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https://github.com/c-sooyoung/fold_slice.git
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220 lines
10 KiB
Matlab
220 lines
10 KiB
Matlab
% Another script for STXM evaluation of round roi scans
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%
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% Does not use Gaussians centered on grid points which leads to inaccuarate
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% values at the center positions (due to adding up all the Gaussians)
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% but rather uses the Matlab's "griddata" function.
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clear all
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import utils.compile_x12sa_filename
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import utils.verbose
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%% scan parameters
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scannumber = 2370;
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scans = ['S' num2str(scannumber,'%05d')];
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asize = [128 128];
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%pathdir = sprintf('/afs/psi.ch/project/cxs/CDI/cSAXS_sxdm_2009_05_tomo/analysis/%s/', scans);
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pathdir = sprintf('../../analysis/%s/', scans);
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datafile = [pathdir, sprintf('%s_data_%03dx%03d.mat', scans, asize(1), asize(2))];
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scan_type = 'round_roi';
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dr = 1.5e-6;
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lx = 30e-6;
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ly = 36e-6;
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nth = 5;
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dx_spec = [65.4e-9 65.4e-9];
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export_figures_to_svg = 0;
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%% create positions
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rmax = sqrt((lx/2)^2 + (ly/2)^2);
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nr = 1 + floor(rmax/dr);
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positions = [];
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for ir=1:nr+1
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rr = ir*dr;
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dth = 2*pi / (nth*ir);
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for ith=0:nth*ir-1
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th = ith*dth;
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x1 = rr * cos(th);
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x2 = rr * sin(th);
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if( abs(x1) > lx/2 || (abs(x2) >= ly/2) )
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continue
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end
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positions(end+1,:) = [x1/dx_spec(2) x2/dx_spec(2)]; %#ok<AGROW>
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end
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end
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numpts = size(positions,1);
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%% load data
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if ~exist(datafile,'file')
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while ~exist(compile_x12sa_filename(scannumber,numpts-1),'file');
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disp(['Waiting for scan ' scans ' to finish.'])
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pause(10)
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end
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verbose(1); core.prepare_data_2d(asize, numpts, scannumber, [100,268],'','','',147576);
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end
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load(datafile)
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%% intialize variables for STXM analysis and upsampling
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upsample =4;
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ndx = ceil(upsample*(2+lx/dr));
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ndy = ceil(upsample*(2+ly/dr));
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[xx,yy] = meshgrid((1:ndx) - ndx/2, (1:ndy) - ndy/2);
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pos = positions;
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pos(:,1) = upsample*pos(:,1)*dx_spec(1)/dr;
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pos(:,2) = upsample*pos(:,2)*dx_spec(2)/dr;
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trans = zeros(ndy,ndx);
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dpcx = zeros(ndy,ndx);
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dpcy = zeros(ndy,ndx);
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% put the STXM results into linear vectors first
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lin_trans = zeros(numpts,1);
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lin_dpcx = zeros(numpts,1);
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lin_dpcy = zeros(numpts,1);
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%% STXM analysis loop
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for ii=1:numpts
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s1 = sum(data(:,:,ii),1);
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s2 = sum(data(:,:,ii),2);
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Atrans = sum(s1);
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Adpcx = sum(((1:asize(1))-asize(1)/2).*s1)/Atrans;
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Adpcy = sum(((1:asize(1))-asize(1)/2)'.*s2)/Atrans;
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lin_trans(ii) = Atrans;
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lin_dpcx(ii) = Adpcx;
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lin_dpcy(ii) = Adpcy;
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end
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%% upsample
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trans=griddata(pos(:,1),pos(:,2),lin_trans,xx,yy,'linear');
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dpcx_nearest=griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'nearest');
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dpcx_linear =griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'linear');
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%dpcy=griddata(pos(:,1),pos(:,2),lin_dpcy,xx,yy,'linear');
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%I0 = mean(trans(10:20,3));
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[n,x] = hist(trans(:),asize(1));
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I0 = x(find(diff(n)>0,1,'last')+1);
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% Compute integrated linear attenuation coefficient
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mu = -log(trans./ I0 );
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%% plot
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%figure(1)
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% scatter(positions(:,1),positions(:,2),300,lin_dpcx,'filled');
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% colormap bone(256)
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%colorbar
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% title([scans ': scattered photons per diffraction pattern'])
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% axis ij image off
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% figure(2);
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%imagesc(dpcx_nearest);
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%axis image ij tight off
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%colormap bone(256); colorbar
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%title([scans ': scattered photons (upsampled by a factor of ' num2str(upsample) ', nearest neighbour interpolation)'])
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%scalebar(dr,'fontsize',20, 'linewidth',10)
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figure(1);
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imagesc(dpcx_linear);
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axis image ij tight off
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colormap bone(256); colorbar
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title([scans ': DPC x'])
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scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
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figure(4)
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imagesc(trans)
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axis image ij tight off
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colormap bone(256); colorbar
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scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
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title([scans ': transmission'])
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figure(5)
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imagesc(mu)
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axis image ij tight off
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colormap bone(256); colorbar
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scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
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%
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% roi_half = floor(upsample*nr/sqrt(2));
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% roi_mask = zeros(size(trans));
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% roi_mask(size(trans,1)/2-roi_half+1:size(trans,1)/2+roi_half,...
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% size(trans,2)/2-roi_half+1:size(trans,2)/2+roi_half) =1;
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% roi_mask(size(trans,1)/2-upsample+1:size(trans,1)/2+upsample,...
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% size(trans,2)/2-upsample+1:size(trans,2)/2+upsample) =0;
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%
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% roi_ind = find(roi_mask == 1);
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%% export figures
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if export_figures_to_svg
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saveas(1,fullfile(pathdir,'/S00327_dpcx_scatterplot.png'))
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%plot2svg(fullfile(pathdir,'/S00327_dpcx_scatterplot.svg'),1)
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plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_nearest.svg'),2)
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plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_linear.svg'),3)
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plot2svg(fullfile(pathdir,'/S00327_trans_interpol_linear.svg'),4)
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plot2svg(fullfile(pathdir,'/S00327_abs_mu_interpol_linear.svg'),5)
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disp(['Image files saved.']);
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end
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
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% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
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% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
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% another computing language:
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% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
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% (doi: 10.1364/OE.24.029089).
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% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
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% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
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% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
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% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
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% the courts of Zürich, Switzerland. |