mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 22:59:07 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,196 @@
|
||||
%PTYCHO_SOLVER_DISTRIBUTED solve asynchronously ptychography, from
|
||||
%"prepare_data_path" load parameters of the current reconstruction, data
|
||||
%and from shared memory load the corresponding initial guess of the object
|
||||
% Finally, run ptychography and return results
|
||||
%
|
||||
% [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path)
|
||||
%
|
||||
% Inputs:
|
||||
% **GPU_id - id of the used GPU
|
||||
% **prepare_data_path - path to the stored initialization files
|
||||
%
|
||||
% *returns*
|
||||
% ++pout - output from ptychography
|
||||
% ++ferr - fourier error reported by ptychography
|
||||
|
||||
% 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 [pout, ferr] = ptycho_solver_distributed(GPU_id, prepare_data_path)
|
||||
|
||||
% fast loading to save time
|
||||
%p = core.ptycho_recons(p, true);
|
||||
% IT IS 2X FASTER TO LOAD IT FROM CACHE
|
||||
load([prepare_data_path, '/prepared_data.mat'], 'p')
|
||||
p.use_display = 0;
|
||||
p.plot.interval = inf;
|
||||
|
||||
[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)) ));
|
||||
|
||||
|
||||
%% load initial guess + specific settings for this angles
|
||||
init = load([prepare_data_path, '/prepared_initial_guess.mat']);
|
||||
% get from the shared memory
|
||||
shm_mem = shm(true, init.p.proj_id);
|
||||
[shm_mem, shm_data] = shm_mem.attach();
|
||||
init.p.object{1} = shm_data+eps;% force matlab to allocate new memory
|
||||
|
||||
|
||||
% apply setttings from initial guess
|
||||
for item = fieldnames(init.p)'
|
||||
if ~isempty(init.p.(item{1}))
|
||||
p.(item{1}) = init.p.(item{1});
|
||||
end
|
||||
end
|
||||
for item = fieldnames(init.engine0)'
|
||||
p.engines{1}.(item{1}) = init.engine0.(item{1});
|
||||
end
|
||||
|
||||
|
||||
p.gpu_id = GPU_id;
|
||||
|
||||
|
||||
|
||||
if isfield(p, 'gpu_id')
|
||||
gpu = gpuDevice();
|
||||
if p.gpu_id ~= gpu.Index
|
||||
gpuDevice(double(p.gpu_id));
|
||||
end
|
||||
end
|
||||
|
||||
if strcmpi(p.engines{1}.name , 'GPU')
|
||||
p.object{1} = gpuArray(p.object{1});
|
||||
p.probes = gpuArray(p.probes);
|
||||
end
|
||||
|
||||
|
||||
%% run all engines
|
||||
utils.verbose(struct('prefix', {'ptycho'}))
|
||||
for ieng=1:length(p.engines)
|
||||
p.ieng = ieng;
|
||||
|
||||
% engine call
|
||||
utils.verbose(1, 'Calling engine %s', p.engines{ieng}.name)
|
||||
utils.verbose(struct('prefix', {p.engines{ieng}.name}))
|
||||
|
||||
%% run engine
|
||||
|
||||
try
|
||||
[pout, fdb] = core.run_engine(p,ieng);
|
||||
catch err
|
||||
disp(err)
|
||||
keyboard
|
||||
end
|
||||
|
||||
utils.verbose(struct('prefix', {'ptycho'}))
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
try
|
||||
ferr = pout.error_metric.value([1,end]);
|
||||
catch
|
||||
ferr = nan(2,1);
|
||||
end
|
||||
|
||||
% delete input data, save time in storing / loading
|
||||
pout.fmag = [];
|
||||
pout.fmask = [];
|
||||
pout.probe = [];
|
||||
pout.simulation = [];
|
||||
|
||||
status = true;
|
||||
for ii = 1:5
|
||||
try
|
||||
shm_mem.free;
|
||||
shm_mem.upload(pout.object{1})
|
||||
status = false;
|
||||
break
|
||||
catch err
|
||||
warning(err.message)
|
||||
end
|
||||
pause(0.1)
|
||||
end
|
||||
|
||||
if status
|
||||
warning('Uploading results to shared mem failed')
|
||||
keyboard
|
||||
end
|
||||
|
||||
% upload to shared memory
|
||||
% utils.add_to_3D_projection(shm_mem.data_handle{1}, real(pout.object{1}), [0,0], 1, false);
|
||||
% utils.add_to_3D_projection(shm_mem.data_handle{2}, imag(pout.object{1}), [0,0], 1, false);
|
||||
|
||||
|
||||
|
||||
% delete the larger arrays from the p-structure
|
||||
% pout.probes = [];
|
||||
pout.object = [];
|
||||
|
||||
% rewrite the structure with the initial guess and store there results
|
||||
save([pout. prepare_data_path, '/output_reconstruction.mat'] ,'ferr', 'pout', '-v6')
|
||||
utils.verbose(-1,'Save data %s', [pout. prepare_data_path, '/output_reconstruction.mat'])
|
||||
|
||||
end
|
||||
Reference in New Issue
Block a user