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