% Another script for STXM evaluation of round roi scans % % Does not use Gaussians centered on grid points which leads to inaccuarate % values at the center positions (due to adding up all the Gaussians) % but rather uses the Matlab's "griddata" function. clear all import utils.compile_x12sa_filename import utils.verbose %% scan parameters scannumber = 2370; scans = ['S' num2str(scannumber,'%05d')]; asize = [128 128]; %pathdir = sprintf('/afs/psi.ch/project/cxs/CDI/cSAXS_sxdm_2009_05_tomo/analysis/%s/', scans); pathdir = sprintf('../../analysis/%s/', scans); datafile = [pathdir, sprintf('%s_data_%03dx%03d.mat', scans, asize(1), asize(2))]; scan_type = 'round_roi'; dr = 1.5e-6; lx = 30e-6; ly = 36e-6; nth = 5; dx_spec = [65.4e-9 65.4e-9]; export_figures_to_svg = 0; %% create positions rmax = sqrt((lx/2)^2 + (ly/2)^2); nr = 1 + floor(rmax/dr); positions = []; for ir=1:nr+1 rr = ir*dr; dth = 2*pi / (nth*ir); for ith=0:nth*ir-1 th = ith*dth; x1 = rr * cos(th); x2 = rr * sin(th); if( abs(x1) > lx/2 || (abs(x2) >= ly/2) ) continue end positions(end+1,:) = [x1/dx_spec(2) x2/dx_spec(2)]; %#ok end end numpts = size(positions,1); %% load data if ~exist(datafile,'file') while ~exist(compile_x12sa_filename(scannumber,numpts-1),'file'); disp(['Waiting for scan ' scans ' to finish.']) pause(10) end verbose(1); core.prepare_data_2d(asize, numpts, scannumber, [100,268],'','','',147576); end load(datafile) %% intialize variables for STXM analysis and upsampling upsample =4; ndx = ceil(upsample*(2+lx/dr)); ndy = ceil(upsample*(2+ly/dr)); [xx,yy] = meshgrid((1:ndx) - ndx/2, (1:ndy) - ndy/2); pos = positions; pos(:,1) = upsample*pos(:,1)*dx_spec(1)/dr; pos(:,2) = upsample*pos(:,2)*dx_spec(2)/dr; trans = zeros(ndy,ndx); dpcx = zeros(ndy,ndx); dpcy = zeros(ndy,ndx); % put the STXM results into linear vectors first lin_trans = zeros(numpts,1); lin_dpcx = zeros(numpts,1); lin_dpcy = zeros(numpts,1); %% STXM analysis loop for ii=1:numpts s1 = sum(data(:,:,ii),1); s2 = sum(data(:,:,ii),2); Atrans = sum(s1); Adpcx = sum(((1:asize(1))-asize(1)/2).*s1)/Atrans; Adpcy = sum(((1:asize(1))-asize(1)/2)'.*s2)/Atrans; lin_trans(ii) = Atrans; lin_dpcx(ii) = Adpcx; lin_dpcy(ii) = Adpcy; end %% upsample trans=griddata(pos(:,1),pos(:,2),lin_trans,xx,yy,'linear'); dpcx_nearest=griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'nearest'); dpcx_linear =griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'linear'); %dpcy=griddata(pos(:,1),pos(:,2),lin_dpcy,xx,yy,'linear'); %I0 = mean(trans(10:20,3)); [n,x] = hist(trans(:),asize(1)); I0 = x(find(diff(n)>0,1,'last')+1); % Compute integrated linear attenuation coefficient mu = -log(trans./ I0 ); %% plot %figure(1) % scatter(positions(:,1),positions(:,2),300,lin_dpcx,'filled'); % colormap bone(256) %colorbar % title([scans ': scattered photons per diffraction pattern']) % axis ij image off % figure(2); %imagesc(dpcx_nearest); %axis image ij tight off %colormap bone(256); colorbar %title([scans ': scattered photons (upsampled by a factor of ' num2str(upsample) ', nearest neighbour interpolation)']) %scalebar(dr,'fontsize',20, 'linewidth',10) figure(1); imagesc(dpcx_linear); axis image ij tight off colormap bone(256); colorbar title([scans ': DPC x']) scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10) figure(4) imagesc(trans) axis image ij tight off colormap bone(256); colorbar scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10) title([scans ': transmission']) figure(5) imagesc(mu) axis image ij tight off colormap bone(256); colorbar scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10) % % roi_half = floor(upsample*nr/sqrt(2)); % roi_mask = zeros(size(trans)); % roi_mask(size(trans,1)/2-roi_half+1:size(trans,1)/2+roi_half,... % size(trans,2)/2-roi_half+1:size(trans,2)/2+roi_half) =1; % roi_mask(size(trans,1)/2-upsample+1:size(trans,1)/2+upsample,... % size(trans,2)/2-upsample+1:size(trans,2)/2+upsample) =0; % % roi_ind = find(roi_mask == 1); %% export figures if export_figures_to_svg saveas(1,fullfile(pathdir,'/S00327_dpcx_scatterplot.png')) %plot2svg(fullfile(pathdir,'/S00327_dpcx_scatterplot.svg'),1) plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_nearest.svg'),2) plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_linear.svg'),3) plot2svg(fullfile(pathdir,'/S00327_trans_interpol_linear.svg'),4) plot2svg(fullfile(pathdir,'/S00327_abs_mu_interpol_linear.svg'),5) disp(['Image files saved.']); 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.