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197 lines
10 KiB
Matlab
197 lines
10 KiB
Matlab
%PTYCHO_SOLVER_DISTRIBUTED solve asynchronously ptychography, from
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%"prepare_data_path" load parameters of the current reconstruction, data
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%and from shared memory load the corresponding initial guess of the object
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% Finally, run ptychography and return results
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%
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% [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path)
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%
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% Inputs:
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% **GPU_id - id of the used GPU
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% **prepare_data_path - path to the stored initialization files
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%
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% *returns*
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% ++pout - output from ptychography
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% ++ferr - fourier error reported by ptychography
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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 PtychoShelves
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% 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 PtychoShelves 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
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% 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
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% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
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% and 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 LSQ-ML:
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% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
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% (doi: 10.1364/OE.26.003108),
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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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% and/or for OPRP:
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% 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.
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% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
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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.
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function [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path)
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% fast loading to save time
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%p = core.ptycho_recons(p, true);
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% IT IS 2X FASTER TO LOAD IT FROM CACHE
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load([prepare_data_path, '/prepared_data.mat'], 'p')
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p.use_display = 0;
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p.plot.interval = inf;
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[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)) ));
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%% load initial guess + specific settings for this angles
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init = load([prepare_data_path, '/prepared_initial_guess.mat']);
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% get from the shared memory
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shm_mem = shm(true, init.p.proj_id);
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[shm_mem, shm_data] = shm_mem.attach();
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init.p.object{1} = shm_data+eps;% force matlab to allocate new memory
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% apply setttings from initial guess
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for item = fieldnames(init.p)'
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if ~isempty(init.p.(item{1}))
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p.(item{1}) = init.p.(item{1});
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end
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end
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for item = fieldnames(init.engine0)'
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p.engines{1}.(item{1}) = init.engine0.(item{1});
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end
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p.gpu_id = GPU_id;
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if isfield(p, 'gpu_id')
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gpu = gpuDevice();
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if p.gpu_id ~= gpu.Index
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gpuDevice(double(p.gpu_id));
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end
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end
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if strcmpi(p.engines{1}.name , 'GPU')
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p.object{1} = gpuArray(p.object{1});
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p.probes = gpuArray(p.probes);
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end
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%% run all engines
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utils.verbose(struct('prefix', {'ptycho'}))
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for ieng=1:length(p.engines)
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p.ieng = ieng;
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% engine call
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utils.verbose(1, 'Calling engine %s', p.engines{ieng}.name)
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utils.verbose(struct('prefix', {p.engines{ieng}.name}))
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%% run engine
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try
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[pout, fdb] = core.run_engine(p,ieng);
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catch err
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disp(err)
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keyboard
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end
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utils.verbose(struct('prefix', {'ptycho'}))
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end
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try
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ferr = pout.error_metric.value([1,end]);
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catch
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ferr = nan(2,1);
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end
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% delete input data, save time in storing / loading
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pout.fmag = [];
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pout.fmask = [];
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pout.probe = [];
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pout.simulation = [];
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status = true;
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for ii = 1:5
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try
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shm_mem.free;
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shm_mem.upload(pout.object{1})
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status = false;
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break
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catch err
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warning(err.message)
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end
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pause(0.1)
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end
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if status
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warning('Uploading results to shared mem failed')
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keyboard
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end
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% upload to shared memory
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% utils.add_to_3D_projection(shm_mem.data_handle{1}, real(pout.object{1}), [0,0], 1, false);
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% utils.add_to_3D_projection(shm_mem.data_handle{2}, imag(pout.object{1}), [0,0], 1, false);
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% delete the larger arrays from the p-structure
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% pout.probes = [];
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pout.object = [];
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% rewrite the structure with the initial guess and store there results
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save([pout. prepare_data_path, '/output_reconstruction.mat'] ,'ferr', 'pout', '-v6')
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utils.verbose(-1,'Save data %s', [pout. prepare_data_path, '/output_reconstruction.mat'])
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end
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