% ACCELERATE_GRADIENTS use the Nesterov's Accelerated Gradient method % % cache = accelerate_gradients(self, par, cache, iter) % % ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, .. % ** par structure containing parameters for the engines % ** cache structure with precalculated values to avoid unnecessary overhead % ** iter number of the current iteration % % returns: % ** self updated structure containing inputs % ** cache structure with precalculated values - stores the previous accelerated gradients updates % % 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 mixed coherent modes: % P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806), % for LSQ-ML method % M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018 % for OPRP method % 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." Optics express 24.8 (2016): 8360-8369 % 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). % 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. 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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 [self,cache] = accelerate_gradients(self, par, cache, iter) %% accelerated gradients extension, tries to look ahead in direction of the last update if iter == par.accelerated_gradients_start cache.object_prev = {self.object, self.object}; cache.probe_prev = {self.probe, self.probe}; for ii = 1:length(cache.illum_sum_0) cache.update_weights{ii} = cache.illum_sum_0{ii}.^2 ./ (cache.illum_sum_0{ii}.^2 + 0.1*cache.MAX_ILLUM(ii)^2); end elseif iter > par.accelerated_gradients_start object_start = max(par.object_change_start, par.accelerated_gradients_start); probe_start = max(par.probe_change_start, par.accelerated_gradients_start); cache.object_prev{1} = cache.object_prev{2}; cache.object_prev{2} = self.object; cache.probe_prev{1} = cache.probe_prev{2}; cache.probe_prev{2} = self.probe; % accelerate the object reconstructions if iter > par.object_change_start beta = (iter-object_start+1)/(iter-object_start+3); for ii = 1:size(self.object,1) for layer = 1:size(self.object,2) if ii == 1 && utils.verbose() > 3 plotting.smart_figure(555) update = cache.update_weights{ii}.* (self.object{ii,layer} - cache.object_prev{1}{ii,layer}); plotting.imagesc3D(update) title('Acceleration step in the Nesterov method') axis xy off utils.verbose(0, 'Norm of accelerated gradient = %g', math.norm2(update) ) drawnow end self.object{ii,layer} = self.object{ii,layer} + ... beta*cache.update_weights{ii}.*(self.object{ii,layer} - cache.object_prev{1}{ii,layer}); end end end % accelerate only the first OPR mode of the probe if iter > par.probe_change_start beta = (iter-probe_start+1)/(iter-probe_start+3); for ii = 1:numel(self.probe) self.probe{ii}(:,:,:,1) = self.probe{ii}(:,:,:,1) + ... beta.*(self.probe{ii}(:,:,:,1) - cache.probe_prev{1}{ii}(:,:,:,1)); end end end end