%PREPARE_DISTRIBUTED_DATA use current tomographic volume reconstruction volData and % previous projection reconstructions projData_rec to create a new initial % guess for the ML ptychography % % [projData_model, projData_rec, shm_mem] = prepare_distributed_data(p, volData, projData_rec, layer_distance, par, init_level, save_init_guess) % % Inputs: % **p - ptycho p structure % **volData - 3D array, linearized tomographic volume (ie tranmission == exp(sum(volData,1)) == prod(exp(volData)) ) % **projData_rec - structure that contains complex projection reconstructed in the previous iteration % **layer_distance - vector, distance between layers in meters % **par - parameter structure for ptychotomo % **init_level - flag: -1 == very first initialization, 0 = no initialization, 1 == force ptychography cache to update % % *returns* % ++projData_model - model projection structure % ++projData_rec - reconstructed projection structure % ++shm_mem - @shm class object that contain reference to the shared memory % 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 [projData_model, projData_rec, shm_mem] = prepare_distributed_data(p, volData, projData_rec, layer_distance, par, init_level, save_init_guess) try %% create initial guess for ptychography, clear object_c if number of layers in increased if isempty(projData_rec.object) projData_rec.object = exp(projData_rec.object_c); warning('Object was missing in projData_rec') end Npx_proj = size(projData_rec.object); Nlayers = length(layer_distance)+1; %%%%%%%%%%%%%%%%%%%%%%%%% GET PROJECTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% projData_model = get_forward_model(projData_rec, volData, Nlayers); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % move on GPU projData_rec.object_c = utils.Garray(projData_rec.object_c); expand_layers = size(projData_rec,3) < Nlayers; if expand_layers % cheaper version but less exact projData_rec.object_c = repmat(sum(projData_rec.object_c,3),1,1,Nlayers)/Nlayers; projData_rec.object = []; end % find reliability region of the current model Npx_proj_small = size(projData_model.object_c); win = utils.Garray(single(tukeywin(Npx_proj_small(2), 0.2))'.*single(tukeywin(Npx_proj_small(1), 0.2))); win = utils.crop_pad(win, Npx_proj(1:2)); win_shifted = utils.imshift_fast(win, projData_rec.position_offset(1), projData_rec.position_offset(2)); weight = utils.Garray(projData_rec.weight) ; if init_level == -1 % first initialization % estimate air region W_tmp = weight .* exp(-abs(sum(projData_model.object_c,3))) .* win_shifted; % remove offset between model and the reconstruction. projData_rec = remove_offset_initial(projData_model,projData_rec, W_tmp, Npx_proj_small); % run only the initialization return end %% merge phase and amplitude from tomo and measurements projData_model.object_c = win_shifted .*projData_model.object_c + (1-win_shifted).* projData_rec.object_c; if ~isempty(weight) projData_rec.object_c = projData_rec.object_c .* (weight~=0); projData_model.object_c = projData_model.object_c .* (weight~=0); end catch err err keyboard end %% get the complex transmission object = exp(projData_model.object_c); projData_model.object = object; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% STORE PREPARED PROJECTION FOR ASYNCHRONOUS SOLVERS %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% object = gather(object); if (init_level && par.force_initialization) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % precache the already initalized p structures to make the solver faster % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% p.ds = []; p.use_gpu = true; p.scan = []; p. scan_number = projData_rec.scan_id; p. rotation_angle = projData_rec.angle; p. proj_id = projData_rec.proj_id; %% prepare data p. prepare_data_path = sprintf(par.prepare_data_path, p.scan_number); p.object = []; p.probe = []; p.probes = []; p.positions_real = []; p.positions_orig = []; %% store data into some fast cache save('-v6', [p.prepare_data_path, '/prepared_data.mat'], 'p') end %% prepare the initial guess and store it p = struct(); p. proj_id = projData_rec.proj_id; p. scan_number = projData_rec.scan_id; p. rotation_angle = projData_rec.angle; p. prepare_data_path = sprintf(par.prepare_data_path, p.scan_number); p. force_preparation_data = false; p. remove_object_ambiguity= false; p. initial_probe_file = ''; p. prefix = ''; p. run_name = '' ; p. save_path = ''; % the input guess should be already optimally shifted p. position_offset = [0,0]; if utils.verbose() engine0.use_display = 1; p. use_display = 0; p. verbose_level = 3; engine0.verbose_level = 3; else p. use_display = 0; p. verbose_level = -1; engine0.verbose_level = -1; end % initialize the reconstruction, load prepared data engine0.delta_z = layer_distance; engine0.N_layer = size(object,3); if init_level == 1 engine0.initial_probe_rescaling = true; else engine0.initial_probe_rescaling = false; end %% load initial guesses p.probes = single(projData_rec.probe); p.positions = projData_rec.positions; % ptychography expects the layers in opposite order object = object(:,:,end:-1:1); p.object{1} = gather(reshape(object, [size(object,1), size(object,2),1,size(object,3)])); p.object_size = [size(object,1), size(object,2)]; ferr = nan; % fourier error is initialized as nan % prevent saving useless variables try; p = rmfield(p, 'simulation'); end try; p = rmfield(p, 'probe'); end if save_init_guess if ~exist(p.prepare_data_path, 'dir') mkdir(p. prepare_data_path); end % upload to the shared memory shm_mem = shm(false, p.proj_id); shm_mem.upload(p.object{1}); shm_mem.detach % delete from p-struct , it is already in the shared memory p.object = []; % save only the empty p-structure save([p. prepare_data_path, '/prepared_initial_guess.mat'] , 'p', 'ferr', 'engine0', '-v6') else shm_mem = []; end end function projData_model = get_forward_model(projData_rec, volData, Nlayers) Npx_vol = size(volData); Nblock = ceil(prod(Npx_vol)*8 / 1e9); % split into 2GB blocks Npx_proj = size(projData_rec.object); % block by block get the projection model projData_model = projData_rec; % create a copy of the input structure projData_model.object_c = gpuArray.zeros([Npx_vol([3,1]),Nlayers], 'single'); for ii = 1:Nblock ind = 1+(ii-1)*ceil(Npx_vol(3)/Nblock):min((ii)*ceil(Npx_vol(3)/Nblock), Npx_vol(3)); volData_block = volData(:,:,ind); volData_block = utils.Garray(volData_block); [object_r] = ptychotomo.fwd_proj(volData_block, projData_rec.angle, Nlayers, 'real'); [object_i] = ptychotomo.fwd_proj(volData_block, projData_rec.angle, Nlayers, 'imag'); projData_model.object_c(ind,:,:) = complex(object_r, object_i); end % pad the geprojData_modelnerated projection to the size of the measured % projections projData_model.object_c = utils.crop_pad(projData_model.object_c,Npx_proj(1:2),0); if any(any(round(projData_rec.position_offset) ~= projData_rec.position_offset)) error('Noninterger shift may result in mixing real and imaginary data') end % apply shifts found by prealignement projData_model.object_c = utils.imshift_fast(projData_model.object_c, ... projData_rec.position_offset(1), ... projData_rec.position_offset(2)); end function [projData_rec, offset] = remove_offset_initial(projData_model,projData_rec, weight, Npx_proj_small) import utils.* W = crop_pad(weight, Npx_proj_small) ; diff = crop_pad(sum(projData_model.object_c,3), Npx_proj_small) - crop_pad(sum(projData_rec.object_c,3), Npx_proj_small); % empirical estimation of weights to subtract the phase / amplitude offset offset = mean(mean(mean(W.*diff,2))) ./ mean(mean(W,2)); % subtract offset plane projData_rec.object_c = projData_rec.object_c + offset ; verbose(0,'Offset removal %3.2e+%3.2ei ', real(offset), imag(offset)); end