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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