mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 21:49:08 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,163 @@
|
||||
%% TEST TEMPLATE FOR FUNTIONALITY CHECK IN GPU ENGINES
|
||||
% 1) call standard template to get fresh settings defaults
|
||||
% 2) generate artificial data that should serve as a standart test "sample"
|
||||
% 3) call GPU engine with different basic functionalities and test if all still works
|
||||
% !! THESE TEST ARE ONLY USEFUL TO FIND CRASHES IN THE CODE, QUALITY OF THE RECONSTRUCTION IS NOT EVALUATED !!
|
||||
|
||||
%% set shared parameters for all test scripts
|
||||
run(fullfile( fileparts(mfilename('fullpath')), 'init_test.m'))
|
||||
|
||||
plot_results = true;
|
||||
|
||||
%% general settings
|
||||
p. artificial_data_file = 'tests/test_data.m'; % artificial data parameters
|
||||
p. asize = [256 256]; % size of the reconstruction probe
|
||||
p. prop_regime = 'nearfield';
|
||||
p. focus_to_sample_distance = 5e-3; % sample to focus distance, very important parameter to be set for nearfield ptychography
|
||||
p. simulation.prop_from_focus = 5e-3;
|
||||
p. scan.lx = 10e-6; % round_roi scan: width of the roi
|
||||
p. scan.ly = 10e-6;
|
||||
|
||||
% first bin the data and then upsample -> use ptychrography to compemsate for the information loss
|
||||
p. binning = 1;
|
||||
p.data_upsampling = 1;
|
||||
|
||||
%% ENGINES
|
||||
% External C++ code
|
||||
|
||||
% --------- GPU engines -------------
|
||||
if 1
|
||||
eng = struct();
|
||||
eng. name = 'GPU';
|
||||
eng. use_gpu = true; % if false, run CPU code, but it will get very slow
|
||||
eng. keep_on_gpu = true; % keep data + projections on GPU, false is useful for large data if DM is used
|
||||
eng. compress_data = true; % use automatic online memory compression to limit meed of GPU memory
|
||||
eng. gpu_id = []; % default GPU id, [] means choosen by matlab
|
||||
eng. check_gpu_load = true; % check available GPU memory before starting GPU engines
|
||||
|
||||
%% general
|
||||
eng. number_iterations = 20; % number of iterations for selected method
|
||||
|
||||
|
||||
% basic recontruction parameters
|
||||
% PIE / ML methods
|
||||
eng. beta_object = 1; % object step size, larger == faster convergence, smaller == more robust, should not exceed 1
|
||||
eng. beta_probe = 1; % probe step size, larger == faster convergence, smaller == more robust, should not exceed 1
|
||||
eng. delta_p = 0.1; % LSQ dumping constant, 0 == no preconditioner, 0.1 is usually safe,
|
||||
% DM
|
||||
eng. pfft_relaxation = 0.1; % Relaxation in the Fourier domain projection, = 0 for full projection
|
||||
eng. probe_regularization = 0.1;% Weigth factor for the probe update (inertia)
|
||||
|
||||
|
||||
% ADVANCED OPTIONS
|
||||
% position refinement
|
||||
eng. apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow
|
||||
eng. probe_pos_search = 10; % reconstruct probe positions, from iteration == probe_pos_search, assume they are independed
|
||||
eng. probe_position_search = inf; % reconstruct probe positions, from iteration == probe_position_search, assume they have to match geometry model with error less than probe_position_error_max
|
||||
eng. probe_position_error_max = 10e-9; % max expected random position error of the stages
|
||||
|
||||
|
||||
end
|
||||
|
||||
eng_0 = eng;
|
||||
|
||||
if 1
|
||||
%% test DM solver
|
||||
eng = eng_0;
|
||||
eng. method = 'DM'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
|
||||
eng.grouping = 100;
|
||||
eng.probe_support_radius = [];
|
||||
eng.number_iterations = 20;
|
||||
|
||||
[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
|
||||
end
|
||||
|
||||
if 1
|
||||
%% test MLc/s codes
|
||||
eng = eng_0;
|
||||
eng. method = 'MLc'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
|
||||
eng.grouping = 50;
|
||||
eng.probe_support_radius = [];
|
||||
eng.number_iterations = 20;
|
||||
eng.accelerated_gradients_start = 2;
|
||||
eng. apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow
|
||||
|
||||
[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
|
||||
end
|
||||
|
||||
|
||||
if 1
|
||||
%% test nearfield propagation refinement
|
||||
eng = eng_0;
|
||||
|
||||
% introduce error in the propagation distance of 1%
|
||||
eng.z = 5.05e-3;
|
||||
|
||||
eng. method = 'MLc'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
|
||||
eng.grouping = 20;
|
||||
eng.probe_support_radius = [];
|
||||
eng.number_iterations = 100;
|
||||
eng.accelerated_gradients_start = 2;
|
||||
eng. estimate_NF_distance = 10; % try to estimate the nearfield propagation distance using gradient descent optimization
|
||||
|
||||
[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
|
||||
end
|
||||
|
||||
|
||||
run(fullfile( fileparts(mfilename('fullpath')), 'run_test.m'))
|
||||
|
||||
|
||||
% 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 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 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).
|
||||
% 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.
|
||||
|
||||
Reference in New Issue
Block a user