%PTYCHO_SOLVER_DISTRIBUTED solve asynchronously ptychography, from %"prepare_data_path" load parameters of the current reconstruction, data %and from shared memory load the corresponding initial guess of the object % Finally, run ptychography and return results % % [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path) % % Inputs: % **GPU_id - id of the used GPU % **prepare_data_path - path to the stored initialization files % % *returns* % ++pout - output from ptychography % ++ferr - fourier error reported by ptychography % 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 [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path) % fast loading to save time %p = core.ptycho_recons(p, true); % IT IS 2X FASTER TO LOAD IT FROM CACHE load([prepare_data_path, '/prepared_data.mat'], 'p') p.use_display = 0; p.plot.interval = inf; [p.fmag, p.fmask, p.positions] = io.load_prepared_data(fullfile( prepare_data_path, sprintf('S%05i_data_%ix%i.h5', p.scan_number, p.asize(1), p.asize(2)) )); %% load initial guess + specific settings for this angles init = load([prepare_data_path, '/prepared_initial_guess.mat']); % get from the shared memory shm_mem = shm(true, init.p.proj_id); [shm_mem, shm_data] = shm_mem.attach(); init.p.object{1} = shm_data+eps;% force matlab to allocate new memory % apply setttings from initial guess for item = fieldnames(init.p)' if ~isempty(init.p.(item{1})) p.(item{1}) = init.p.(item{1}); end end for item = fieldnames(init.engine0)' p.engines{1}.(item{1}) = init.engine0.(item{1}); end p.gpu_id = GPU_id; if isfield(p, 'gpu_id') gpu = gpuDevice(); if p.gpu_id ~= gpu.Index gpuDevice(double(p.gpu_id)); end end if strcmpi(p.engines{1}.name , 'GPU') p.object{1} = gpuArray(p.object{1}); p.probes = gpuArray(p.probes); end %% run all engines utils.verbose(struct('prefix', {'ptycho'})) for ieng=1:length(p.engines) p.ieng = ieng; % engine call utils.verbose(1, 'Calling engine %s', p.engines{ieng}.name) utils.verbose(struct('prefix', {p.engines{ieng}.name})) %% run engine try [pout, fdb] = core.run_engine(p,ieng); catch err disp(err) keyboard end utils.verbose(struct('prefix', {'ptycho'})) end try ferr = pout.error_metric.value([1,end]); catch ferr = nan(2,1); end % delete input data, save time in storing / loading pout.fmag = []; pout.fmask = []; pout.probe = []; pout.simulation = []; status = true; for ii = 1:5 try shm_mem.free; shm_mem.upload(pout.object{1}) status = false; break catch err warning(err.message) end pause(0.1) end if status warning('Uploading results to shared mem failed') keyboard end % upload to shared memory % utils.add_to_3D_projection(shm_mem.data_handle{1}, real(pout.object{1}), [0,0], 1, false); % utils.add_to_3D_projection(shm_mem.data_handle{2}, imag(pout.object{1}), [0,0], 1, false); % delete the larger arrays from the p-structure % pout.probes = []; pout.object = []; % rewrite the structure with the initial guess and store there results save([pout. prepare_data_path, '/output_reconstruction.mat'] ,'ferr', 'pout', '-v6') utils.verbose(-1,'Save data %s', [pout. prepare_data_path, '/output_reconstruction.mat']) end