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%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