%GATHER_DISTRIBUTED_RECONSTRUCTIONS gather object reconstructions from the shared % memory, calculate difference from the initial reconstruction, and apply % update into the full tomographic volume. % % [volData,projData_new, fourier_error, update_norm] = ... % gather_distributed_reconstructions(volData, projData_model, ptycho_results, par) % % Inputs: % **volData - 3D array, linearized tomographic volume (ie tranmission == exp(sum(volData,1)) == prod(exp(volData)) ) % **projData_model - structure that contain complex projection, initial guess and other values related to the currently processed angle % **ptycho_results - output from ptychography, if empty, load it from the share memory array % **par - parameter structure for ptychotomo % % *returns* % ++volData - updated tomographic volume % ++projData_new - updated projection structure % ++fourier_error - vector, fourier error reported by ptychography % ++update_norm - scalar, difference between original and new tomo volume % 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. function [volData,projData_new, fourier_error, update_norm] = ... gather_distributed_reconstructions(volData, projData_model, ptycho_results, par) % prepare path p.prepare_data_path = sprintf(par.prepare_data_path, projData_model.scan_id); Npx_proj = size(projData_model.object); %% GATHER DATA FROM SHARED MEMORY if ~isempty(ptycho_results) && isstruct(ptycho_results) % avoid loading from disk if the cached data are available data.pout = ptycho_results; data.ferr = nan; else % load reoonstruction from disk, calculate optimal update for given angle, use it to calculate % optimal volume update for ii = 1:3 % try twice before failing try data = load([p. prepare_data_path, '/output_reconstruction.mat'], 'pout', 'ferr'); assert(isfield(data, 'ferr'), 'Results not loeaded correctly') break end pause(0.5) end if ~exist('data', 'var') error('Reconstruction %s not found', p. prepare_data_path) end for ii = 1:3 try % gather to the shared memory [ptycho_results, data_shm] = ptycho_results.attach(); break end pause(0.5) end if isempty(ptycho_results) keyboard end if ~exist('data_shm', 'var') error('Shared data not found') end data.pout.object{1} = data_shm;% force matlab to allocate new memory if numel(data_shm) ~= prod(Npx_proj) warning('Wrong object size returned') keyboard end if isreal(data_shm) || any(all(all(imag(data_shm)==0))) warning('Something went wrong, skipping projection update') % something wrong happened with the data in the shared memory, it % seems that the complex part was lost at least partly -> skip % this update and try next projection projData_new = projData_model; fourier_error= nan; update_norm= nan; return end clear ptycho_results end %% GET UPDATE FROM THE COMPLEX VALUED PROJECTION projData_new = projData_model; % make a new structure by a compy of the previous one % return sorted for ptychography projData_new.object = utils.Garray(squeeze(data.pout.object{1}(:,:,:,end:-1:1))); projData_new.probe = squeeze(data.pout.probes); projData_new.positions = data.pout.positions; % enforce full transmission in the nonmeasured regions missing = (projData_new.weight)==0; projData_new.object = projData_new.object .* ~missing + missing; % compare the model object_c and the updated object, use the difference to find new object_c projData_new.object_c = ptychotomo.prepare_projections(projData_new.object, Npx_proj, data.pout.asize, false, projData_model.object_c, projData_model.weight); projData_new.object = gather(projData_new.object); projData_new.weight = gather(projData_new.weight); projData_c_upd = gpuArray(projData_new.object_c - projData_model.object_c); % subtract potential offset in the global phase or aplitude offset_tot = 0; for ii = 1:3 offset = mean(mean(mean((projData_c_upd),3) .* projData_new.weight)) ./ mean(mean( projData_new.weight)); projData_c_upd = (projData_c_upd-offset) .* projData_new.weight; offset_tot = offset_tot + offset; end utils.verbose(1,'Offset removal gather %3.2e+%3.2ei', real(offset_tot), imag(offset_tot)); if 2*sum(math.norm2(projData_c_upd)) > 0.5 warning('Probably some convergence issue') keyboard end %%%%%%%%%%%%%%%%%% BACKPROJECT THE UPDATE TO THE VOLUME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% [volData, update_norm] = ptychotomo.update_volume(volData, projData_c_upd, par.update_step, projData_model, par); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if update_norm > 0.1 warning('Probably some convergence issue') keyboard end % store the filtered / regularized version for the next iteration guess projData_new.object_c = gather((projData_model.object_c + projData_c_upd)); % already a version with corrections projData_new.object = exp(projData_new.object_c); try fourier_error = data.ferr ; catch fourier_error = nan(2,1); end end