min(p.plot.scrsz(3)-ceil(p.plot.scrsz(4)/2), ceil(p.plot.scrsz(4)*pos/horiz_fact))) ceil(p.plot.scrsz(4)/2) ceil(p.plot.scrsz(4)/horiz_fact) ceil(p.plot.scrsz(4)/2)]) %[left, bottom, width, height
end
ax.play(ax);
end
ptycho/+core/+analysis/plot_results.m
+322
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%%% PLOT_RESULTS plotting routine for ptychographic reconstructions
% ** p p structure from a ptychographic reconstruction
%
% *optional*
% ** use_display show plots (default: true)
% ** store_images write images to disk (default: false)
% ** final show all error metrics for a final plot (default: false)
% ** save_path change default save_path (p.save_path) for saving jpgs
%
% EXAMPLES:
% core.analysis.plot_results(p);
% core.analysis.plot_results(p, 'store_images', true);
% core.analysis.plot_results(p, 'use_display', false, 'store_images', true);
%
%
% see also: plotting.ptycho_show_recons
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function plot_results(p, varargin)
import plotting.*
import utils.*
import math.sp_quantile
% parse p.plot inputs
check_input = @(x) islogical(x) || isnumeric(x);
parse_p = inputParser;
parse_p.KeepUnmatched = true;
parse_p.addParameter('fourier_ptycho', false, check_input)
parse_p.addParameter('object_spectrum', [], check_input)
parse_p.addParameter('filt', true, check_input)
parse_p.addParameter('plot_layers', true, check_input)
parse_p.addParameter('plot_layers_stack', true, check_input)
parse_p.addParameter('remove_phase_ramp', false, check_input)
parse_p.addParameter('prop_obj',0, check_input)
parse_p.addParameter('plot_conj', false, check_input)
parse_p.addParameter('obj_apod', false, check_input)
parse_p.parse(p.plot);
p.plot = utils.update_param(p.plot, parse_p.Results);
% parse p.save
parse_p = inputParser;
parse_p.KeepUnmatched = true;
parse_p.addParameter('store_images_format', 'png', @(x)ismember(x, {'png', 'jpg'}))
parse_p.addParameter('store_images_dpi', 150, @math.isint)
parse_p.parse(p.save);
p.save = utils.update_param(p.save, parse_p.Results);
if isempty(varargin) || ischar(varargin{1})
par = inputParser;
par.addParameter('use_display', true, check_input)
par.addParameter('store_images', false, check_input)
par.addParameter('final', false, check_input)
par.addParameter('save_path',[], @ischar)
par.parse(varargin{:})
vars = par.Results;
end
if p.fourier_ptycho
p.plot.fov_box = false;
end
if isempty(p.plot.object_spectrum)
p.plot.object_spectrum = (utils.verbose>=3);
end
if ~isfield(p.plot, 'log_scale')
p.plot.log_scale = [false false];
elseif isscalar(p.plot.log_scale)
p.plot.log_scale = repmat(p.plot.log_scale,1,2);
end
% Subplot geometry
% p.subplwin = [floor(sqrt(p.numscans)) ceil(p.numscans/floor(sqrt(p.numscans)))];
numwinobj = p.numobjs*p.object_modes;
p.plot.subplwinobj = [floor(sqrt(numwinobj)) ceil(numwinobj/floor(sqrt(numwinobj)))];
if p.numprobs == 1 || p.probe_modes == 1
% distribute as efficiently as possible
numwinprob = p.numprobs*p.probe_modes;
p.plot.subplwinprob = [floor(sqrt(numwinprob)) ceil(numwinprob/floor(sqrt(numwinprob)))];
else
% show scans in columns and probe modes in rows
p.plot.subplwinprob = [p.probe_modes, p.numprobs];
end
if check_option(p.plot, 'subplwinobj_dir', 'vertical') || (p.plot.show_layers && size(p.object{1},4) > 1)
% prefer to stack the object verticaly , useful for multilayer object plotting
p.plot.subplwinobj = sort(p.plot.subplwinobj, 'descend');
end
%%%%%%%%%%%%%%%%%%%%
%%%%%% OBJECTS %%%%%
%%%%%%%%%%%%%%%%%%%%
[fig1, fig2] = core.analysis.plot_objects(p, vars.use_display);
%%%%%%%%%%%%%%%%%%%%
%%%%%% PROBES %%%%%%
%%%%%%%%%%%%%%%%%%%%
fig3 = core.analysis.plot_probes(p, vars.use_display);
%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% ERROR METRIC %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%
try
fig4 = core.analysis.plot_error_metric(p, vars.final, vars.use_display);
catch ME
warning('Failed to plot error metrics.')
disp([ME.getReport]);
fig4 = plotting.smart_figure(4);
end
%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% POSITIONS %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%
if p.plot.positions
core.analysis.plot_positions(p);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% PROBES @ DETECTOR %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.plot.probe_spectrum
fig5 = core.analysis.plot_probes_at_detector(p, vars.use_display);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% OBJECT SPECTRUM %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.plot.object_spectrum
fig6 = core.analysis.plot_object_spectrum(p, vars.use_display);
end
drawnow;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Write in figures folder %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% If you configured to dump it also saves the figures in
% analysis/online/ptycho
if vars.store_images
if isempty(vars.save_path)
% split the save_path and find the last occurrence of 'analysis'
tmpPath = strsplit(p.save_path{1}, '/');
analysisPos = find(strcmpi(tmpPath, 'analysis'));
save_path_online = strjoin(tmpPath(1:max(1,analysisPos(end)-1)),'/');
if ~isfield(p, 'datasetID')
p.datasetID = 0;
end
% load sample name if provided in .dat files and append it to the
% save name suffix
if isfield(p, 'samplename')
suffix = sprintf('dset_%s_%05d', p.samplename, p.datasetID);
else
suffix = sprintf('dset_%05d', p.datasetID);
end
subdir = fullfile(save_path_online,'analysis/online/ptycho/', suffix);
gallery = fullfile(save_path_online,'analysis/online/ptycho/gallery/');
else
subdir = vars.save_path;
gallery = fullfile(subdir,'/gallery/');
end
if ~exist(gallery,'dir')
mkdir(gallery);
end
if ~exist(subdir,'dir')
mkdir(subdir);
end
utils.verbose(0, 'Saving images to %s', subdir)
% ignore prefix in the run name -> make sorting by name equivalent to
% sorting by scan number -> easier preview and browsing through image
% gallery
image_name = p.run_name(1+length(p.prefix):end);
width = 6*p.plot.subplwinobj(2);
height = 4*p.plot.subplwinobj(1);
if any(p.save.store_images_ids == 1)
fig1.PaperPosition = [3 3 width height]; % adjust size of the resulting image
save_figs(fig1, '%s_amplitude.%s', image_name, subdir, gallery, p.save);
end
if any(p.save.store_images_ids == 2)
fig2.PaperPosition = [3 3 width height]; % adjust size of the resulting image
save_figs(fig2, '%s_phase.%s', image_name, subdir, gallery, p.save);
end
if any(p.save.store_images_ids == 6)
fig6.PaperPosition = [3 3 width height]; % adjust size of the resulting image
save_figs(fig6, '%s_object_spectrum.%s', image_name, subdir, gallery, p.save);
end
width = 4*p.plot.subplwinprob(2);
height = 4*p.plot.subplwinprob(1);
if any(p.save.store_images_ids == 3)
fig3.PaperPosition = [3 3 width height]; % adjust size of the resulting image
save_figs(fig3, '%s_probe.%s', image_name, subdir, gallery, p.save);
end
if any(p.save.store_images_ids == 4)
save_figs(fig4, '%s_err.%s', image_name, subdir, gallery, p.save);
end
if any(p.save.store_images_ids == 5)
fig5.PaperPosition = [3 3 width height]; % adjust size of the resulting image
save_figs(fig5, '%s_probe_spectrum.%s', image_name, subdir, gallery, p.save);
end
end
end
function save_figs(fig_handle, fname,run_name, subdir, gallery, params)
try
fname = sprintf(fname,run_name, params.store_images_format);
utils.verbose(3, 'saving %s',fullfile(subdir,fname));
switch params.store_images_format
case 'png' , printer = '-dpng';
case 'jpg' , printer = '-djpeg';
otherwise, error('Unsupported image extension')
end
print(fig_handle, printer,['-r', num2str(params.store_images_dpi)],fullfile(subdir,fname));
% trim borders around the images
system(sprintf('convert -trim %s %s', fullfile(subdir,fname), fullfile(subdir,fname)));
% make a symbolic link to a gallery folder
system(sprintf('ln -sf %s %s', fullfile(subdir,fname), fullfile(gallery, fname)));
catch err
warning('Saving plot handle fig%i failed: %s',fig_handle.Number, err.message)
end
end
ptycho/+core/+analysis/private/get_object_pixel_size.m
+80
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@@ -0,0 +1,80 @@
%GET_OBJECT_PIXEL_SIZE
% calculate object pixel size, for conventional ptycho it is p.dx_spec
%
% ** p p structure
%
% Outputs:
% ++
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [objpix, FP_pre_phase_factor] = get_object_pixel_size(p)
import utils.get_grid
if p.fourier_ptycho
k = 2*pi/p.lambda;
objpix = p.lambda*p.z_lens./(p.object_size.*p.dx_spec);
for ii=1:p.numobjs
[Xp,Yp] = get_grid(p.object_size(ii,:), objpix(1));
FP_pre_phase_factor{ii} = exp(1i*k*((Xp).^2+(Yp).^2)/(2*p.z_lens));
end
else
objpix = p.dx_spec;
FP_pre_phase_factor = [];
end
end
ptycho/+core/+save/extract4saving.m
+208
View File
@@ -0,0 +1,208 @@
%EXTRACT4SAVING extracts datasets and parameters from p and creates HDF5
%structure
% ** p p structure
% ** append boolean; true if data will be appended to an existing file
%
% returns:
% ++ s structure for save2hdf5
%
% see also: io.HDF.save2hdf5
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ s ] = extract4saving(p, append)
import utils.update_param
import math.double2int
s = [];
p = rmfield_safe(p, 'probe');
p = rmfield_safe(p, 'positions_temp');
p = rmfield_safe(p, 'scanidxs');
p = rmfield_safe(p, 'share_pos');
p.positions = transpose(p.positions);
p.positions_real = transpose(p.positions_real);
p.positions_orig = transpose(p.positions_orig);
%%%%%%%%%%%%%%%%%%%
%%% measurement %%%
%%%%%%%%%%%%%%%%%%%
%% external link to data file
% should be saved with a relative path
% s.measurement.data = ['ext:' p.prepare_data_path p.prepare_data_filename ':/'];
%% Meta data
if ~isempty(p.meta)
s.measurement.meta_all = p.meta;
end
p = rmfield_safe(p, 'meta');
%% Detector settings
% s.measurement.detector
p = rmfield_safe(p, p.detector.name);
%% fmask and fmag
p = rmfield_safe(p, 'fmask');
p = rmfield_safe(p, 'fmag');
%%%%%%%%%%%%%%%%%%%%%%
%%% reconstruction %%%
%%%%%%%%%%%%%%%%%%%%%%
%% engines
em_indx = 0;
for ii=1:length(p.engines)
tmp = p.engines{ii};
% % add object_final
% if ~isempty(tmp.object_final)
% s.reconstruction.engines{ii}.object_final = tmp.object_final;
% end
% % add probes_final
% if ~isempty(tmp.probes_final)
% s.reconstruction.engines{ii}.probes_final = tmp.probes_final;
% end
if isfield(tmp, 'error_metric_final')
for jj=1:length(tmp.error_metric_final)
% add error_metric_final
if iscell(tmp.error_metric_final)
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).iteration = tmp.error_metric_final{jj}.iteration;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).value = tmp.error_metric_final{jj}.value;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).method = tmp.error_metric_final{jj}.method;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).err_metric = tmp.error_metric_final{jj}.err_metric;
s.reconstruction.p.engines{ii}.error_metric_final.Attributes.MATLAB_class = 'cell';
else
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).iteration = tmp.error_metric_final.iteration;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).value = tmp.error_metric_final.value;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).method = tmp.error_metric_final.method;
s.reconstruction.p.engines{ii}.error_metric_final.(['em_' num2str(jj-1)]).err_metric = tmp.error_metric_final.err_metric;
s.reconstruction.p.engines{ii}.error_metric_final.Attributes.MATLAB_class = 'cell';
end
% add error_metric
% s.reconstruction.p.error_metric.(['em_' num2str(em_indx)]) = ['int_soft:/reconstruction/p/engines/' fn{ii} '/error_metric_final/em_' num2str(jj-1)];
% em_indx = em_indx + 1;
end
s.reconstruction.p.engines{ii} = update_param(s.reconstruction.p.engines{ii}, double2int(tmp), 'force_update', 0);
end
tmp = rmfield_safe(tmp, 'object_final');
tmp = rmfield_safe(tmp, 'probes_final');
tmp = rmfield_safe(tmp, 'error_metric_final');
tmp = rmfield_safe(tmp, 'fdb');
end
p = rmfield_safe(p, 'engines');
p = rmfield_safe(p, 'error_metric');
% p = rmfield_safe(p, 'err');
% p = rmfield_safe(p, 'rfact');
%% probe (dataset)
if ~append
for ii=1:p.numprobs
s.reconstruction.p.probes.(['probe_' num2str(ii-1)]) = permute(squeeze(p.probes(:,:,ii,:)), [2 1 3]);
end
end
p = rmfield_safe(p, 'probes');
%% object (dataset)
if ~append
for ii=1:p.numobjs
s.reconstruction.p.objects.(['object_' num2str(ii-1)]) = permute(p.object{ii}, [2 1 3 4]);
end
end
p = rmfield_safe(p, 'object');
%% probe mask
if isfield(p, 'probe_mask')
s.reconstruction.p.probe_mask = p.probe_mask;
p = rmfield_safe(p, 'probe_mask');
end
%% ctr
s.reconstruction.p.ctr = uint32(transpose(p.ctr));
p = rmfield_safe(p, 'ctr');
%% everything else
s.reconstruction.p = update_param(s.reconstruction.p, double2int(p), 'force_update', 0);
end
function p = rmfield_safe(p, val)
if isfield(p, val)
p = rmfield(p, val);
end
end
ptycho/+core/+save/reconstructions_as_h5.m
+153
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@@ -0,0 +1,153 @@
%RECONSTRUCTIONS_AS_MAT
% Save reconstruction into a h5 file
%
% ** p p structure
% ** final boolean; false for intermediate saving routines
%
% returns:
% ++ p p structure
%
% see also: core.save.save_results
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function p = reconstructions_as_h5(p, final)
import utils.verbose
import utils.relative_path
import io.HDF.*
if final
p.plot.extratitlestring = sprintf(' (%dx%d) - Final', p.asize(2), p.asize(1));
end
% check if last engine was c_solver
if strcmpi(p.engines{p.current_engine_id}.name, 'c_solver')
append2file = true;
else
append2file = false;
end
s = core.save.extract4saving(p, append2file);
for ii=1:p.numscans
if p.share_object
obnum = 1;
else
obnum = ii;
end
if p.share_probe
prnum = 1;
else
prnum = ii;
end
s.reconstruction.object = ['int_soft:/reconstruction/p/objects/object_' num2str(obnum-1)];
s.reconstruction.probes = ['int_soft:/reconstruction/p/probes/probe_' num2str(prnum-1)];
s.reconstruction.Attributes.obnum = obnum;
s.reconstruction.Attributes.prnum = prnum;
if isfield(p, 'recon_filename')
filename_with_path = p.recon_filename{ii};
if p.queue.isreplica
[~, fname, ext] = fileparts(p.recon_filename{ii});
filename_with_path = fullfile(p.save_path{ii}, [fname ext]);
end
else
recons_filename = sprintf('%s_recons.%s',p.run_name, p.save.output_file);
filename_with_path = fullfile(p.save_path{ii}, recons_filename);
if exist(filename_with_path, 'file')
verbose(3,'File %s exists!', filename_with_path);
alt_filename = filename_with_path;
[~, fbase,f2] = fileparts(filename_with_path);
append_number = 0;
while exist(alt_filename, 'file')
f1 = sprintf('%s_%02d', fbase, append_number);
alt_filename = fullfile(p.save_path{ii}, [f1 f2]);
append_number = append_number + 1;
end
filename_with_path = alt_filename;
end
end
if ii==1
% If the last engine was c_solver, we can use the already existing
% h5 file.
if append2file
movefile(p.recon_filename_c, filename_with_path);
end
root_file = filename_with_path;
s.measurement.data = ['ext:' relative_path(filename_with_path, [p.prepare_data_path p.prepare_data_filename]) ':/'];
else
hdf5_cp_file(relative_path(filename_with_path, root_file), filename_with_path, 'groups', {'/measurement/data'; '/measurement/meta_all'; '/reconstruction/p'});
end
s.measurement.meta = ['int_soft:/measurement/meta_all/meta_all_' num2str(ii-1)];
save2hdf5(filename_with_path, s, 'comp', p.io.file_compression);
try
fsz = dir(filename_with_path);
verbose(0, 'Reconstructed scan S%05d: %s', p.scan_number(ii), filename_with_path)
verbose(2, 'File size: %0.4f MB', fsz.bytes/1e6)
catch
verbose(0, 'Saved reconstruction to file %s.', filename_with_path);
end
s = [];
end
end
ptycho/+core/+save/reconstructions_as_mat.m
+145
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@@ -0,0 +1,145 @@
%RECONSTRUCTIONS_AS_MAT
% Save reconstruction into the MAT file
%
% ** p p structure
% ** final boolean; false for intermediate saving routines
%
% returns:
% ++ p p structure
%
% see also: core.save.save_results
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function p = reconstructions_as_mat(p, final)
import utils.verbose
import utils.relative_path
import io.HDF.*
if ~isfield(p.save, 'exclude')
p.save.exclude = {'fmag'; 'fmask'};
end
if final
p.plot.extratitlestring = sprintf(' (%dx%d) - Final', p.asize(2), p.asize(1));
end
recons_filename = sprintf('%s_recons.mat',p.run_name);
for ii = 1:p.numscans
if p.share_object
obnum = 1;
else
obnum = ii;
end
if p.share_probe
prnum = 1;
else
prnum = ii;
end
object = p.object{obnum};
probe = p.probes(:,:,prnum,:);
% if isfield(p.meta,'spec')
% p.spec = p.meta.spec{ii};
% end
filename_with_path = fullfile(p.save_path{ii}, recons_filename);
if exist(filename_with_path, 'file')
verbose(3,'File %s exists!', filename_with_path);
alt_filename = filename_with_path;
[~, fbase,f2] = fileparts(filename_with_path);
append_number = 0;
while exist(alt_filename, 'file')
f1 = sprintf('%s_%02d', fbase, append_number);
alt_filename = fullfile(p.save_path{ii}, [f1 f2]);
append_number = append_number + 1;
end
verbose(1, 'Saving reconstruction to file %s', alt_filename);
filename_with_path = alt_filename;
end
% avoid saving unnecesary data => speed up loading during tomography
probe = single(squeeze(probe));
object = single(object);
if ~p.save.save_reconstructions_intermediate
for ieng = 1:length(p.engines)
p.engines{ieng}.object_final = [];
p.engines{ieng}.probes_final = [];
end
end
for ex=1:size(p.save.exclude,1)
temp.(p.save.exclude{ex}) = p.(p.save.exclude{ex});
p.(p.save.exclude{ex}) = [];
end
% save it to HDF5 without compression (faster saving / loading)
save(filename_with_path,'p','object','probe', '-v6' );
% note that the -v6 option makes the saving 10x faster and
% loading 5x faster compared to option -v7 and 30x faster
% saving compared to -v7.3
verbose(0, 'Saved reconstruction to file %s.', filename_with_path);
for ex=1:size(p.save.exclude,1)
p.(p.save.exclude{ex}) = temp.(p.save.exclude{ex});
end
clear temp;
end
end
ptycho/+core/+save/save_results.m
+134
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@@ -0,0 +1,134 @@
%SAVE_RESULTS
% Save reconstruction and parameter file
%
% ** p p structure
% ** final boolean; false for intermediate saving routines
%
% returns:
% ++ p p structure
%
% see also: core.ptycho_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p] = save_results(p, final)
import utils.verbose
import utils.relative_path
import io.HDF.*
print_FSC = false;
if p.plot.calc_FSC
if p.numscans ~= 2 && ~(isfield(p, 'simulation')&&isfield(p.simulation, 'obj'))
warning('FRC calculation is implemented for 2 scans only.')
else
try
[p, resolution] = core.analysis.calc_FSC(p);
print_FSC = true;
catch ME
if p.verbose_level > 3
keyboard
else
warning('Failed to calculate FSC.')
end
end
end
end
if p.save.save_reconstructions
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% Save reconstruction and parameter file %%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmpi(p.save.output_file, 'h5') || strcmpi(p.save.output_file, 'cxs')
p = core.save.reconstructions_as_h5(p, final);
elseif strcmpi(p.save.output_file, 'mat')
p = core.save.reconstructions_as_mat(p, final);
else
error('Unknown file extension .%s', p.save.output_file);
end
end
%%%%%%%%%%%%
%%% Plot %%%
%%%%%%%%%%%%
if final && p.save.external && p.verbose_level <=2
verbose(2, 'Starting new matlab session to save figures.')
recons_filename = sprintf('%s_recons.%s',p.run_name, p.save.output_file);
filename_with_path = fullfile(p.save_path{1}, recons_filename);
ext_call = ['addpath(genpath(''../'')); try;' ...
'plotting.ptycho_show_recons(''' filename_with_path ''');catch ME;'...
'fprintf([ME.getReport ''\n\n\n'']); end; quit'];
system(['matlab -nosplash -nodisplay -r "' ext_call '" &']);
else
if p.use_display||p.save.store_images
core.analysis.plot_results(p, 'use_display', p.use_display, 'store_images', p.save.store_images, 'final', final);
end
end
if print_FSC
fprintf('\n');
utils.verbose(2,'Resolution (FSC): (%.2f, %.2f) nm\n', resolution)
end
end
ptycho/+core/append_engine.m
+82
View File
@@ -0,0 +1,82 @@
%APPEND_ENGINE appends engine specified in new_eng to p
% Adds engines with index, starting at 1
% 1st engine: p.engines{1}
%
% ** p p structure
% ** new_eng structure containing information about the new engine
%
% returns:
% ++ p p structure
% ++ new_eng empty container; useful if one does not want to propagate changes between engines
%
% see also: core.ptycho_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p, new_eng] = append_engine(p, new_eng )
% check if it is the first engine, otherwise get the current index
if ~isfield(p, 'engines')
p.engines = {};
end
% append engine
p.engines{end+1} = new_eng;
% clear engine structure
new_eng = struct();
end
ptycho/+core/apply_binning.m
+50
View File
@@ -0,0 +1,50 @@
% APPLY_BINNING apply binning / upsampling on all relevant parameters except data and mask
%
% p = apply_binning(p, bin_data)
%
% ** p p structure
% ** binning if binning > 1, then data are binned , if binning < 1, data will be upsampled
% returns:
% ++ p p structure
%
function p = apply_binning(p, binning)
% apply binning / upsampling on all relevant parameters except data and mask
if binning > 0
assert(all(rem(p.asize, binning)==0), 'Array size cannot be divided for binning')
end
% Modify variables for binning
p.ds = p.ds*binning;
if check_option(p,'prop_regime', 'farfield')
p.object_size = p.object_size + ( 1/binning-1)*p.asize ;
for ii = 1:p.numobjs
p.object{ii} = utils.crop_pad(p.object{ii},p.object_size(ii,:)); % crop_pad is better when if the binned reconstruction is loaded from file as an initial guess
end
p.asize = p.asize/binning;
%% always assume that no binning was applied on the provided probes
p.probe_initial = utils.crop_pad( p.probe_initial, p.asize);
p.probes = utils.crop_pad( p.probes, p.asize);
else
p.object_size = ceil(p.object_size / binning);
for ii = 1:p.numobjs
p.object{ii} = utils.interpolateFT(p.object{ii},p.object_size(ii,:)); % crop_pad is better when if the binned reconstruction is loaded from file as an initial guess
end
p.asize = p.asize/binning;
%% always assume that no binning was applied on the provided probes
p.probe_initial = utils.interpolateFT( p.probe_initial, p.asize);
p.probes = utils.interpolateFT( p.probes, p.asize);
p.dx_spec = p.dx_spec * binning;
p.positions = p.positions / binning; % in nearfield the pixel size also changes
end
end
ptycho/+core/check_prepared_data.m
+166
View File
@@ -0,0 +1,166 @@
%CHECK_PREPARED_DATA compares prepared data file with current
%reconstruction parameters. If force_update == true, data preparation will
%be forced (see core.ptycho_prepare_scans)
% ** p p structure
%
% returns:
% ++ force_update true if data preparation has be done enforced
%
% see also: core.ptycho_prepare_scans
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ force_update ] = check_prepared_data( p )
force_update = false;
file = fullfile(p.prepare_data_path, p.prepare_data_filename);
if ~exist(file, 'file')
error('Prepared data file %s does not exist!', file);
end
h = h5info(file);
if ~isempty(find(contains({h.Attributes.Name}, 'format'),1)) && h.Attributes(find(contains({h.Attributes.Name}, 'format'),1)).Value==2
h5format = 'LibDetXR';
else
h5format = 'Matlab';
end
switch h5format
case 'LibDetXR'
% check for sharing, asize and numpts
idx = contains({h.Groups.Name}, '/measurement');
fn = length(h.Groups(idx).Groups);
probe_ID = zeros(1,fn);
object_ID = zeros(1,fn);
data_size = zeros(fn,3);
for ii=1:fn
group = h.Groups(idx).Groups;
idx_sub = ismember({group.Name}, ['/measurement/n' num2str(ii-1)]);
attrib = group(idx_sub).Attributes;
idx_pr = ismember({attrib.Name}, 'probe');
probe_ID(ii) = attrib(idx_pr).Value + 1;
idx_ob = ismember({attrib.Name}, 'object');
object_ID(ii) = attrib(idx_ob).Value + 1;
data_size(ii,:) = group(idx_sub).Datasets(find(contains({group(idx_sub).Datasets.Name}, 'data'),1)).Dataspace.Size;
end
if any(data_size(1,[2,1])~=p.asize/2^p.detector.binning)
force_update = true;
end
if (size(data_size,1) ~= length(p.numpts) || any(data_size(:,3)'~=p.numpts)) && ~p.fourier_ptycho
force_update = true;
end
if length(unique(probe_ID))~=length(unique(p.share_probe_ID)) || any(probe_ID~=p.share_probe_ID)
force_update = true;
end
if length(unique(object_ID))~=length(unique(p.share_object_ID)) || any(object_ID~=p.share_object_ID)
force_update = true;
end
case 'Matlab'
idx = contains({h.Groups.Name}, '/measurements');
fn = length(h.Groups(idx).Groups);
probe_ID = zeros(1,fn);
object_ID = zeros(1,fn);
scan_ID = zeros(1,fn);
for ii=1:fn
idx_pr = contains({h.Groups(idx).Groups(ii).Attributes.Name}, 'probe');
idx_det = contains({h.Groups(idx).Groups(ii).Attributes.Name}, 'detector');
idx_ob = contains({h.Groups(idx).Groups(ii).Attributes.Name}, 'object');
scan_ID(ii) = h.Groups(idx).Groups(ii).Attributes(idx_det).Value + 1;
probe_ID(ii) = h.Groups(idx).Groups(ii).Attributes(idx_pr).Value + 1;
object_ID(ii) = h.Groups(idx).Groups(ii).Attributes(idx_ob).Value + 1;
end
numscans = unique(scan_ID);
numpts = zeros(1,numel(numscans));
for ii=1:numel(numscans)
numpts(ii) = sum(scan_ID==numscans(ii));
if ~all(object_ID(scan_ID==numscans(ii)) == p.share_object_ID(ii)) || ~all(probe_ID(scan_ID==numscans(ii)) == p.share_probe_ID(ii))
force_update = true;
end
end
if (numel(numpts) ~= numel(p.numpts)) || any(numpts~=p.numpts)
force_update = true;
end
% asize
asize = hdf5_load(file, '/probes');
asize = asize(1:2);
if any(asize ~= p.asize)
force_update = true;
end
otherwise
error('Unknown prepared data format')
end
end
ptycho/+core/engine_status.m
+101
View File
@@ -0,0 +1,101 @@
% ENGINE_STATUS use persisten variables to store error messages
% Error code: 0 for 'everything OK' and ~=0 for 'error' (return values of matlab's system function)
%
% *usage:*
% engine_status(status) to set persisten variable engine_stat to
% status
%
% engine_status to read persisten variables
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [eng_stat] = engine_status(varargin)
persistent engine_stat
persistent engine_stat_ln
if isempty(engine_stat)
engine_stat = 0;
end
if isempty(engine_stat_ln)
engine_stat_ln = [];
end
eng_stat.status = engine_stat;
eng_stat.ln = engine_stat_ln;
if nargin == 0
return
end
if nargin == 1
if ischar(varargin{1})
engine_stat = str2num(varargin{1});
else
engine_stat = varargin{1};
end
if engine_stat ~= 0
engine_stat_ln = dbstack(1);
end
eng_stat.status = engine_stat;
eng_stat.ln = engine_stat_ln;
return
end
ptycho/+core/errorplot.m
+74
View File
@@ -0,0 +1,74 @@
% Build an errormetric plot vs iteration number
%
% *usage*
% e = errorplot Clears the persistent variable
% e = errorplot(x) Appends x to the persistent variable
% e = errorplot([]) Only reads the persistent variable
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function outerror = errorplot(argin)
persistent errormetric,
if exist('argin') == 0,
errormetric = [];
else
errormetric = [errormetric ; argin];
end
outerror = errormetric;
end
ptycho/+core/export4remote.m
+115
View File
@@ -0,0 +1,115 @@
%EXPORT4REMOTE
% Export the meta data using a .mat file for remote reconstruction
%
% ** p p structure
%
% returns:
% ++ p updated p structure
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function p = export4remote(p)
import utils.verbose
if ~isfield(p.queue, 'remote_path') || isempty(p.queue.remote_path)
error('Shared directory for remote host has to be specified.')
end
if ~exist(p.queue.remote_path, 'dir')
try
mkdir(fullfile(p.queue.remote_path))
catch
error('Failed to create remote queue directory.')
end
end
if ~exist(fullfile(p.queue.remote_path,'in_progress'))
mkdir(fullfile(p.queue.remote_path,'in_progress'));
end
if ~exist(fullfile(p.queue.remote_path,'failed'))
mkdir(fullfile(p.queue.remote_path,'failed'));
end
if ~exist(fullfile(p.queue.remote_path,'done'))
mkdir(fullfile(p.queue.remote_path,'done'));
end
p = core.ptycho_prepare_paths(p);
recons_filename = sprintf('%s_recons.%s',p.run_name, p.save.output_file);
for ii=1:numel(p.scan_number)
filename_with_path = fullfile(p.save_path{ii}, recons_filename);
if exist(filename_with_path, 'file')
verbose(3,'File %s exists!', filename_with_path);
alt_filename = filename_with_path;
[~, fbase,f2] = fileparts(filename_with_path);
append_number = 0;
while exist(alt_filename, 'file')
f1 = sprintf('%s_%02d', fbase, append_number);
alt_filename = fullfile(p.save_path{ii}, [f1 f2]);
append_number = append_number + 1;
end
filename_with_path = alt_filename;
end
p.recon_filename{ii} = filename_with_path;
end
p.queue.remote_file_this_recons = fullfile(p.queue.remote_path, [p.run_name '.mat']);
save(fullfile(p.queue.remote_path, [p.run_name '.mat']), 'p', '-v6');
end
ptycho/+core/find_base_package.m
+82
View File
@@ -0,0 +1,82 @@
%FIND_BASE_PACKAGE
% finds the path to the cSAXS base package by looking for a specific file (+math)
%
% returns:
% ++ base_package_path path to the cSAXS base package
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function base_package_path = find_base_package()
maxdepth = 3;
test_path = '+math'; % one file to find them all
lvl = 1;
cpath = '';
ret = '';
while isempty(ret) && ~contains(strtrim(ret), test_path)
[~, ret] = system(sprintf('find %s -maxdepth 2 -type d -name "%s"', cpath, test_path));
if lvl > maxdepth
break
end
lvl = lvl + 1;
cpath = [cpath '../'];
end
ret = split(ret);
base_package_path = strtrim(ret{1});
base_package_path = base_package_path(1:end-length(test_path));
end
ptycho/+core/find_shared_IDs.m
+133
View File
@@ -0,0 +1,133 @@
%FIND_SHARED_IDS find which positions belong to each object / probe
%
% ** p p structure
% returns:
% ++ p p structure
%
% see also: core.initialize_ptycho
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ p ] = find_shared_IDs( p )
% Shared scans
if all(p.share_object==0)
p.share_object_ID = 1:p.numscans;
else
for ii=1:length(p.share_object)
if ~p.share_object(ii)
p.share_object_ID(ii) = ii;
else
p.share_object_ID(ii) = p.share_object(ii);
end
end
if length(p.share_object)<p.numscans
for ii=length(p.share_object)+1:p.numscans
p.share_object_ID = [p.share_object_ID p.share_object_ID(end)];
end
elseif length(p.share_object)>p.numscans
p.share_object_ID(p.numscans+1:end) = [];
end
if max(p.share_object_ID)> length(p.scan_number)
error('Shared object ID must be in the range of length(scan_number)')
end
end
p.share_object_ID = squeeze_num(p.share_object_ID);
p.numobjs = length(unique(p.share_object_ID));
if all(p.share_probe==0)
p.share_probe_ID = 1:p.numscans;
else
for ii=1:length(p.share_probe)
if ~p.share_probe(ii)
p.share_probe_ID(ii) = ii;
else
p.share_probe_ID(ii) = p.share_probe(ii);
end
end
if length(p.share_probe)<p.numscans
for ii=length(p.share_probe)+1:p.numscans
p.share_probe_ID = [p.share_probe_ID p.share_probe_ID(end)];
end
elseif length(p.share_probe)>p.numscans
p.share_probe_ID(p.numscans+1:end) = [];
end
if max(p.share_probe_ID)> length(p.scan_number)
error('Shared object ID must be in the range of length(scan_number)')
end
end
p.share_probe_ID = squeeze_num(p.share_probe_ID);
p.numprobs = length(unique(p.share_probe_ID));
end
function ret = squeeze_num(n)
% squeeze number to be consecutive
uval = unique(n);
if length(n)==length(uval)
ret = n;
else
ret = n;
for ii=1:length(n)
if ~any(n==ii)
ret(ret>ii) = ret(ret>ii)-1;
end
end
end
end
ptycho/+core/generate_scan_name.m
+87
View File
@@ -0,0 +1,87 @@
%GENERATE_SCAN_NAME
% Auxilialy function to generate scan names
%
% ** p p structure
%
% returns:
% ++ scan_name scan names
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function scan_name = generate_scan_name(p)
if length(p.scan_number) <= 2
% original naming conventioon
scan_name = sprintf('S%05d_',p.scan_number);
else
% in case of large scans with continuous scan range use a
% shorter name notation to avoid filesystem errors
scan_range_start = setdiff(p.scan_number, p.scan_number+1);
scan_range_end = setdiff(p.scan_number, p.scan_number-1);
scan_name = '';
for ii = 1:length(scan_range_start)
if scan_range_start(ii) ~= scan_range_end(ii)
scan_name = [scan_name, sprintf('S%05d-S%05d_',scan_range_start(ii), scan_range_end(ii))];
else
scan_name = [scan_name, sprintf('S%05d_',scan_range_start(ii))];
end
end
end
scan_name = scan_name(1:end-1);
end
ptycho/+core/get_projections.m
+106
View File
@@ -0,0 +1,106 @@
%GET_PROJECTIONS
%
% ** p p structure
% ** object full-size object
% ** scan_id ID of the current scan
% ** obj_proj container for object projections
%
% returns:
% ++ obj_proj updated container for object projections
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function obj_proj = get_projections(p, object, scan_id, obj_proj)
import utils.verbose
Npos = length(p.scanidxs{scan_id});
Nmodes = size(object,4);
if nargin < 4
obj_proj = zeros([p.asize, Npos, Nmodes], 'like', object);
end
if any(max(round(p.positions(p.scanidxs{scan_id},:)))+p.asize > [size(object,1),size(object,2)])
error('Object is too small for given positions')
end
if Nmodes == 1 && (isa(object, 'gpuArray') || isa(obj_proj, 'gpuArray'))
% use function from GPU engine
cache.skip_ind = [];
positions = round(p.positions(p.scanidxs{scan_id},:));
cache.oROI_s{1}{1} = uint32(positions(:,1));
cache.oROI_s{1}{2} = uint32(positions(:,2));
obj_proj = engines.GPU.shared.get_views(object, obj_proj, 1,1,int32(1:Npos),cache);
return
end
if Nmodes == 1 && ~verLessThan('matlab', '9.4')
% faster MEX based function
positions = int32(p.positions(p.scanidxs{scan_id},:));
indices = int32(1:Npos);
obj_proj = utils.get_from_3D_projection(obj_proj,object,positions,indices);
return
end
verbose(3, 'Using slow nonMEX version of get_projections')
id_0 = p.scanidxs{scan_id}(1)-1;
for jj = p.scanidxs{scan_id}
Indy = round(p.positions(jj,1)) + (1:p.asize(1));
Indx = round(p.positions(jj,2)) + (1:p.asize(2));
obj_proj(:,:,jj-id_0,:) = object(Indy,Indx,:);
end
end
ptycho/+core/hermite_like.m
+110
View File
@@ -0,0 +1,110 @@
%HERMITE_LIKE
% Receives a probe and maximum x and y order M N. Based on the given probe
% and multiplying by a Hermitian function new modes are computed. The modes
% are then orthonormalized.
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function H = hermite_like(fundam,X,Y,M,N)
import plotting.c2image
% corresponding to this. Returns all
m = [0:M];
n = [0:N];
% fundam = abs(probe);
cenx = sum(sum(X.*abs(fundam).^2))/sum(sum(abs(fundam).^2));
ceny = sum(sum(Y.*abs(fundam).^2))/sum(sum(abs(fundam).^2));
varx = sum(sum((X-cenx).^2.*abs(fundam).^2))/sum(sum(abs(fundam).^2));
vary = sum(sum((Y-ceny).^2.*abs(fundam).^2))/sum(sum(abs(fundam).^2));
counter = 1;
% Create basis
for nii = n
for mii = m
auxfunc = ((X-cenx).^mii).*((Y-ceny).^nii).*fundam;
if counter == 1
auxfunc = auxfunc/sqrt(sum(abs(auxfunc(:)).^2));
else
auxfunc = auxfunc.*exp(-((X-cenx).^2/(2*varx))-((Y-ceny).^2/(2*vary)));
auxfunc = auxfunc/sqrt(sum(abs(auxfunc(:)).^2));
end
% Now make it orthogonal to the previous ones
for ii = 1:counter-1 % The other ones
auxfunc = auxfunc - H(:,:,ii)*sum(sum(H(:,:,ii).*conj(auxfunc),1),2);
end
auxfunc = auxfunc/sqrt(sum(abs(auxfunc(:)).^2));
H(:,:,counter) = auxfunc;
index(counter,:) = [mii nii];
% figure(1)
% subplot(3,3,counter)
% imagesc(c2image(H(:,:,counter)));
% title(num2str(index(counter,:)))
% axis xy equal tight
counter = counter+1;
end
end
% hermite_gauss - Recieves X, Y and gaussian waist (w) and computes the
% Hermite Gauss beam
end
ptycho/+core/initial_checks.m
+351
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%INITIAL_CHECKS set default values for the most common variables
%
% ** p p structure
%
% returns:
% ++ p p structure
%
% see also: core.initialize_ptycho
%
function [p] = initial_checks(p)
import utils.*
import io.*
%%%%%%%%%%%%%
%% General %%
%%%%%%%%%%%%%
% check matlab version
check_matlab_version('9.3');
if ~isfield(p, 'use_display') || isempty(p.use_display)
if verbose > 1
p.use_display = true;
else
p.use_display = false;
end
end
if ~usejava('desktop')
% test if matlab was called with -nodisplay option, if yes then
% use_display should be false
p.use_display = false;
end
% check if fourier ptycho recon is needed
if ~isfield(p, 'fourier_ptycho')
p.fourier_ptycho = false;
end
if ~isfield(p, 'sample_rotation_angles')
p.sample_rotation_angles = [0,0,0]; % 3x1 vector rotation around [X,Y,beam] axes in degrees , apply a correction accounting for tilted plane oR the sample and ewald sphere curvature (high NA correction)
end
%%% Derived quantities %%%
assert(~isempty(p.energy), 'Provide p.energy or source of metadata p.src_metadata')
% modified by YJ for electron pty
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
%use relativistic corrected formula for electron pty
p.lambda = 12.3986/sqrt((2*511.0+p.energy).*p.energy); %angstrom
else
p.lambda = 1.23984193e-9/p.energy; % wavelength
end
if isscalar(p.asize); p.asize = [p.asize p.asize]; end
%%%%%%%%%%%%%%%%%%%%
%% Scan meta data %%
%%%%%%%%%%%%%%%%%%%%
% calculate fourier ptycho geometry
if p.fourier_ptycho
if ~isfield(p, 'FP_focal_distance')
error('For running Fourier Ptychography, please specify the focal length of your objective lens (p.FP_focal_distance)');
end
if ~get_option(p, 'z_lens')
p.z_lens = 1/(1/(p.FP_focal_distance)-1/(p.z));
end
end
%%%%%%%%%%%%%%%%
%% Scan queue %%
%%%%%%%%%%%%%%%%
% number of attempts to reconstruct the given dataset
if ~isfield(p.queue, 'max_attempts')
p.queue.max_attempts = 5;
end
% lock files
if ~isfield(p.queue, 'lockfile') || isempty(p.queue.lockfile)
if verbose > 2
p.queue.lockfile = false;
else
p.queue.lockfile = true;
end
end
if ~isfield(p.queue, 'file_queue_timeout')
p.queue.file_queue_timeout = 10; % time to wait for a new dataset in queue
end
%%%%%%%%%%%%%%%%%%%%%%
%% Data preparation %%
%%%%%%%%%%%%%%%%%%%%%%
% data prefix
if isempty(p.detector.data_prefix)
import beamline.identify_eaccount %% not included in the ptychoshelves package
eaccount = identify_eaccount;
if ~isempty(eaccount) && eaccount(1) == 'e'
% default setting for cSAXS beamline
p.detector.data_prefix = [eaccount '_1_'];
else
verbose(3,'p.detector.data_prefix is not defined')
end
end
% suffix for prepared data file
if ~isfield(p.prepare, 'prep_data_suffix')
p.prepare.prep_data_suffix = '';
end
if p.asize(1) ~= p.asize(2) && (~isfield(p.prepare, 'data_preparator') || any(strcmpi(p.prepare.data_preparator, {'python', 'libDetXR','json'})))
p.prepare.data_preparator = 'matlab_ps';
verbose(1, 'Python preparator does not support asymmetric probe dimensions, switching to matlab_ps')
end
if p.asize(1) ~= p.asize(2) && p.prepare.force_preparation_data == false
verbose(1, 'Loading prepared data is not supported for asymmetric p.asize, enforce load from raw data ')
p.prepare.force_preparation_data = true;
end
% data preparator
if ~isfield(p.prepare, 'data_preparator') || any(strcmpi(p.prepare.data_preparator, {'python', 'libDetXR','json'}))
p.prepare.data_preparator = 'libDetXR';
verbose(3, 'Using python data preparator.')
elseif any(strcmpi(p.prepare.data_preparator, {'matlab', 'matlab_ps','mex'}))
p.prepare.data_preparator = 'matlab_ps';
verbose(3, 'Using matlab data preparator.')
elseif any(strcmpi(p.prepare.data_preparator, {'matlab_aps'})) %% adde by YJ
p.prepare.data_preparator = 'matlab_aps';
verbose(3, 'Using matlab APS data preparator.')
elseif any(strcmpi(p.prepare.data_preparator, {'matlab_aps_lynx'})) %% adde by YJ
p.prepare.data_preparator = 'matlab_aps_lynx';
verbose(3, 'Using matlab APS-LYNX data preparator.')
else
error('Unknown data preparator %s', p.prepare.data_preparator);
end
if ~isfield(p.prepare,'data_preparator') || isempty(p.prepare.data_preparator)
error(' p.prepare.data_preparator is not set')
end
if strcmpi(p.prepare.data_preparator, 'matlab')
p.prepare.data_preparator = 'matlab_ps';
elseif strcmpi(p.prepare.data_preparator, 'python')
p.prepare.data_preparator = 'libDetXR';
end
% binning is only supported by Matlab data preparation
if isfield(p.detector,'binning')&& p.detector.binning
p.prepare.data_preparator = 'matlab_ps';
verbose(1, 'Using binning %ix%i, switching to matlab data loading', 2^p.detector.binning, 2^p.detector.binning)
else
p.detector.binning = false;
end
% binning is only supported by Matlab data preparation
if isfield(p.detector,'upsampling') && p.detector.upsampling
if strcmp(p.prepare.data_preparator,'matlab_ps')
%p.prepare.data_preparator = 'matlab_ps';
p.prepare.data_preparator = 'matlab_aps'; %modified by YJ for APS data
end
verbose(1, 'Using data upsampling %ix%i, switching to matlab data loading', 2^p.detector.upsampling, 2^p.detector.upsampling)
else
p.detector.upsampling = false;
end
% prealignment for Fourier Ptychography
if check_option(p, 'FP_focal_distance')
p. fourier_ptycho = true; % set to true for Fourier Ptychography
else
p. fourier_ptycho = false;
end
if ~isfield(p, 'prealign_FP')
p.prealign_FP = false;
end
% Fourier Ptycho is only supported by Matlab data preparation
if p.fourier_ptycho
p.prepare.data_preparator = 'matlab_ps';
verbose(1, 'Switching to matlab data loading for Fourier Ptycho.')
% set prealign_data to true if not distortion correction is available
if p.prealign_FP && ~p.prealign.prealign_data && isempty(p.prealign.distortion_corr)
p.prealign.prealign_data = true;
end
end
% set defaults for matlab_ps
if strcmpi(p.prepare.data_preparator, 'matlab_ps')
if ~isfield(p.io, 'data_precision')
p.io.data_precision = 'single';
end
if ~isfield(p.io, 'data_nthreads')
p.io.data_nthreads = 2;
end
end
if isfield(p, 'prop_regime') && ~ismember(p.prop_regime, {'nearfield', 'farfield'})
error(['Nonexistent propagation regime ', p.prop_regime ])
end
% store prepared data
if ~isfield(p.prepare, 'store_prepared_data')
p.prepare.store_prepared_data = true;
end
%%%%%%%%%%%%%%%%%%%%
%% Scan positions %%
%%%%%%%%%%%%%%%%%%%%
% load positions from prepared file
if ~isfield(p.io, 'load_prep_pos')
p.io.load_prep_pos = false;
end
%%%%%%%%%
%% I/O %%
%%%%%%%%%
% file compression
if ~isfield(p.io, 'file_compression')
p.io.file_compression = 0;
end
if ~isfield(p.io, 'data_compression')
p.io.data_compression = 3;
end
% run name
if ~check_option(p, 'run_name')
% check if prefix is defined
if isempty(p.prefix)
if iscell(p.scan_str)
p.prefix = p.scan_str{1};
else
p.prefix = p.scan_str;
end
end
p.run_name = sprintf('%s_%s', p.prefix, datestr(now, 'yyyy_mm_dd'));
end
verbose(3, 'run_name = %s', p.run_name);
%%%%%%%%%%%%%%%%%%%%
%% Reconstruction %%
%%%%%%%%%%%%%%%%%%%%
% backward compatibilty for initial_iterate
if isfield(p, 'initial_iterate') && ~isfield(p, 'initial_iterate_object')
p.initial_iterate_object = p.initial_iterate;
p = rmfield(p, 'initial_iterate');
end
if isfield(p, 'initial_iterate_file') && ~isfield(p, 'initial_iterate_object_file')
p.initial_iterate_object_file = p.initial_iterate_file;
p = rmfield(p, 'initial_iterate_file');
end
% model probe
if ~isfield(p.model, 'probe_central_stop')
p.model.probe_central_stop = false;
end
if ~isfield(p.model, 'probe_central_stop_diameter') && p.model.probe_central_stop
p.model.probe_central_stop_diameter = 50e-6;
end
%%%%%%%%%%%%%%%%%%%
%% Plot and save %%
%%%%%%%%%%%%%%%%%%%
% plot prepared data
if ~isfield(p.plot, 'prepared_data') || (isfield(p.plot, 'prepared_data')&& isempty(p.plot.prepared_data))
if p.verbose_level > 2
p.plot.prepared_data = true;
else
p.plot.prepared_data = false;
end
end
% plotting
if ~isfield(p.plot, 'interval') || isempty(p.plot.interval)
if verbose > 2
p.plot.interval = 10;
else
p.plot.interval = 200;
end
end
% external call to save figures
if ~isfield(p.save, 'external')
p.save.external = false;
end
% propagation and apodization
if ~isfield(p.plot, 'obj_apod')
p.plot.obj_apod = false;
end
if ~isfield(p.plot, 'prop_obj')
p.plot.prop_obj = 0;
end
% calculate FSC
if ~isfield(p.plot, 'calc_FSC')
p.plot.calc_FSC = false;
end
if ~isfield(p.plot, 'show_FSC')
p.plot.show_FSC = utils.verbose>2;
end
if ~isfield(p.plot, 'probe_spectrum')|| isempty(p.plot.probe_spectrum)
p.plot.probe_spectrum = utils.verbose>2;
end
if ~isfield(p.plot, 'object_spectrum')|| isempty(p.plot.object_spectrum)
p.plot.object_spectrum = utils.verbose>2;
end
if ~isfield(p.save, 'store_images_ids' )|| isempty(p.save.store_images_ids)
p.save.store_images_ids = 1:4;
end
%%%%%%%%%%%%%
%% Engines %%
%%%%%%%%%%%%%
% at least one engine has to be specified
if ~isfield(p, 'engines')
error('At least one reconstruction engine has to be selected. Please check your template.')
end
% first engine is external
p.external_engine0 = strcmpi(p.engines{1}.name, 'c_solver') || ...
(isfield(p.engines{1}, 'external') && p.engines{1}.external);
if ~isfield(p,'remove_scaling_ambiguity')
% if true. try to keep norm(probe) constant during the reconstruction
p.remove_scaling_ambiguity = true;
end
end
ptycho/+core/initialize_ptycho.m
+279
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%INITIALIZE_PTYCHO
% everything that needs to be done before triggering the reconstruction. This includes
% inter alia initial checks, intial guess preparations and loading the data.
%
% ** p p structure
%
% returns:
% ++ p p structure
% ++ status status flag
%
%
% see also: core.ptycho_recons
%
% Based on cSAXS code, modified by Yi Jiang
function [ p, status ] = initialize_ptycho( p )
import utils.*
import io.*
%%% read meta data %%%
if ~isfield(p, 'src_metadata')
verbose(0,' p.src_metadata is not set, using default p.src_metadata = ''spec''')
p. src_metadata = 'spec'; % load meta data from file; currently only 'spec' is supported;
end
% check store_images flag
if ~isfield(p.save, 'store_images')
p.save.store_images = true;
end
if ~p.save.store_images
close all
end
% prepare container for meta data
assert( isnumeric(p.scan_number), 'p.scan_number has to contain an integer number')
p.numscans = length(p.scan_number); % Number of scans
p.meta = cell(1,length(p.scan_number));
p = scans.read_metadata(p);
for ii = 1:p.numscans
p. scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
% write procID
write_procID(p);
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Checks and defaults %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
p = core.initial_checks(p);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%% LOAD DATA %%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% prepare paths, note that it was already initialized in ptycho_recons %%%
p = core.ptycho_prepare_paths(p);
%%% load detector settings %%%
p = detector.load_detector(p);
if isfield(p, 'ds') && ~isempty(p.ds)
warning(['Defining ds in the template is not supported anymore and ' ...
'will not change the pixel size. Please make sure '...
'that it is set correctly in +detector/+%s/%s.m and remove ds from your template.'], p.detector, p.detector)
end
for ii=1:length(p.detectors)
assert(p.detectors(1).params.pixel_size==p.detectors(ii).params.pixel_size, 'Different detector pixel sizes are not supported at the moment.')
end
p.ds = p.detectors(1).params.pixel_size;
if check_option(p, 'prop_regime', 'nearfield')
% nearfield ptychography
assert(check_option(p,'focus_to_sample_distance'), 'Undefined p.focus_to_sample_distance that is required for nearfield ptychography')
p.nearfield_magnification = (p.z-p.focus_to_sample_distance)/p.focus_to_sample_distance;
verbose(1, 'Propagation in nearfield regime, magnification = %g', p.nearfield_magnification)
p.dx_spec = [p.ds,p.ds] / p.nearfield_magnification;
p.z = p.z / p.nearfield_magnification;
else
% standard farfield ptychography
% modified by YJ for electron pty
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
if isfield(p,'dk') %A^-1/pix
p.dx_spec = 1./p.asize./p.dk; %angstrom
elseif isfield(p,'d_alpha') % mrad/pix
p.dx_spec = 1./p.asize./(p.d_alpha/1e3/p.lambda); %angstrom
else
error('dk or d_alpha are not speficied!')
end
else
p.dx_spec = p.lambda*p.z ./ (p.asize*p.ds); % resolution in the specimen plane
end
p.dx_spec = p.dx_spec ./ cosd(p.sample_rotation_angles(1:2)); % account for a tilted sample ptychography
end
%%% prepare positions %%%
p = scans.read_positions(p);
%%% find which positions belongs to each object
p = core.find_shared_IDs(p);
%%% prepare positions
% Prepare positions, note the output is already in probe positions which
% are different from object (scan) positions by a minus sign
p = core.ptycho_adjust_positions(p);
% p.positions_orig = p.positions;
% p.numpts_orig = p.numpts;
p.numpos = sum(p.numpts);
p.asize_nobin = p.asize;
%%%%%%%%%%%%%%%%%%%%%%
%%% prepare scans %%%%
%%%%%%%%%%%%%%%%%%%%%%
% make sure that all scans have a ctr
numctr = size(p.ctr,1);
if p.numscans > numctr
for ii=numctr+1:p.numscans
p.ctr(end+1,:) = p.ctr(numctr,:);
end
elseif p.numscans < numctr
p.ctr(p.numscans+1:end,:) = [];
end
%%%% load data, mask and generate initial estimate of the probe
if p.prepare.auto_prepare_data
[p, status]=core.ptycho_prepare_scans(p);
else
if ~isa(p.prepare.prepare_data_function, 'function_handle')
error(['Expected function handle as p.prepare.prepare_data_function. '...
'Please update p.prepare.auto_prepare_data or set p.prepare.auto_prepare_data=true.'])
else
[p, status] = p.prepare.prepare_data_function(p);
end
end
if ~status
return
end
% Added by YJ: remove bad data with very low counts
% p.avg_photon_threshold is defined same as the one in GPU engines
if isfield(p, 'avg_photon_threshold') && p.avg_photon_threshold > 0
diffraction = (single(p.fmag .* p.fmask) / single(p.renorm) ).^2;
good_dp_ind = squeeze(sum(sum(diffraction)) / prod(p.asize) >= p.avg_photon_threshold);
%remove bad scan points from p
p.positions_real = p.positions_real(good_dp_ind,:);
p.positions_orig = p.positions_orig(good_dp_ind,:);
p.positions = p.positions(good_dp_ind,:);
p.fmag = p.fmag(:,:,good_dp_ind);
p.fmask = p.fmask(:,:,good_dp_ind);
low_count_dp_ind = find((1-good_dp_ind)==1);
for ii=1:length(p.scanidxs)
scan_ind_temp = p.scanidxs{ii};
N_scan_pts = length(scan_ind_temp);
[val, pos]=intersect(scan_ind_temp,low_count_dp_ind);
num_bad_pts = length(val); % get the # of bad pts for current scan
p.share_pos{ii}(pos,:) = []; %remove positions for current scan
if ii == 1
scanidxs_lb = 1;
else
scanidxs_lb = p.scanidxs{ii-1}(end)+1;
end
p.numpts(ii) = N_scan_pts-num_bad_pts;
p.scanindexrange(ii,:) = [scanidxs_lb, scanidxs_lb+p.numpts(ii)-1];
p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,2);
end
p.numpos = sum(p.numpts);
%store indices for bad data
p.low_count_dp = 1-good_dp_ind;
if any(p.low_count_dp)
verbose(1, 'Remove %d diffraction pattern(s) with low counts', sum(p.low_count_dp))
end
end
% Added by YJ: remove bad data with very high counts
% p.avg_photon_threshold_ub is defined similar to p.avg_photon_threshold
if isfield(p, 'avg_photon_threshold_ub') && p.avg_photon_threshold_ub > 0 && p.avg_photon_threshold_ub < inf
diffraction = (single(p.fmag .* p.fmask) / single(p.renorm) ).^2;
good_dp_ind = squeeze(sum(sum(diffraction)) / prod(p.asize) <= p.avg_photon_threshold_ub);
%remove bad scan points from p
p.positions_real = p.positions_real(good_dp_ind,:);
p.positions_orig = p.positions_orig(good_dp_ind,:);
p.positions = p.positions(good_dp_ind,:);
p.fmag = p.fmag(:,:,good_dp_ind);
p.fmask = p.fmask(:,:,good_dp_ind);
high_count_dp_ind = find((1-good_dp_ind)==1);
for ii=1:length(p.scanidxs)
scan_ind_temp = p.scanidxs{ii};
N_scan_pts = length(scan_ind_temp);
[val, pos]=intersect(scan_ind_temp,high_count_dp_ind);
num_bad_pts = length(val); % get the # of bad pts for current scan
p.share_pos{ii}(pos,:) = []; %remove positions for current scan
if ii == 1
scanidxs_lb = 1;
else
scanidxs_lb = p.scanidxs{ii-1}(end)+1;
end
p.numpts(ii) = N_scan_pts-num_bad_pts;
p.scanindexrange(ii,:) = [scanidxs_lb, scanidxs_lb+p.numpts(ii)-1];
p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,2);
end
p.numpos = sum(p.numpts);
%store indices for bad data
p.high_count_dp = 1-good_dp_ind;
if any(p.high_count_dp)
verbose(1, 'Remove %d diffraction pattern(s) with high counts', sum(p.high_count_dp))
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% plot prepared data %%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.plot.prepared_data && p.use_display
core.analysis.plot_raw_data(p)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% Plot initial guess %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Define combined strings for figure title
p.plot.obtitlestring = '';
p.plot.prtitlestring = '';
p.plot.errtitlestring = '';
if p.share_object
p.plot.obtitlestring = [core.generate_scan_name(p) ' '];
end
if p.share_probe
p.plot.prtitlestring = [core.generate_scan_name(p) ' '];
end
p.plot.errtitlestring = [core.generate_scan_name(p) ' '];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% Plot initial guess %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.use_display
p.plot.extratitlestring = sprintf(' (%dx%d) - Initial guess', p.asize(2), p.asize(1));
core.analysis.plot_results(p, 'use_display', p.use_display);
end
p.plot.extratitlestring = sprintf(' (%dx%d)', p.asize(2), p.asize(1));
if ~isfield(p.plot, 'windowautopos')
p.plot.windowautopos = false; % So resizing after first time display is respected
end
verbose(1, 'Finished data preparation and initialization.')
end
ptycho/+core/prep_h5data.m
+234
View File
@@ -0,0 +1,234 @@
%PREP_H5DATA prepare data and save it to disk
% prep_h5data expects that fmask and fmag already exist, prepares them
% for the C++ code and saves everything to disk.
%
% ** p p structure
%
% see also: core.ptycho_prepare_scans
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function prep_h5data(p)
import utils.verbose
import io.HDF.save2hdf5
fmask = p.fmask;
fmag = p.fmag;
single_mask = true;
for ii=1:size(fmask,3)-1
if ~isequaln(fmask(:,:,ii),fmask(:,:,ii+1))
single_mask = false;
break;
end
end
%%%%% Prepare object and probe for hdf5 file %%%%%
for obnum = p.share_object_ID
object_c(obnum) = struct('data',p.object{obnum}(:,:,1));
end
for prnum = p.share_probe_ID
probe_c(prnum) = struct('data',p.probes(:,:,prnum));
end
%%%%% Prepare data for hdf5 file %%%%%
bad_pixels = cell(p.numscans,1);
bad_pixels_index = cell(p.numscans,1);
% Assumes that detector position is the same within a scan
for ii = 1:p.numscans % loop over scans
% Prepare structure for detector %
% Here I detect the module gaps, can be later given by the
% prepare_data function
fmaski = fmask(:,:,p.scanindexrange(ii,1)); % First mask to detect modules (gaps)
auxmodxo = any(fmaski,1);
if auxmodxo(1)
indbeginmodx = 1;
else
indbeginmodx = [];
end
auxmodx = diff(auxmodxo);
indbeginmodx = [indbeginmodx find(auxmodx==1)+1];
nummodx = length(indbeginmodx);
indendmodx = find(auxmodx==-1);
if auxmodxo(end)
indendmodx = [indendmodx p.asize(2)];
end
auxmodyo = any(fmaski,2);
if auxmodyo(1)
indbeginmody = 1;
else
indbeginmody = [];
end
auxmody = diff(auxmodyo);
indbeginmody = [indbeginmody find(auxmody==1).'+1];
nummody = length(indbeginmody);
indendmody = find(auxmody==-1).';
if auxmodyo(end)
indendmody = [indendmody p.asize(1)];
end
modulearray = zeros(nummody*nummodx,4);
fmaskdet = zeros(p.asize); % Module mask for current detector position
counter = 0;
for kk = 1:nummody
for jj = 1:nummodx
counter = counter+1;
numrows = indendmody(kk) - indbeginmody(kk) + 1;
numcols = indendmodx(jj) - indbeginmodx(jj) + 1;
fmaskdet(indbeginmody(kk):indendmody(kk),indbeginmodx(jj):indendmodx(jj))=1;
modulearray(counter,:) = [numrows,numcols,indbeginmody(kk)-1,indbeginmodx(jj)-1]; %% Minus one to go to indexing convention in C
end
end
verbose(3,['Detected ' num2str(nummodx*nummody) ' modules'])
if verbose >= 3
disp([num2str(modulearray)])
end
%%% Here there is the posibility to add bad pixels that are common
%%% to all diffraction patterns. Could be identified in prepare
%%% data
%detector(ii) = struct('rows', uint32(192), 'columns', uint32(192), 'modules', transpose(uint32([192,192,0,0])), 'bad_pixels', transpose(uint32([9,10; 11,12; 13,14])));
detector(ii) = struct('rows', uint32(p.asize(1)), 'columns', uint32(p.asize(2)),...
'modules', transpose(uint32(modulearray)),'bad_pixels',uint32([]));
if ~single_mask
idx = 0;
for jj = p.scanindexrange(ii,1):p.scanindexrange(ii,2) % loop over corresponding diffraction patterns
[y, x] = find(1+fmask(:,:,jj)-fmaskdet==0);
bps = transpose(reshape([y, x], length(x), 2))-1;
idx = length(bps)+idx;
bad_pixels_index{ii} = [bad_pixels_index{ii} idx];
bad_pixels{ii} = [bad_pixels{ii} bps];
end
else
[y, x] = find(1+fmaski-fmaskdet==0);
bad_pixels{ii} = transpose(reshape([y, x], length(x), 2))-1;
end
% Prepare structure for measurement %
% for jj = p.scanindexrange(ii,1):p.scanindexrange(ii,2) % loop over corresponding diffraction patterns
% %%%%% Prepare bad pixels %%%%%
% [y, x] = find(1+fmaski-fmaskdet==0);
% bad_pixels(jj) = transpose(reshape([y, x], length(x), 2))-1;
% measurement(jj) = struct('data', fmag(:,:,jj), 'position', uint32((p.positions(jj,:))),...
% 'object', uint32(p.share_object_ID(ii)-1), 'probe', uint32(p.share_probe_ID(ii)-1),...
% 'detector', uint32(ii-1));
% end
end
%% prepare output
h5_struc = [];
h5_struc.Attributes.format = 2;
for ii=1:size(probe_c,2)
h5_struc.probes(:,ii) = uint64(size(probe_c(ii).data));
end
for ii=1:size(object_c,2)
h5_struc.objects(:,ii) = uint64(size(object_c(ii).data));
end
%% detectors
h5_struc.detector = [];
for ii=1:p.numscans
temp = detector(ii);
h5_struc.detector.(['n' num2str(ii-1)]).Attributes.rows = temp.rows;
h5_struc.detector.(['n' num2str(ii-1)]).Attributes.columns = temp.columns;
if single_mask && ~isempty(bad_pixels{ii})
h5_struc.detector.(['n' num2str(ii-1)]).bad_pixels = bad_pixels{ii};
end
h5_struc.detector.(['n' num2str(ii-1)]).modules = temp.modules;
end
%% measurements
h5_struc.measurement = [];
h5_struc.measurement.Attributes.max_power = 1/p.renorm^2;
for ii=1:p.numscans
% attributes
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.detector = uint32(ii-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.probe = uint32(p.share_probe_ID(ii)-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.object = uint32(p.share_object_ID(ii)-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.max_sum = uint32(p.max_sum(ii));
% datasets
h5_struc.measurement.(['n' num2str(ii-1)]).positions = uint32(transpose(round(p.positions(p.scanidxs{ii},:))));
h5_struc.measurement.(['n' num2str(ii-1)]).data = permute((fmag(:,:,p.scanidxs{ii})/p.renorm).^2, [2 1 3]);
if ~single_mask
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels = bad_pixels{ii};
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels_index.Value = uint64(transpose(bad_pixels_index{ii}));
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels_index.Attributes.save2hdf5DataShape = size(uint64(transpose(bad_pixels_index{ii})),1);
end
end
%% save to disk
if ~exist(p.prepare_data_path, 'dir')
mkdir(p.prepare_data_path)
end
verbose(2,'Writing H5 data file: %s',[p.prepare_data_path p.prepare_data_filename]);
save2hdf5([p.prepare_data_path p.prepare_data_filename], h5_struc, 'overwrite', true, 'comp', p.io.data_compression);
end
ptycho/+core/prepare_initial_guess.m
+85
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@@ -0,0 +1,85 @@
%PREPARE_INITIAL_GUESS
% prepare an initial guess for the object and probe reconstruction
%
% ** p p structure
%
% returns:
% ++ p p structure
%
% see also: core.prepare_initial_guess
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p] = prepare_initial_guess(p)
import utils.verbose
verbose(1, 'Preparing initial guess.')
%% prepare objects
p = core.update_object_size(p);
p = core.prepare_initial_object(p);
%% prepare probes
p = core.prepare_initial_probes(p);
if ~isfield(p,'center_probe')
p.center_probe = false;
end
end
ptycho/+core/prepare_initial_object.m
+113
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@@ -0,0 +1,113 @@
%PREPARE_INITIAL_OBJECT
% prepare an initial guess for the object reconstruction
%
% ** p p structure
%
% returns:
% ++ p p structure
%
% see also: core.prepare_initial_guess
%
function [ p ] = prepare_initial_object( p )
import utils.verbose
import utils.crop_pad
import utils.interpolateFT
if p.model_object
switch p.model.object_type
case 'rand'
verbose(2,'Using random object as initial guess.')
case 'amplitude'
% create dummy object which will be overwritten once the
% prepared data is available
assert(p.fourier_ptycho, 'An initial guess based on the prepared data is only suited for Fourier ptychography.')
end
for obnum = 1:p.numobjs
p.object{obnum} = (1+1i*1e-6*rand([p.object_size(obnum,:) p.object_modes])).*ones([p.object_size(obnum,:) p.object_modes]);
end
else
if isfield(p, 'initial_iterate_object')
warning('Loading initial object guess from file given by p.initial_iterate_object_file.')
end
verbose(2,'Using loaded object as initial guess.')
if numel(p.initial_iterate_object_file) ~= p.numobjs
verbose(2,'Number of initial iterate files and number of objects does not match')
for ii=numel(p.initial_iterate_object_file):p.numobjs
p.initial_iterate_object_file{ii} = p.initial_iterate_object_file{end};
end
end
% make a bit smarter the use of initial_iterate_object_file and allow
% some automatic patten filling + file search
for obnum = unique(p.share_object_ID)
% if string allows it, fill in the scan numbers
p.initial_iterate_object_file{obnum} = sprintf(p.initial_iterate_object_file{obnum}, p.scan_number(obnum));
if contains(p.initial_iterate_object_file{obnum}, '*') % if string contains wild character *, try to find the file
fpath = dir(p.initial_iterate_object_file{obnum}) ;
if isempty(fpath)
warning('No file corresponding to pattern %s was found, using random initial guess', p.initial_iterate_object_file{obnum})
p.object{obnum} = (1+1i*1e-6*rand([p.object_size(obnum,:) p.object_modes])).*ones([p.object_size(obnum,:) p.object_modes]);
p.initial_iterate_object_file{obnum} = [];
continue
elseif length(fpath) > 1
warning('Too many files corresponding to pattern %s were found, using the last', p.initial_iterate_object_file{obnum})
fpath = fpath(end);
end
p.initial_iterate_object_file{obnum} = [fpath.folder,'/',fpath.name];
end
end
% load data from disk
for ii = unique(p.share_object_ID) % avoid loading datasets twice
if isempty(p.initial_iterate_object_file{ii})
continue
end
if ~exist(p.initial_iterate_object_file{ii}, 'file')
error(['Did not find initial iterate: ' p.initial_iterate_object_file{ii}])
end
verbose(2,'Loading object %d from: %s',ii,p.initial_iterate_object_file{ii})
S = io.load_ptycho_recons(p.initial_iterate_object_file{ii});
object = double(S.object);
% reinterpolate to the right pixel size
if isfield(S, 'p') && any(S.p.dx_spec ~= p.dx_spec)
verbose(2, 'Warning: Reinterpolate loaded object to new pixels size')
object = interpolateFT(object, ceil(size(object(:,:,1)).*S.p.dx_spec./p.dx_spec));
end
%%% check the object size
if ~isequal(size(squeeze(object(:,:,1))), squeeze(p.object_size(ii,:)))
% if the loaded dataset does not have the expected object size,
% crop/pad it to p.object_size
verbose(2, 'Warning: Object taken from file %s does not have the expected size of %d x %d.', ...
p.initial_iterate_object_file{ii}, p.object_size(ii,1), ...
p.object_size(ii,2))
p.object{ii} = crop_pad(object, p.object_size(ii,:));
else
% the the object sizes are the same, just copy everything
% to p.object
p.object{ii} = object;
end
% now let's check the object modes
mode_diff = p.object_modes-size(object,3);
if mode_diff > 0
% add (random) object modes
p.object{ii}(:,:,size(object,3)+1:p.object_modes,:) = (1+1i*1e-6*rand([p.object_size(ii,:) mode_diff])).*ones([p.object_size(ii,:) mode_diff]);
elseif mode_diff < 0
% modified by YJ. keep all layers for multi-layer object
if isfield(p,'multiple_layers_obj') && p.multiple_layers_obj
%add an extra axis that is needed by GPU_MS
object_temp(:,:,1,:) = p.object{ii};
p.object{ii} = object_temp;
else
% remove object modes
p.object{ii}(:,:,p.object_modes+1:size(object,3),:) = [];
end
end
end
end
end
ptycho/+core/prepare_initial_probes.m
+157
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@@ -0,0 +1,157 @@
% Prepare probe - Only single file supported, either the file has a 3D matrix
% of many probes or the probe will be repeated for the number of probes
% needed for reconstruction
function [ p ] = prepare_initial_probes( p )
p = core.ptycho_model_probe(p);
p.probes = double(p.probe_initial);
if size(p.probes,3) ~= p.numprobs
p.probes = repmat(p.probes,[1 1 p.numprobs]);
end
% If prepared without modes, but reconstruction needs modes
% allocate initial guess.
if size(p.probes,4) ~= p.probe_modes
% Determine mode energies
Emod = zeros(p.probe_modes,1);
for jj = 1:numel(Emod)-1
if jj <= numel(p.mode_start_pow)
Emod(jj+1) = p.mode_start_pow(jj);
else
Emod(jj+1) = p.mode_start_pow(end);
end
end
% if (numel(p.mode_start_pow) == 1)||(numel(p.mode_start_pow) == p.probe_modes-1)
% Emod(2:end) = p.mode_start_pow;
if sum(Emod) > 1
error('Energy distribution between modes exceeds 1, see p.mode_start_pow')
else
Emod(1) = 1-sum(Emod);
end
Emod_init = Emod;
%disp(p.numprobs)
for prnum = 1:p.numprobs
% Determine the total energy of the probe first mode
aux = p.probes(:,:,prnum,1);
Etot = sum(abs(aux(:)).^2);
Emod = Emod_init*Etot; % Now Emod has really the expected total sum
if strcmpi(p.mode_start,'rand')
for prmode = 2:p.probe_modes
p.probes(:,:,prnum,prmode) = p.probes(:,:,prnum,1).*(2*rand(p.asize)-1);
end
elseif strfind(p.mode_start,'herm')
if strcmpi(p.mode_start,'herm')
M = ceil(sqrt(p.probe_modes))-1;
N = ceil(p.probe_modes/(M+1))-1;
elseif strcmpi(p.mode_start,'hermver')
M = 0;
N = p.probe_modes-1;
elseif strcmpi(p.mode_start,'hermhor')
M = p.probe_modes-1;
N = 0;
else
error('Unknown p.mode_start')
end
x = [1:size(p.probes,2)]-size(p.probes,2)/2;
y = [1:size(p.probes,1)]-size(p.probes,1)/2;
[X Y] = meshgrid(x,y);
H = core.hermite_like(squeeze(p.probes(:,:,prnum,1)),X,Y,M,N);
if prnum == 1
p.probes(:,:,:,2:p.probe_modes) = 0;
end
p.probes(:,:,prnum,2:p.probe_modes) = reshape(H(:,:,2:p.probe_modes),size(p.probes(:,:,prnum,2:p.probe_modes)));
else
error('Undefined p.mode_start')
end
% Normalization
for prmode = 1:p.probe_modes
p.probes(:,:,prnum,prmode) = p.probes(:,:,prnum,prmode)*sqrt(Emod(prmode)/(sum(sum(abs(p.probes(:,:,prnum,prmode)).^2))));
end
% p. mode_start_pow = [0.02] ; % Integrated intensity on modes. Can be a number (all modes equal) or a vector
% p. mode_start = 'rand' % (for probe) = 'rand', = 'her' (Hermitian-like base), = 'herver' (vertical modes only), = 'herhor' (horizontal modes only)
% p. mode_her_ord = []; % (for probe) Specify a 2xn vector with the (m,n) starting orders, leave = [] for default
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*(1+0.01.*rand(p.asize))*0.5;
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*exp(1i*0.1*pi.*rand(p.asize))*0.1;
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*(2*rand(p.asize)-1)*5;
end
end
%Added by YJ. Force orthogonalization of initial probes
if isfield(p,'ortho_init_probes') && p.ortho_init_probes
% Determine mode energies
Emod = zeros(p.probe_modes,1);
for jj = 1:numel(Emod)-1
if jj <= numel(p.mode_start_pow)
Emod(jj+1) = p.mode_start_pow(jj);
else
Emod(jj+1) = p.mode_start_pow(end);
end
end
% if (numel(p.mode_start_pow) == 1)||(numel(p.mode_start_pow) == p.probe_modes-1)
% Emod(2:end) = p.mode_start_pow;
if sum(Emod) > 1
error('Energy distribution between modes exceeds 1, see p.mode_start_pow')
else
Emod(1) = 1-sum(Emod);
end
Emod_init = Emod;
for prnum = 1:p.numprobs
% Determine the total energy of the probe first mode
aux = p.probes(:,:,prnum,1);
Etot = sum(abs(aux(:)).^2);
Emod = Emod_init*Etot; % Now Emod has really the expected total sum
if strcmpi(p.mode_start,'rand')
for prmode = 2:p.probe_modes
p.probes(:,:,prnum,prmode) = p.probes(:,:,prnum,1).*(2*rand(p.asize)-1);
end
elseif strcmpi(p.mode_start,'zeros') %added by YJ
for prmode = 2:p.probe_modes
p.probes(:,:,prnum,prmode) = ones(p.asize)*eps;
end
elseif strfind(p.mode_start,'herm')
if strcmpi(p.mode_start,'herm')
M = ceil(sqrt(p.probe_modes))-1;
N = ceil(p.probe_modes/(M+1))-1;
elseif strcmpi(p.mode_start,'hermver')
M = 0;
N = p.probe_modes-1;
elseif strcmpi(p.mode_start,'hermhor')
M = p.probe_modes-1;
N = 0;
else
error('Unknown p.mode_start')
end
x = [1:size(p.probes,2)]-size(p.probes,2)/2;
y = [1:size(p.probes,1)]-size(p.probes,1)/2;
[X Y] = meshgrid(x,y);
H = core.hermite_like(squeeze(p.probes(:,:,prnum,1)),X,Y,M,N);
%disp(size(H))
if prnum == 1
p.probes(:,:,:,2:p.probe_modes) = 0;
end
p.probes(:,:,prnum,2:p.probe_modes) = reshape(H(:,:,2:p.probe_modes),size(p.probes(:,:,prnum,2:p.probe_modes)));
else
error('Undefined p.mode_start')
end
% Normalization
for prmode = 1:p.probe_modes
p.probes(:,:,prnum,prmode) = p.probes(:,:,prnum,prmode)*sqrt(Emod(prmode)/(sum(sum(abs(p.probes(:,:,prnum,prmode)).^2))));
end
% p. mode_start_pow = [0.02] ; % Integrated intensity on modes. Can be a number (all modes equal) or a vector
% p. mode_start = 'rand' % (for probe) = 'rand', = 'her' (Hermitian-like base), = 'herver' (vertical modes only), = 'herhor' (horizontal modes only)
% p. mode_her_ord = []; % (for probe) Specify a 2xn vector with the (m,n) starting orders, leave = [] for default
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*(1+0.01.*rand(p.asize))*0.5;
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*exp(1i*0.1*pi.*rand(p.asize))*0.1;
% p.probes(:,:,:,prmode) = p.probes(:,:,:,1).*(2*rand(p.asize)-1)*5;
end
end
end
ptycho/+core/private/get_projections_cpu_mex.c
+169
View File
@@ -0,0 +1,169 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_projections_cpu_mex.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
hereinafter set out and until termination of this license as set forth below.
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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
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
in the commercial use, application or exploitation of works similar to the PROGRAM.
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
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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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:
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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,
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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
the courts of Zürich, Switzerland.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type single. */
for (i=0; i < 2; i++) {
if (mxIsSingle(prhs[i]) != 1){
printf("Input %d is not single\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* Check that arrays are complex */
if(mxIsComplex(prhs[0]) != 1) {
printf("object input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
if(mxIsComplex(prhs[1]) != 1) {
printf("probe input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
float const *object_r, *object_i;
float *projection_r,*projection_i;
const int *positions, *ind_ok;
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (float*)mxGetData(prhs[0]);
projection_r = (float*)mxGetData(prhs[1]);
/* get pointers to input data */
object_i = (float*)mxGetImagData(prhs[0]);
projection_i = (float*)mxGetImagData(prhs[1]);
/* Get dimension of probe and object */
mwSize const * dims;
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[3]) > dims[2])) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
int id_small, id_large, pos, col, row, p;
#pragma omp parallel for private(p,pos,col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
projection_r[id_small] = object_r[id_large];
projection_i[id_small] = object_i[id_large];
}
}
}
return;
}
ptycho/+core/private/get_projections_cpu_mex_double.c
+169
View File
@@ -0,0 +1,169 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_projections_cpu_mex_double.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
hereinafter set out and until termination of this license as set forth below.
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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
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
in the commercial use, application or exploitation of works similar to the PROGRAM.
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
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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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:
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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,
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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
the courts of Zürich, Switzerland.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsDouble(prhs[i]) != 1){
printf("Input %d is not double\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* Check that arrays are complex */
if(mxIsComplex(prhs[0]) != 1) {
printf("object input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
if(mxIsComplex(prhs[1]) != 1) {
printf("probe input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
double const *object_r, *object_i;
double *projection_r,*projection_i;
int *positions, *ind_ok;
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (double*)mxGetData(prhs[0]);
projection_r = (double*)mxGetData(prhs[1]);
/* get pointers to input data */
object_i = (double*)mxGetImagData(prhs[0]);
projection_i = (double*)mxGetImagData(prhs[1]);
/* Get dimension of probe and object */
mwSize const * dims;
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[3]) > dims[2])) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
int id_small, id_large, pos, col, row, p;
#pragma omp parallel for private(p,pos,col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
projection_r[id_small] = object_r[id_large];
projection_i[id_small] = object_i[id_large];
}
}
}
return;
}
ptycho/+core/private/ptycho_exit.m
+245
View File
@@ -0,0 +1,245 @@
%PTYCHO_EXIT
%onCleanup function for core.ptycho_recons
%
% ** p p structure
%
% see also: core.ptycho_recons
% modified by YJ
function ptycho_exit(p)
import utils.*
if ~isfield(p.io,'data_descriptor')
p.io.data_descriptor = '';
end
if isfield(p.getReport, 'crashed') && p.getReport.crashed
fprintf('\n\n\n###############################################################\n')
fprintf('########################## PONG! ##############################\n')
fprintf('###############################################################\n')
disp([p.getReport.ME.getReport '\n\n\n']);
fprintf('Reconstruction stopped! Set verbose level to >3 for debugging. \n')
if ~p.getReport.completed
if ~isempty(p.io.phone_number) && p.io.send_crashed_recon_SMS
%modified by YJ
subject = 'Ptycho recon crashed!';
message = sprintf('User %s''s ptycho recon of %s scan%s crashed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
if isfield(p.queue, 'file_this_recons')
disp('test test test test')
try
fprintf('Moving queue file file back to %s.\n', fullfile(p.queue.path, p.queue.file_this_recons))
% get log file name
[~, ~, fext] = fileparts(p.queue.file_this_recons);
log_dir = fullfile(p.queue.path, 'failed', 'log');
if ~exist(log_dir, 'dir')
mkdir(log_dir)
end
log_file = fullfile(log_dir, strrep(p.queue.file_this_recons, fext, '.log'));
% check if log file extists and update its content; move
% queue file back to in_progess
if exist(log_file, 'file')
fid = fopen(log_file);
log_line = fgetl(fid);
fclose(fid);
log_int = strtrim(strsplit(log_line, ':'));
log_int = log_int{end};
log_int = str2double(log_int);
if ~isfield(p, 'queue_max_attempts')
p.queue.max_attempts = 5;
fprintf('Code crashed before parsing p.queue.max_attempts.\n')
end
if log_int >= p.queue.max_attempts
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, 'failed', p.queue.file_this_recons))
fid = fopen(log_file, 'w');
fprintf(fid, [p.getReport.ME.getReport '\n\n\n']);
fprintf('Failed more than %u times. Moving file to ''failed''.\n', p.queue.max_attempts);
fclose(fid);
if ~isempty(p.io.phone_number) && p.io.send_failed_scans_SMS
io.sendSMS(p.io.phone_number, sprintf('Failed to reconstruct scan %s. I will move it to "failed".', num2str(p.scan_number)), 'sleep', p.SMS_sleep, 'logfile', fullfile(log_dir, 'sendSMS.log'));
end
else
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons));
fid = fopen(log_file, 'w');
fprintf(fid, 'failed attempts: %u\n\n', log_int+1);
fprintf(fid, [p.getReport.ME.getReport '\n\n\n']);
fclose(fid);
end
else
fid = fopen(log_file, 'w');
fprintf(fid, 'failed attempts: 1');
fclose(fid);
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons))
end
catch
fprintf('Failed to move file back to queue search path.\n')
end
end
if isfield(p.queue, 'lockfile')
if isempty(p.queue.lockfile)
if verbose > 2
p.queue.lockfile = false;
else
p.queue.lockfile = true;
end
end
if p.queue.lockfile
if isempty(p.save_path{1})
try
for ii = 1:length(p.scan_number)
p.scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
p = core.ptycho_prepare_paths(p);
catch
fprintf('Could not find lock file. \n')
end
end
for ii=1:length(p.save_path)
lock_filename = [p.save_path{ii} '/' p.run_name '_lock'];
if exist(lock_filename, 'file')
try
unix(['rm ' lock_filename]);
fprintf('Removing lock file %s\n',lock_filename)
catch
fprintf('Removing lock file %s failed\n',lock_filename)
end
end
end
end
end
if isfield(p.queue, 'remote_recons') && p.queue.remote_recons
keyboard
end
end
fprintf('Pausing for 5 seconds.\n')
fprintf('###############################################################\n\n')
pause(5);
elseif ~p.getReport.completed
if isfield(p, 'remote_failed') && p.remote_failed
try
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, 'failed', p.queue.file_this_recons));
catch
fprintf('Failed to move file to failed.\n')
end
elseif isfield(p.queue, 'file_this_recons')
try
fprintf('Reconstruction stopped, moving file to %s.\n', fullfile(p.queue.path, p.queue.file_this_recons))
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons))
catch
fprintf('Failed to move file back to queue search path.\n')
end
end
if isfield(p.queue, 'lockfile')
if isempty(p.queue.lockfile)
if verbose > 2
p.queue.lockfile = false;
else
p.queue.lockfile = true;
end
end
if p.queue.lockfile
if isempty(p.save_path{1})
try
for ii = 1:length(p.scan_number)
p.scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
p = core.ptycho_prepare_paths(p);
catch
fprintf('Could not find lock file. \n')
end
end
if isfield(p, 'run_name') && ~isempty(p.run_name)
for ii=1:length(p.save_path)
lock_filename = [p.save_path{ii} '/' p.run_name '_lock'];
if exist(lock_filename, 'file')
try
delete(lock_filename);
fprintf('Removing lock file %s\n',lock_filename)
catch
fprintf('Removing lock file %s failed\n',lock_filename)
end
end
end
end
end
end
if isfield(p, 'remote_file_this_recons')
try
fprintf('Removing remote file.\n')
if exist(p.queue.remote_file_this_recons, 'file')
delete(p.queue.remote_file_this_recons)
end
[~, this_file] = fileparts(p.queue.remote_file_this_recons);
if p.queue.isreplica
system(['touch ' fullfile(p.queue.remote_path, [this_file '.crash'])]);
end
this_file = [this_file '.mat'];
if exist(fullfile(p.queue.remote_path, 'in_progress', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'in_progress', this_file));
end
if exist(fullfile(p.queue.remote_path, 'done', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'done', this_file));
end
if exist(fullfile(p.queue.remote_path, 'done', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'done', this_file));
end
catch
fprintf('Failed to remove remote file.\n')
end
end
if ~isempty(p.io.phone_number) && p.io.send_crashed_recon_SMS
%modified by YJ
subject = 'Ptycho recon crashed!';
message = sprintf('User %s''s ptycho recon of %s scan%s crashed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
end
pid = [p.ptycho_matlab_path './utils/.tmp_procID/proc_' num2str(feature('getpid')) '.dat'];
if exist(pid, 'file')
delete(pid)
end
if ~isempty(p.io.phone_number) && p.io.send_finished_recon_SMS && p.getReport.completed
%modified by YJ
subject = 'Ptycho recon completed!';
message = sprintf('User %s''s ptycho recon of %s scan%s completed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
try
verbose(struct('prefix', {[]}))
catch
end
end
ptycho/+core/private/set_projections_cpu_mex.c
+188
View File
@@ -0,0 +1,188 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" set_projections_cpu_mex.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
hereinafter set out and until termination of this license as set forth below.
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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
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
in the commercial use, application or exploitation of works similar to the PROGRAM.
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
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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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:
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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,
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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
the courts of Zürich, Switzerland.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsSingle(prhs[i]) != 1){
printf("Input %d is not single\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// /* Check that arrays are complex */
// if(mxIsComplex(prhs[0]) != 1) {
// printf("object input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
// if(mxIsComplex(prhs[1]) != 1) {
// printf("probe input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
float *object_r, *object_i, *probe_r,*probe_i;
int *positions, *ind_ok;
bool cprobe, cobject;
cobject = mxIsComplex(prhs[0]);
cprobe = mxIsComplex(prhs[1]);
if( cobject != cobject)
{
printf("probe/object input argument must be complex/real-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected both complex / real arrays");
}
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (float*)mxGetData(prhs[0]);
probe_r = (float*)mxGetData(prhs[1]);
if(cprobe)
{
/* get pointers to input data */
object_i = (float*)mxGetImagData(prhs[0]);
probe_i = (float*)mxGetImagData(prhs[1]);
}
/* Get dimension of probe and object */
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
mwSize const * dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[2]) != dims[2]) && (Ndims == 3)) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
mwSize id_small, id_large, pos, col, row, o, p;
bool flat_probe = Ndims == 2;
#pragma omp parallel for private(p,pos, col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
if(flat_probe)
id_small = row + col*Np_y;
else
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
#pragma omp atomic
object_r[id_large] += probe_r[id_small];
if(cprobe) {
#pragma omp atomic
object_i[id_large] += probe_i[id_small];
}
}
}
}
return;
}
ptycho/+core/private/set_projections_cpu_mex_double.c
+188
View File
@@ -0,0 +1,188 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" set_projections_cpu_mex_double.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
hereinafter set out and until termination of this license as set forth below.
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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
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
in the commercial use, application or exploitation of works similar to the PROGRAM.
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
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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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:
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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,
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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
the courts of Zürich, Switzerland.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsDouble(prhs[i]) != 1){
printf("Input %d is not double\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// /* Check that arrays are complex */
// if(mxIsComplex(prhs[0]) != 1) {
// printf("object input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
// if(mxIsComplex(prhs[1]) != 1) {
// printf("probe input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
double *object_r, *object_i, *probe_r,*probe_i;
int *positions, *ind_ok;
bool cprobe, cobject;
cobject = mxIsComplex(prhs[0]);
cprobe = mxIsComplex(prhs[1]);
if( cobject != cobject)
{
printf("probe/object input argument must be complex/real-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected both complex / real arrays");
}
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (double*)mxGetData(prhs[0]);
probe_r = (double*)mxGetData(prhs[1]);
if(cprobe)
{
/* get pointers to input data */
object_i = (double*)mxGetImagData(prhs[0]);
probe_i = (double*)mxGetImagData(prhs[1]);
}
/* Get dimension of probe and object */
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
mwSize const * dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[2]) != dims[2]) && (Ndims == 3)) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
mwSize id_small, id_large, pos, col, row, o, p;
bool flat_probe = Ndims == 2;
#pragma omp parallel for private(p,pos, col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
if(flat_probe)
id_small = row + col*Np_y;
else
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
#pragma omp atomic
object_r[id_large] += probe_r[id_small];
if(cprobe) {
#pragma omp atomic
object_i[id_large] += probe_i[id_small];
}
}
}
}
return;
}
ptycho/+core/private/write_procID.m
+84
View File
@@ -0,0 +1,84 @@
%WRITE_PROCID
% writes .dat files to utils/.tmp_procID to keep track of current
% reconstructions
% ** p p structure
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function write_procID(p)
try
if ~exist(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID'), 'dir')
mkdir(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID'))
end
if ispc
hostname = getenv('COMPUTERNAME');
else
hostname = getenv('HOSTNAME');
end
% calling system('hostname') has large overhead, try to avoid if not needed
if isempty(hostname)
[~, hostname] = system('hostname');
hostname = hostname(1:end-1);
end
caller = dbstack;
f = fopen(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID', ['proc_' num2str(feature('getpid')) '.dat']), 'w');
fprintf(f, [hostname ' ' strrep(num2str(p.scan_number), ' ', '-') ' ' datestr(datetime('now')) ' ' caller(end).name]);
fclose(f);
catch
utils.verbose(0, 'Failed to write process ID.')
end
ptycho/+core/probe_modes_ortho.m
+120
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@@ -0,0 +1,120 @@
% ORTHO Orthogonalize the given list of modes using SVD.
% [pr, I_n, eval] = probe_modes_ortho(modes)
% pr Orthogonalized (eigen) modes
% I_n Normalized intensity of the mode (relative contribution to total intensity)
% eval SVD eigenvalues
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [pr, I_n, eval] = probe_modes_ortho(modes)
% SVD decomposition of matrix M
% M = U S V*
% where U is a unitary matrix, S is a diagonal matrix with singular
% values and V* is a unitary matrix.
%
% M M* = U S V* V S* U* = U (S S*) U*
% M* M = V S* U* U S V* = V (S* S) V*
% If probes are given as a 4D array, it will be assumed that the 3rd axis
% is the scan index
if ndims(modes)==4
nscans = size(modes,3);
I_n = cell(nscans,1);
eval = cell(nscans,1);
N = size(modes,4);
pr = zeros(size(modes));
for scanindx=1:nscans
[pr(:,:,scanindx,:), I_n{scanindx}, eval{scanindx}] = core.probe_modes_ortho(squeeze(modes(:,:,scanindx,:)));
end
else
%% calculate M M* and its eigenvectors
N = size(modes,3);
A = zeros(N,N,'like',modes);
for ii=1:N
p2 = modes(:,:,ii);
for jj=1:N
p1 = modes(:,:,jj);
A(ii,jj) = sum(dot(p2,p1));
end
end
A(isnan(A)) = 0;
[evec,eval] = eig(A);
%% sort modes by their contribution
[~,I] = sort(diag(eval), 'descend');
%% orthogonalize probes
pr = zeros(size(modes,1), size(modes,2), N, 'like', modes);
for jj = 1:N
for ii = 1:N
pr(:,:,jj) = pr(:,:,jj) + modes(:,:,ii) * evec(ii,I(jj));
end
end
%% calculate intensity contribution
I_n = zeros(N,1, 'like', modes);
for ii = 1:N
I_n(ii,:) = sum(sum(abs(pr(:,:,ii)).^2));
end
I_n = I_n ./ sum(I_n(:));
end
ptycho/+core/ptycho_adjust_positions.m
+132
View File
@@ -0,0 +1,132 @@
%PTYCHO_ADJUST_POSITIONS
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ p ] = ptycho_adjust_positions( p )
p.positions_real = -p.positions_real;
% Affine transform on probe positions (this will modify the object
% according to the transformation matrix)
if isfield(p,'affine_matrix')&&(~isempty(p.affine_matrix))&&any(any(p.affine_matrix ~= eye(2)))
utils.verbose(1, 'Applying custom affine matrix to measured positions')
p.positions_real = p.affine_matrix*p.positions_real.';
p.positions_real = p.positions_real.';
end
%Add coarse translation for slow axis (substract because we are in probe
%positions)
if isfield(p, 'spec') && (check_option(p.spec.motor,'coarse_motors') && length(p.spec.motor.coarse_motors) == 2)
assert(check_option(p.spec.motor,'coarse_motors_scale'), 'Provide scale of the coarse motors in p.spec.motor.coarse_motors_scale ')
for ii = 1:length(p.scan_number)
p.positions_real(p.scanidxs{ii},1) = p.positions_real(p.scanidxs{ii},1)-getfield(p.meta{ii}.spec,p.spec.motor.coarse_motors{2})*p.spec.motor.coarse_motors_scale(min(end,2));
p.positions_real(p.scanidxs{ii},2) = p.positions_real(p.scanidxs{ii},2)-getfield(p.meta{ii}.spec,p.spec.motor.coarse_motors{1})*p.spec.motor.coarse_motors_scale(1);
end
end
% Convert to pixels
p.positions = p.positions_real./p.dx_spec;
% prepare positions offset
if ~isfield(p, 'positions_pad')
p.positions_pad = [0 0];
else
if size(p.positions_pad,2) == 1
p.positions_pad = [p.positions_pad p.positions_pad];
end
end
% compute positions for shared reconstruction
share_pos{length(unique(p.share_object_ID))} = [];
for jj=1:p.numscans
if isempty(share_pos{p.share_object_ID(jj)})
share_pos{p.share_object_ID(jj)} = p.positions(p.scanidxs{jj},:);
else
tmp = share_pos{p.share_object_ID(jj)};
share_pos{p.share_object_ID(jj)} = [];
share_pos{p.share_object_ID(jj)} = cat(1, tmp, p.positions(p.scanidxs{jj},:));
end
end
% Convenient offset of positions
if length(unique(p.share_object_ID))==1
p.positions = p.positions - min(p.positions) + p.positions_pad;
else
for ii=1:length(p.scan_number)
p.positions(p.scanidxs{ii},:) = ...
p.positions(p.scanidxs{ii},:) - ...
min(share_pos{p.share_object_ID(ii)}) + p.positions_pad;
end
end
% update shared positions with new positions
clear share_pos;
share_pos{length(unique(p.share_object_ID))} = [];
for jj=1:p.numscans
if isempty(share_pos{p.share_object_ID(jj)})
share_pos{p.share_object_ID(jj)} = p.positions(p.scanidxs{jj},:);
else
tmp = share_pos{p.share_object_ID(jj)};
share_pos{p.share_object_ID(jj)} = [];
share_pos{p.share_object_ID(jj)} = cat(1, tmp, p.positions(p.scanidxs{jj},:));
end
end
p.share_pos = share_pos;
end
ptycho/+core/ptycho_model_probe.m
+233
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@@ -0,0 +1,233 @@
% pout = ptycho_model_probe(p)
function pout = ptycho_model_probe(p)
import utils.*
import io.*
% Define often-used variables
lambda = p.lambda;
asize = p.asize; % Diffr. patt. array size
% added by YJ for up-sampled diffraction patterns.
if p.detector.upsampling >0
asize = asize*2^p.detector.upsampling;
end
dx_spec = p.dx_spec;
a2 = prod(asize);
if check_option(p, 'prop_regime', 'nearfield')
% for this task use original values of the pixel sizes
dx_spec = p.lambda*p.z*p.nearfield_magnification ./ (p.asize*p.ds);
end
% Prepare probe
if p.model_probe
% STEM probe: based on Eq.(2.10) in Advanced Computing in Electron
% Microscopy (2nd edition) by Dr.Kirkland
if isfield(p,'beam_source') && strcmp(p.beam_source, 'electron')
df = p.model.probe_df;
alpha_max = p.model.probe_alpha_max;
amax = alpha_max*1e-3; %in rad
amin = 0;
klimitmax = amax/lambda;
klimitmin = amin/lambda;
N = asize(1);
dk = 1/(dx_spec(1)*N);
kx = linspace(-floor(N/2),ceil(N/2)-1,N);
[kX,kY] = meshgrid(kx,kx);
kX = kX.*dk;
kY = kY.*dk;
kR = sqrt(kX.^2+kY.^2);
theta = atan2(kY,kX);
mask = single(kR<=klimitmax).*single(kR>=klimitmin);
chi = -pi*lambda*kR.^2*df;
%third-order spherical aberration in angstrom
if isfield(p.model,'probe_c3') && p.model.probe_c3~=0
chi = chi + pi/2*p.model.probe_c3*lambda^3*kR.^4;
end
%fifth-order spherical aberration in angstrom
if isfield(p.model,'probe_c5') && p.model.probe_c5~=0
chi = chi + pi/3*p.model.probe_c5*lambda^5*kR.^6;
end
%seventh-order spherical aberration in angstrom
if isfield(p.model,'probe_c7') && p.model.probe_c7~=0
chi = chi + pi/4*p.model.probe_c7*lambda^7*kR.^8;
end
%twofold astigmatism in angstrom & azimuthal orientation in radian
if isfield(p.model,'probe_f_a2') && isfield(p.model,'probe_theta_a2') && p.model.probe_f_a2~=0
chi = chi + pi*p.model.probe_f_a2*lambda*kR.^2*sin(2*(theta-p.model.probe_theta_a2));
end
%threefold astigmatism in angstrom & azimuthal orientation in radian
if isfield(p.model,'probe_f_a3') && isfield(p.model,'probe_theta_a3') && p.model.probe_f_a3~=0
chi = chi + 2*pi/3*p.model.probe_f_a3*lambda^2*kR.^3*sin(3*(theta-p.model.probe_theta_a3));
end
%coma in angstrom & azimuthal orientation in radian
if isfield(p.model,'probe_f_c3') && isfield(p.model,'probe_theta_c3') && p.model.probe_f_c3~=0
chi = chi + 2*pi/3*p.model.probe_f_c3*lambda^2*kR.^3*sin(theta-p.model.probe_theta_c3);
end
probe = mask.*exp(-1i.*chi);
probe = fftshift(ifft2(ifftshift(probe)));
probe = probe/sum(sum(abs(probe)));
else %X-ray probe
if p.model.probe_is_focused
verbose(2, 'Using focused probe as initial model.');
if asize(1) ~= asize(2)
error('Focused probe modeling is only implemented for square arrays (please feel free to change that).');
end
if isempty(p.model.probe_zone_plate_diameter) || isempty(p.model.probe_outer_zone_width)
zp_f = p.model.probe_focal_length;
verbose(3, 'Using model.probe_focal_length for modeled probe.');
else
zp_f = p.model.probe_zone_plate_diameter * p.model.probe_outer_zone_width / lambda;
end
% The probe is generated in a larger array to avoid aliasing
upsample = p.model.probe_upsample;
defocus = p.model.probe_propagation_dist;
Nprobe = upsample*asize(1); % Array dimension for the simulation
dx = (zp_f+defocus)*lambda/(Nprobe*dx_spec(1)); % pixel size in the pupil plane
r1_pix = p.model.probe_diameter / dx; % size in pixels of first pinhole
r2_pix = p.model.probe_central_stop_diameter / dx; % size in pixels of central stop
% Pupil
[x,y] = meshgrid(-Nprobe/2:floor((Nprobe-1)/2),-Nprobe/2:floor((Nprobe-1)/2));
r2 = x.^2 + y.^2;
% w = (r2 < (r1_pix)^2);
if upsample*asize(1) < round(r1_pix)-5
error(sprintf('For this experimental parameters asize must be at least %d in order for the lens to fit in the window.',ceil((round(r1_pix)-5)./upsample+1)))
end
w = fftshift(filt2d_pad(upsample*asize(1), round(r1_pix)+5, round(r1_pix)-5, 'circ'));
if p.model.probe_central_stop
w = w .*(1-fftshift(filt2d_pad(upsample*asize(1), round(r2_pix)+2, round(r2_pix-2), 'circ')));
end
if isfield(p.model,'probe_structured_illum_power') && p.model.probe_structured_illum_power
%rng default
r = utils.imgaussfilt2_fft(randn(upsample*p.asize),upsample*2);
r = r / math.norm2(r);
r = exp(1i*r*p.model.probe_structured_illum_power);
w = imgaussfilt(w,upsample/2).*r;
end
% Propagation
probe_hr = prop_free_ff(w .* exp(-1i * pi * r2 * dx^2 / (lambda * zp_f)), lambda, zp_f + defocus, dx);
% Cropping back to field of view
probe = crop_pad(probe_hr, asize);
% prevent unreal sharp edges from the cropped tails in probe
[probe] = utils.apply_3D_apodization(probe, 0);
probe = probe .* sqrt(1e5/sum(sum(abs(probe).^2)));
clear x y r2 w probe_hr
else
verbose(2, 'Using circular pinhole as initial model.');
[x1,x2] = ndgrid(-asize(1)/2:floor((asize(1)-1)/2),-asize(2)/2:floor((asize(2)-1)/2));
probe = ( (x1 * dx_spec(1)).^2 + (x2 * dx_spec(2)).^2 < (p.model.probe_diameter/2)^2);
probe = prop_free_nf(double(probe), lambda, p.model.probe_propagation_dist, dx_spec);
clear x1 x2
end
end
verbose(3, 'Successfully generated model probe.');
else
if ~isfield(p,'probe_file_propagation')
p.probe_file_propagation = [];
end
verbose(2, 'Using previous run as initial probe.');
% if string allows it, fill in the scan numbers
p.initial_probe_file = sprintf(replace(p.initial_probe_file,'\','\\'), p.scan_number(1));
for searchpath = {'', p.ptycho_matlab_path}
fpath = dir(fullfile(searchpath{1},p.initial_probe_file));
% check if only one unique file is found
if length(fpath) > 1
error('Too many paths corresponding to patterns %s were found', p.initial_probe_file)
elseif length(fpath) == 1
p.initial_probe_file = fullfile(fpath.folder, fpath.name);
break
end
end
if isempty(fpath)
error(['Did not find initial probe file: ' p.initial_probe_file])
end
fileokflag = 0;
while ~fileokflag
try
S = load_ptycho_recons(p.initial_probe_file, 'probe'); % avoid object loading when it is not needed
probe = S.probe;
probe = probe(:,:,:,1); %%added by YJ. Force to ignore the 4-th dimension (used for storing OPR modes)
%disp(size(probe))
S = load_ptycho_recons(p.initial_probe_file, 'p');
fileokflag = 1;
verbose(2, 'Loaded probe from: %s',p.initial_probe_file );
%% check if the loaded probe was binned or no
if isfield(S, 'p') && isfield(S.p, 'binning')
binning = S.p.binning;
elseif isfield(S, 'p') && isfield(S.p, 'detector') && isfield(S.p.detector, 'binning')
binning = S.p.detector.binning;
else
if verbose() > 0
binning = [];
while isempty(binning)
binning = str2num(input('Define binning factor 2^x for loaded initial probe (i.e. 0 for no binning):','s'));
end
% save provided binning option to the loaded probe file
S.p.detector.binning = binning;
save(p.initial_probe_file, '-append', '-struct', 'S')
else
% prevent stopping code if automatic reconstructions are running
verbose(0, 'Initial probe binning could not be determined, assuming no binning')
binning = 0;
end
end
% modify the loaded probe into a nonbinned version
probe = crop_pad(probe, [size(probe,1),size(probe,2)]*2^binning);
catch err
disp(['File corrupt: ' p.initial_probe_file])
disp(err.message)
disp('Retrying')
pause(1)
end
end
if ndims(probe)==3
sz_pr = size(probe);
probe = reshape(probe, [sz_pr(1) sz_pr(2) 1 sz_pr(3)]);
end
verbose(3, 'File %s loaded successfully.', p.initial_probe_file);
if ~all([size(probe,1) size(probe,2)] == asize)
verbose(2,'Loaded probe has the wrong size.');
if isfield(p,'crop_pad_init_probe') && p.crop_pad_init_probe %added by YJ
verbose(2,'Crop/pad probe in file %s, from (%d,%d) to (%d,%d).', p.initial_probe_file,size(probe,1),size(probe,2),asize(1),asize(2));
probe = crop_pad(probe, asize);
else
verbose(2,'Interpolating probe in file %s, from (%d,%d) to (%d,%d).', p.initial_probe_file,size(probe,1),size(probe,2),asize(1),asize(2));
probe = interpolateFT(probe,asize);
end
end
if ~isempty(p.probe_file_propagation) && any(p.probe_file_propagation ~= 0)
verbose(2,'Propagating probe from file by %f mm',p.probe_file_propagation*1e3);
probe= prop_free_nf(double(probe), lambda, p.probe_file_propagation, dx_spec);
end
end
if isfield(p,'normalize_init_probe') %%added by YJ
if p.normalize_init_probe
probe = probe .* sqrt(a2 ./ sum(sum(abs(probe).^2)));
end
else
probe = probe .* sqrt(a2 ./ sum(sum(abs(probe).^2)));
end
pout = p;
pout.probe_initial = probe;
ptycho/+core/ptycho_prepare_paths.m
+312
View File
@@ -0,0 +1,312 @@
%PTYCHO_PREPARE_PATHS Prepare paths and check defaults
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ p ] = ptycho_prepare_paths( p, varargin)
import utils.*
if nargin > 1
init = varargin{1};
else
init = false;
end
if init
verbose(p.verbose_level);
verbose(1, 'Preparing paths.')
% base paths
if isempty(p.base_path)
p.base_path = './';
verbose(3, 'Using default value for base_path: %s', p.base_path)
end
p.base_path = abspath(p.base_path);
% specfile
if isfield(p, 'specfile')
if isempty(p.specfile) && isfield(p, 'src_metadata') && strcmp(p.src_metadata, 'spec')
p.specfile = p.base_path;
verbose(3, 'Using default value for specfile: %s', p.specfile )
end
p.specfile = abspath(p.specfile);
end
% ptycho path
if isempty(p.ptycho_matlab_path)
% find template_ptycho and assume that the base path is there
p.ptycho_matlab_path = fileparts(which('template_ptycho.m'));
verbose(3, 'Using default value for ptycho_matlab_path: %s', p.ptycho_matlab_path )
end
% base package path
if isempty(p.cSAXS_matlab_path)
if exist(fullfile(p.base_path,'matlab'), 'dir')
p.cSAXS_matlab_path = fullfile(p.base_path,'matlab');
verbose(3, 'Using default value for cSAXS_matlab_path: %s', p.cSAXS_matlab_path )
end
end
% do some basic corrections of the paths
for path = {'base_path', 'ptycho_matlab_path', 'cSAXS_matlab_path', 'prepare_data_path', 'positions_file'}
if isfield(p, path{1}) && ~isempty(p.(path{1}))
p.(path{1}) = abspath(p.(path{1}));
end
end
%% add paths, but only if not included already
if exist(p.ptycho_matlab_path, 'dir') && ~exist(fullfile('+core', 'get_projections.m'),'file')
addpath(p.ptycho_matlab_path)
% check if ptycho_matlab_path is already included
elseif ~exist( fullfile('+core', 'get_projections.m'), 'file')
verbose(1,'Nonexistent ptycho_matlab_path: "%s"', p.ptycho_matlab_path)
end
if exist(fullfile(p.ptycho_matlab_path, 'utils'), 'dir') && ~exist(fullfile('aligned_FSC.m'),'file')
addpath(fullfile(p.ptycho_matlab_path, 'utils'))
% check if ptycho_matlab_path/utils is already included
elseif ~exist(fullfile('aligned_FSC.m'),'file')
verbose(1,'Nonexistent ptycho_matlab_path: "%s/utils"', p.ptycho_matlab_path)
end
if exist(p.cSAXS_matlab_path, 'dir') && ~exist(fullfile('+math', 'argmax.m'), 'file')
addpath(p.cSAXS_matlab_path);
% check if cSAXS_matlab_path is already included
elseif ~exist(fullfile('+math', 'argmax.m'), 'file')
verbose(1,'Nonexistent cSAXS_matlab_path: "%s"', p.cSAXS_matlab_path)
end
verbose(p.verbose_level);
else
% base path
if ~exist(p.base_path, 'dir')
error('base_path = %s : Base directory does not exist.', p.base_path);
end
verbose(2, 'base_path = %s', p.base_path);
% Save data path
for ii = 1:length(p.scan_number)
p. scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
if isempty(p.save_path) || iscell(p.save_path)&&isempty(p.save_path{1})
verbose(3, 'Using default save_path');
for ii = 1:length(p.scan_number)
p.save_path{ii} = fullfile(p.base_path, 'analysis',utils.compile_aps_dirname(p.scan_number(ii)),'');
if ~exist(p.save_path{ii}, 'dir')
mkdir(p.save_path{ii})
end
verbose(2, 'save_path = %s', p.save_path{ii});
end
else
% not enough save paths; replicate
if length(p.scan_number) > length(p.save_path)
verbose(1, 'Number of save paths does not match number of scans. I will use only the first save path.')
if contains(p.save_path{1}, '%')
% fill in the scan number if needed
container = p.save_path{1};
for ii=1:length(p.scan_number)
p.save_path{ii} = sprintf(container, p.scan_number(ii));
end
else
% if there is no variable to fill, append the scan number to
% the given path
container = p.save_path{1};
for ii=1:length(p.scan_number)
p.save_path{ii} = fullfile(container, p.scan_str{ii});
end
end
clear container
else
if contains(p.save_path{1}, '%')
% fill in the scan number if needed
for ii=1:length(p.scan_number)
p.save_path{ii} = sprintf(p.save_path{ii}, p.scan_number(ii));
end
else
% if there is no variable to fill, append the scan number to
% the given path
for ii=1:length(p.scan_number)
p.save_path{ii} = fullfile(p.save_path{ii}, p.scan_str{ii});
end
end
end
for ii = 1:length(p.scan_number)
p.save_path{ii} = rm_delimiter(p.save_path{ii});
if ~exist(p.save_path{ii}, 'dir')
mkdir(p.save_path{ii})
end
verbose(2, 'save_path = %s', p.save_path{ii});
end
end
% Prepare data path
if isempty(p.prepare_data_path)|| iscell(p.prepare_data_path)&&isempty(p.prepare_data_path{1})
verbose(3, 'Using default prepared data path');
p.prepare_data_path = p.save_path{1};
else
if iscell(p.prepare_data_path)
p.prepare_data_path = cell2str(p.prepare_data_path);
end
if contains(p.prepare_data_path, '%')
% fill in the scan number if needed
p.prepare_data_path = sprintf(p.prepare_data_path, p.scan_number(1));
else
% if there is no variable to fill, append the scan number to
% the given path
p.prepare_data_path = fullfile(p.prepare_data_path, p.scan_str{1});
end
end
p.prepare_data_path = replace(p.prepare_data_path,'\','\\');
p.prepare_data_path = add_delimiter(p.prepare_data_path);
if ~exist(p.prepare_data_path, 'dir')
mkdir(p.prepare_data_path)
end
verbose(2, 'prepare_data_path = %s', p.prepare_data_path);
% prepare data filename
if isempty(p.prepare_data_filename)
verbose(3, 'Using default prepared data filename');
if ~p.detector.binning
p.prepare_data_filename = [sprintf('S%05d_data_%03dx%03d',p.scan_number(1), p.asize(1), p.asize(2)) p.prepare.prep_data_suffix '.h5'];
else
p.prepare_data_filename = [sprintf('S%05d_data_%03dx%03d_b%i',p.scan_number(1), p.asize(1), p.asize(2),p.detector.binning) p.prepare.prep_data_suffix '.h5'];
end
verbose(2, 'prepare_data_filename = %s', p.prepare_data_filename);
end
% raw data path
if p.prepare.auto_prepare_data
if isempty(p.raw_data_path) || iscell(p.raw_data_path)&&isempty(p.raw_data_path{1})
for ii = 1:length(p.scan_number)
p.raw_data_path{ii} = p.base_path;
%disp(p.raw_data_path{ii})
end
else
if length(p.raw_data_path) ~= length(p.scan_number)
if ~iscell(p.raw_data_path)
p = str2cell(p, 'raw_data_path');
end
for ii = 2:length(p.scan_number)
p.raw_data_path{ii} = p.raw_data_path{1};
end
end
end
% do some basic replacement to get the real path
for ii = 1:length( p.raw_data_path)
p.raw_data_path{ii} = abspath(p.raw_data_path{ii});
p.raw_data_path{ii} = sprintf(replace(p.raw_data_path{ii},'\','\\') , p.scan_number(1));
end
else
prepare_data_full_filename = fullfile(p.prepare_data_path, p.prepare_data_filename);
if ~exist(prepare_data_full_filename, 'file'); error('prepared data file does not exist (%s).', prepare_data_full_filename); end
end
% do some basic corrections of the paths
for path = {'base_path', 'specfile', 'ptycho_matlab_path', 'cSAXS_matlab_path', 'prepare_data_path'}
p.(path{1}) = abspath(p.(path{1}));
end
end
end
% convert single cell entry to string
function p = cell2str(p, fn)
tmp = p.(fn){1};
p = rmfield(p, fn);
p.(fn) = tmp;
end
% convert string to cell
function p = str2cell(p, fn)
tmp = p.(fn);
p = rmfield(p, fn);
p.(fn){1} = tmp;
end
% make sure that the path does not end with /
function path = rm_delimiter(path)
if ~isempty(path) && any(strcmp(path(end), {'\', '/'}))
path = path(1:end-1);
end
end
% make sure that the path ends with /
function path = add_delimiter(path)
if ispc
delimiter = '\';
else
delimiter = '/';
end
if ~isempty(path) && ~strcmp(path(end), delimiter)
path = [path, delimiter];
end
end
ptycho/+core/ptycho_prepare_scans.m
+241
View File
@@ -0,0 +1,241 @@
%PTYCHO_PREPARE_SCANS Load data from disk and prepare the scan for the
%ptychographic reconstruction.
%
% ** p p structure
%
% returns:
% ++ p p structure
% ++ status status flag
%
%
% see also: core.initialize_ptycho
%
%
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [ p, status] = ptycho_prepare_scans( p )
import utils.verbose
import utils.get_option
status=1;
% legacy
if ~check_option(p.prepare, 'legacy')
p.prepare.legacy = false;
end
%% check for lock file
for ii = 1:length(p.scan_number)
% Write lock file
if p.queue.lockfile
lock_filename = [p.save_path{ii} '/' p.run_name '_lock'];
if exist(lock_filename, 'file')
verbose(1,sprintf('%s locked by other instance of this script. Continue with next scan.', p.scan_str{ii}));
out = [];
status = 0;
p.getReport.completed = true;
return
else
if ~exist(p.save_path{ii},'dir')
mkdir(p.save_path{ii});
end
verbose(2, 'Creating lock file: %s', lock_filename);
unix(['touch ' lock_filename]);
end
end
end
%% prepare data
% check prepared data file
if ~p.prepare.force_preparation_data
if ~exist(fullfile(p.prepare_data_path, p.prepare_data_filename), 'file')
verbose(1,'Missing prepared data %s, Forcing data preparation',fullfile(p.prepare_data_path, p.prepare_data_filename) )
p.prepare.force_preparation_data = true;
else
try
if core.check_prepared_data(p)
verbose(2, 'Prepared data does not match reconstruction parameters. Forcing data preparation.')
p.prepare.force_preparation_data = true;
end
catch ME
verbose(2, [ME.getReport '\n']);
verbose(2, 'Prepared data check failed. Forcing data preparation.')
p.prepare.force_preparation_data = true;
end
end
end
% check if we need to prepare the data
if p.prepare.auto_prepare_data && (~exist(fullfile(p.prepare_data_path, p.prepare_data_filename),'file')||p.prepare.force_preparation_data)
prepare_data_bool = true;
else
prepare_data_bool = false;
end
% prepare initial object and probes
p = core.prepare_initial_guess(p);
if prepare_data_bool && ~p.prepare.legacy
verbose(2, 'Loading raw data')
p = core.run_data_preparator(p);
elseif p.prepare.legacy
%% prepare.legacy mode to load prepared data from mat files
% Prepare data path
error('Loading from .mat files is not supported anymore.')
end
%% convert function handles to strings
for jj=1:length(p.detectors)
fn = fieldnames(p.detectors(jj).params);
for ii=1:length(fn)
if isa(p.detectors(jj).params.(fn{ii}) , 'function_handle')
p.detectors(jj).params.(fn{ii}) = func2str(p.detectors(jj).params.(fn{ii}));
end
end
funcs_nm = fieldnames(p.detectors(jj).funcs);
for ii=1:length(funcs_nm)
p.detectors(jj).funcs.(funcs_nm{ii}) = func2str(p.detectors(jj).funcs.(funcs_nm{ii}));
end
end
% cleanup detector storage
if isfield(p.detectors, 'detStorage')
p.detectors = rmfield(p.detectors, 'detStorage');
end
p.detectors = struct2cell(p.detectors);
%% output
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% save/load prepared data to/from disk %%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.prepare.store_prepared_data && (prepare_data_bool || p.prepare.legacy) && ~strcmpi(p.prepare.data_preparator, 'libDetXR')
core.prep_h5data(p);
end
% check if data needs to be loaded from disk
if (~isfield(p,'fmag') || isempty(p.fmag) )&& (p.plot.prepared_data || ~p.external_engine0 || check_option(p, 'force_prepare_h5_files'))
%% TO BE DELETED
% if (~p.external_engine0 && (~isfield(p,'fmag')) ) || p.external_engine0 && ...
% (isfield(p.engines{1}, 'force_prepare_h5_files') && p.engines{1}.force_prepare_h5_files) || ...
% (prepare_data_bool && strcmpi(p.prepare.data_preparator,'libDetXR') && p.plot.prepared_data && ~p.prepare.legacy)|| ...
% (~prepare_data_bool && p.plot.prepared_data) || (p.model_object && strcmpi(p.model_object_type, 'prep_data') && ~prepare_data_bool)
verbose(2, 'Loading already prepared data.');
[p.fmag, p.fmask, pos, max_power, scanindexrange, p.max_sum] = io.load_prepared_data(fullfile(p.prepare_data_path ,p.prepare_data_filename));
p.renorm = sqrt(1/max_power);
p.Nphot = sum((p.fmag(:)/p.renorm).^2.*p.fmask(:));
p.fmask_per_scan = (length(size(p.fmask)) == 3);
% shall the positions be overwritten?
if p.io.load_prep_pos
verbose(2,'Overwriting positions with values from prepared data.')
p.positions = pos;
p.scanindexrange = scanindexrange;
p.numpts = diff(reshape(scanindexrange', 2, []),1);
p.numpts(1) = p.numpts(1)+1; % scanindexrange starts at 1
for ii = 1:p.numscans
p.scanidxs{ii} = scanindexrange(ii,1):scanindexrange(ii,2);
end
end
end
% if not yet done,
% apply binning on all relevant
% parameters except data and mask that are already done
if (p.detector.binning || p.detector.upsampling) && any(p.asize ~= (p.asize_nobin .* 2^-p.detector.binning * 2^p.detector.upsampling))
if p.detector.binning
p = core.apply_binning(p, 2^p.detector.binning);
end
if p.detector.upsampling
% just reverse operation to the binning
p = core.apply_binning(p, 2^(-p.detector.upsampling) );
end
end
% initial guess for Fourier ptychography
if p.model_object && strcmpi(p.model.object_type, 'amplitude')
k = 2*pi/p.lambda;
objpix = p.lambda*p.z_lens./(p.asize.*p.dx_spec);
for ii=1:length(p.object)
[Xp,Yp] = utils.get_grid(p.object_size(ii,:), objpix(1));
pre_phase_factor = exp(-1i*k*((Xp./(p.object_size(ii,2)/(p.asize(2)))).^2+(Yp./(p.object_size(ii,1)/(p.asize(1)))).^2)/(2*p.z_lens));
init_guess = rot90(mean(p.fmag,3),2);
init_guess = init_guess./(max(max(init_guess)))./(p.asize(1).*p.asize(2)).*p.numpts;
p.object{ii} = fftshift(fft2(ifft2(ifftshift(utils.crop_pad(fftshift(fft2(init_guess.*exp(-1j.*(init_guess./(max(max(init_guess))).*2*pi-pi)))), p.object_size(ii,:)))).*fftshift(pre_phase_factor)));
end
end
end
ptycho/+core/ptycho_recons.m
+309
View File
@@ -0,0 +1,309 @@
% [OUT, STATUS] = PTYCHO_RECONS(P, PREPARE_ONLY = false)
% Runs the reconstruction using parameters in the structure p.
% Returns a structure OUT containing all necessary information.
%
% ** p p structure
%
% *optional*
% ** prepare_only stop after the data preparation; default: false
%
% returns:
% out updated p structure
%
% see also: template_ptycho
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [out,status] = ptycho_recons(p, prepare_only)
if ~exist('+math/argmax.m','file')
if exist(p.cSAXS_matlab_path, 'dir') %% avoid repeated loading by testing availibility of argmax.m file
addpath(p.cSAXS_matlab_path);
elseif ~isempty(p.cSAXS_matlab_path)
warning('Nonexistent cSAXS_matlab_path: "%s"', p.cSAXS_matlab_path)
end
end
import utils.*
if nargin < 2
prepare_only = false;
end
caller = dbstack;
p.caller = caller(end).name;
if ~isfield(p, 'queue')
p.queue = struct();
end
if ~isfield(p, 'io')
p.io = struct();
end
if ~isfield(p.io, 'SMS_sleep')
p.io.SMS_sleep = 1800;
end
if ~isfield(p.io, 'phone_number')
p.io.phone_number = [];
end
if ~isfield(p.io, 'send_failed_scans_SMS')
p.io.send_failed_scans_SMS = false;
end
if ~isfield(p.io, 'send_finished_recon_SMS')
p.io.send_finished_recon_SMS = false;
end
if ~isfield(p.io, 'send_crashed_recon_SMS')
p.io.send_crashed_recon_SMS = false;
end
utils.verbose(struct('prefix', {'init'}))
p. run_name = '';
p.getReport.completed = false;
p = core.ptycho_prepare_paths(p, true);
if isfield(p.queue,'path')&&~isempty(p.queue.path) && ~isfield(p.queue, 'name')
verbose(0,'Missing setting of p.queue.name, using default p.queue.name=''filelist'' ')
p.queue.name = 'filelist';
end
if ~isfield(p.queue, 'isreplica')
p.queue.isreplica = false;
end
if ~isfield(p.queue, 'remote_recons')
p.queue.remote_recons = false;
end
p.recon_success = false; %% added by YJ
% the existence of this file will cancel the calculation,
% CTRL-C replacement, checked each iteration
p.io.break_check_name = '/tmp/break_ptycho';
% Function for clean exit, currently used to exit matlab to clean memory
% from MEX upon Ctrl-c
% c = onCleanup(@()ptycho_exit);
% Check screen size
try
p.plot.scrsz = get(0,'ScreenSize');
catch
p.plot.scrsz = [1 1 2560 1024];
end
finishup = utils.onCleanup(@(x) ptycho_exit(x), p);
function ptycho_call()
import utils.*
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Check for file queue %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[p, status] = scans.get_queue(p, false);
if ~status
return
end
p. run_name = [p.prefix core.generate_scan_name(p) '_' num2str(p.asize(1)/2^p.detector.binning) 'x' num2str(p.asize(2)/2^p.detector.binning) '_b' num2str(p.detector.binning) '_' p.suffix]; % If empty: automatically generated
finishup.update(p);
if ~p.queue.remote_recons || p.queue.isreplica
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% initialize ptycho and prepare object and probe
[p, status] = core.initialize_ptycho(p); %p.positions are created here. unit: pxiel
if ~status || prepare_only
finishup.update(p);
out = {p};
return;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
verbose(struct('prefix', {'ptycho'}))
verbose(0, ['Reconstructing ' repmat('S%05d ', 1, numel(p.scan_number))], p.scan_number)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%% MAIN PTYCHOGRAPHY CODE %%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% get all engines
verbose(struct('prefix', {'ptycho'}))
for ieng=1:length(p.engines)
etic = tic();
p.current_engine_id = ieng;
% engine call
verbose(1, 'Calling engine %s', p.engines{ieng}.name)
verbose(struct('prefix', {p.engines{ieng}.name}))
[p, fdb] = core.run_engine(p,ieng);
if fdb.status.status ~= 0
error('Engine %s returned with exit status %d from %s [%d].\n', p.engines{ieng}.name, fdb.status.status, fdb.status.ln(1).name, fdb.status.ln(1).line);
end
fdb = [];
if p.ortho_probes && size(p.probes,4)>1
% orthogonalize probes
p.probes = core.probe_modes_ortho(p.probes);
end
% save reconstructed object, probe and feedback in the p structure of
% the currently used engine
p.engines{ieng}.object_final = p.object;
p.engines{ieng}.probes_final = p.probes;
p.engines{ieng}.error_metric_final = p.error_metric;
% store images of current engine
if p.save.store_images_intermediate
p = core.save.save_results(p, 0);
end
if ieng~=length(p.engines) && p.use_display
% intermediate results, not yet final plotting
core.analysis.plot_results(p);
end
etoc = toc(etic);
verbose(struct('prefix', {'ptycho'}))
verbose(1, 'Elapsed time for engine %s: %0.1f s', p.engines{ieng}.name, etoc)
end
verbose(struct('prefix', {'saving'}))
try
p = core.save.save_results(p, 1);
catch ME
if p.verbose_level > 3
keyboard
else
disp('####### Failed to save data. ##########');
rethrow(ME)
end
end
else
% remote reconstruction
% p.queue.isreplica = false;
p = core.export4remote(p);
finishup.update(p);
[p, status] = core.remote_status(p);
if ~status
core.remote_cleanup(p, status);
finishup.update(p);
out = {p};
return;
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if p.queue.remote_recons
status = core.remote_cleanup(p, true);
end
[p, status] = scans.get_queue(p, true);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
p.getReport.completed = true;
finishup.update(p);
end
if p.verbose_level > 3
fprintf('\n###############################################################\n')
fprintf('########################## DEBUG MODE #########################\n')
fprintf('###############################################################\n')
ptycho_call();
else
try
ptycho_call();
p.recon_success = true; %% added by YJ
catch ME
p.getReport.ME = ME;
p.getReport.crashed = true;
finishup.update(p);
status = false;
p.recon_success = false; %% added by YJ
end
end
out = p;
return
end
ptycho/+core/remote_cleanup.m
+123
View File
@@ -0,0 +1,123 @@
%REMOTE_CLEANUP
% remove temporary files on the remote machine and move the reconstruction
% to the save path on the primary machine
%
% ** p p structure
% ** completed boolean; true if reconstruction finished properly
%
% returns:
% ++ status status flag
%
% see also: core.ptycho_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function status = remote_cleanup(p, completed)
import utils.verbose
logfile = [p.run_name '.mat'];
status = 1;
if ~completed
try
if exist(fullfile(p.queue.remote_path, 'failed', logfile), 'file')
delete(fullfile(p.queue.remote_path, 'failed', logfile))
delete(fullfile(p.queue.remote_path, 'failed', [p.run_name '.log']))
end
catch
status = false;
verbose(1, 'Failed to remove logfile.')
end
else
% copy reconstruction to output directory
for ii = 1:length(p.scan_number)
p. scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
% Save data path
if isempty(p.save_path) || iscell(p.save_path)&&isempty(p.save_path{1})
verbose(3, 'Using default save_path');
for ii = 1:length(p.scan_number)
p.save_path{ii} = fullfile(p.base_path, 'analysis',p.scan_str{ii},'');
if ~exist(p.save_path{ii}, 'dir')
mkdir(p.save_path{ii})
end
verbose(2, 'save_path = %s', p.save_path{ii});
end
else
if length(p.scan_number) ~= length(p.save_path)
error('Number of specified save paths does not match the scan number.')
else
for ii = 1:length(p.scan_number)
if ~exist(p.save_path{ii}, 'dir')
mkdir(p.save_path{ii})
end
verbose(2, 'save_path = %s', p.save_path{ii});
end
end
end
for ii=1:numel(p.scan)
system(['mv ' fullfile(p.queue.tmp_dir_remote, 'analysis', p.scan_str{ii}, '*') ' ' p.save_path{ii}]);
end
verbose(2, 'Deleting remote logfile.')
delete(fullfile(p.queue.remote_path, 'done', logfile))
end
end
ptycho/+core/remote_status.m
+122
View File
@@ -0,0 +1,122 @@
%REMOTE_STATUS
% Check the current status of the remote reconstruction
%
% ** p p structure
%
% returns:
% ++ p updated p structure
% ++ status status flag
%
% see also: core.ptycho_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p, status] = remote_status(p)
import utils.verbose
status = 1;
logfile = [p.run_name '.mat'];
if exist(fullfile(p.queue.remote_path, logfile), 'file')
verbose(2, 'Waiting for remote replica to start the reconstruction.')
end
recon_started = false;
log_int_prev = 0;
while true
if ~recon_started && exist(fullfile(p.queue.remote_path, 'in_progress', logfile), 'file')
verbose(2, 'Reconstruction started...')
recon_started = true;
end
if exist(fullfile(p.queue.remote_path, 'done', logfile), 'file')
verbose(2, 'Reconstruction finished on remote replica.')
break;
elseif exist(fullfile(p.queue.remote_path, 'failed', logfile), 'file')
verbose(2, 'Reconstruction failed on remote replica.')
p.remote_failed = true;
status = 0;
break;
else
if exist(fullfile(p.queue.remote_path, 'failed', strrep(logfile, 'mat', 'log')), 'file')
fid = fopen(fullfile(p.queue.remote_path, 'failed', strrep(logfile, 'mat', 'log')));
log_line = fgetl(fid);
fclose(fid);
log_int = strtrim(strsplit(log_line, ':'));
log_int = log_int{end};
log_int = str2double(log_int);
if log_int>log_int_prev
verbose(2, 'Reconstruction failed on remote replica %u time(s).', log_int)
log_int_prev = log_int;
end
end
if exist(fullfile(p.queue.remote_path, strrep(logfile, 'mat', 'crash')), 'file')
delete(fullfile(p.queue.remote_path, strrep(logfile, 'mat', 'crash')));
status=0;
break;
end
pause(0.5)
end
end
end
ptycho/+core/run_data_preparator.m
+75
View File
@@ -0,0 +1,75 @@
%RUN_DATA_PREPARATOR
% prepare the function handle and call the data preparator
%
% ** p p structure
%
% returns:
% ++ p updated p structure
%
% see also: core.ptycho_prepare_scans
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function p = run_data_preparator(p)
import utils.verbose
%% run data preparator
data_prep_func = str2func(sprintf('detector.prep_data.%s.%s', p.prepare.data_preparator, p.prepare.data_preparator));
p = data_prep_func(p);
end
ptycho/+core/run_engine.m
+106
View File
@@ -0,0 +1,106 @@
%RUN_ENGINE
% calls engine 'eng'
%
% ** p p structure
% ** eng name of the current engine
%
% returns:
% ++ p update p structure
% ++ fdb feedback structure of the engine
%
% see also: core.ptycho_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function [p, fdb] = run_engine(p, ieng)
if isfield(p, 'error_metric')
p_eng = rmfield(p, 'error_metric');
else
p_eng = p;
end
%% load settings from engine structure to the param structure
[p_eng, items] = update_structure(p_eng, p_eng.engines{ieng});
%% call engine
core.engine_status(0);
engine_fnct = str2func(['engines.' p.engines{ieng}.name]);
[p_eng, fdb] = engine_fnct(p_eng);
%% adjust output, remove items in p.engines{ieng} from p
for item=1:size(items,1)
if isfield(p_eng, items{item})
p_eng = rmfield(p_eng, items{item});
end
end
p = utils.update_param(p, p_eng, 'force_update', 2);
end
function [struct_0, items] = update_structure(struct_0, struct_new)
% recursively update structures and values in the struct_0 by values
% in struct_new. Return updated struct_0 and list of the updated field
% in the ground level
items = fieldnames(struct_new);
for item=1:size(items,1)
if ~isstruct(struct_new.(items{item}))
struct_0.(items{item}) = struct_new.(items{item});
else
struct_0.(items{item}) = update_structure(struct_0.(items{item}), struct_new.(items{item}));
end
end
end
ptycho/+core/run_receiver.m
+83
View File
@@ -0,0 +1,83 @@
% RUN_RECEIVER
% modify p structure and run ptycho_recons.
%
% ** p p structure
%
% see also: setup_remote_recons
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function run_receiver(p)
if isempty(p.cSAXS_matlab_path)
error('p.cSAXS_matlab_path has to be specified for the remote reconstruction.')
end
if isempty(p.ptycho_matlab_path)
error('p.ptycho_matlab_path has to be specified for the remote reconstruction.')
end
if isempty(p.queue.remote_path)
error('p.queue.remote_path has to be specified for the remote reconstruction.')
end
p.queue.name = 'remote_queue';
p.queue.isreplica = true;
p.save_path = '';
p.queue.path = p.queue.remote_path;
core.ptycho_recons(p);
end
ptycho/+core/set_projections.m
+102
View File
@@ -0,0 +1,102 @@
%SET_PROJETIONS
%
% ** p p structure
% ** object full-size object
% ** obj_update container for object projections
% ** scan_id ID of the current scan
%
% return:
% ++ object updated object
% 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. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% 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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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
% the courts of Zürich, Switzerland.
function object = set_projections(p, object, obj_update, scan_id)
import utils.verbose
Npos = length(p.scanidxs{scan_id});
Nmodes = size(object,4);
if any(double(max(round(p.positions(p.scanidxs{scan_id},:))))+(p.asize) > size(object))
error('Object is too small for given positions')
end
if Nmodes == 1 && (isa(object, 'gpuArray') || isa(obj_update, 'gpuArray'))
% use function from GPU engine
cache.skip_ind = [];
positions = round(p.positions(p.scanidxs{scan_id},:));
cache.oROI_s{1}{1} = uint32(positions(:,1));
cache.oROI_s{1}{2} = uint32(positions(:,2));
object = engines.GPU.shared.set_views(object, obj_update, 1,1,int32(1:Npos),cache);
return
end
if Nmodes == 1
% faster MEX based function
positions = int32(p.positions(p.scanidxs{scan_id},:));
indices = int32(1:Npos);
object = utils.add_to_3D_projection(obj_update,object,positions,indices, true);
else
verbose(3, 'Using slow nonMEX version of set_projections')
id_0 = p.scanidxs{scan_id}(1)-1;
for jj = p.scanidxs{scan_id}
Indy = round(p.positions(jj,1)) + (1:p.asize(1));
Indx = round(p.positions(jj,2)) + (1:p.asize(2));
object(Indy,Indx,:) = object(Indy,Indx,:) + obj_update(:,:,min(jj-id_0,end),:);
end
end
end
ptycho/+core/update_object_size.m
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%UPDATE_OBJECT_SIZE updates size of the object so that all probe positions
%are withing this regions
% 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
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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,
% "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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% 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
% 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
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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:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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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
% the courts of Zürich, Switzerland.
function p = update_object_size(p)
import utils.verbose
% Compute object sizes
if length(unique(p.share_object_ID))==1 || strcmp(p.engines{1}.name,'ML_MS') % If the other scans have different object sizes as that of the first scan, else matlab-ML_MS crashes
%p.object_size = p.asize + max(round(p.positions),[],1) + p.positions_pad;
%modified by YJ s.t. object_size is consistent with the one
%calculated by GPU engine
p.object_size = p.asize + max(ceil(p.positions),[],1) + p.positions_pad;
verbose(2, 'Computed object size: %d x %d', p.object_size(1), p.object_size(2));
else
for ii = unique(p.share_object_ID)
p.object_size(ii,:) = p.asize + max(round(p.share_pos{ii}),[],1) + p.positions_pad;
verbose(2, 'Computed object size: %d x %d', p.object_size(ii,1), p.object_size(ii,2));
end
end
end