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135 lines
9.1 KiB
Matlab
135 lines
9.1 KiB
Matlab
% PREPARE_FLYSCAN_POSITIONS from finit number of measured position interpolate possitions for each
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% measured frame when fly scan is used
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%
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% self = prepare_flyscan_positions(self, par)
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%
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%
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% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
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% ** par structure containing parameters for the engines
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%
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% returns:
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% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
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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 cSAXS
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% ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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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% for LSQ-ML method
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% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
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% for OPRP method
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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." Optics express 24.8 (2016): 8360-8369
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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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% 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 self = prepare_flyscan_positions(self, par)
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import engines.GPU.GPU_wrapper.*
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import math.*
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import utils.*
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import plotting.*
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jumps = diff(self.probe_positions_0);
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step = median(jumps,1);
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jumps = sum(abs(jumps),2);
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% empirical condition
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jumps = find(jumps > 10*median(jumps));
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%% ADVANCED FLY SCAN - LINE SCAN
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% interpolate the other modes into new positions
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%pos = self.modes{1}.probe_positions;
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pos = self.probe_positions_0; %% modified by YJ, use initial position
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%scatter(pos(:,1),pos(:,2),'.'); axis image
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%hold on
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for ll = 1:par.Nmodes
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ratio = par.flyscan_dutycycle*(ll-1)/par.Nmodes;
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self.modes{ll}.probe_positions = pos(min((1:self.Npos)+1,self.Npos),:)*ratio + (1-ratio)*pos;
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%disp(ll)
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%scatter(self.modes{ll}.probe_positions(:,1),self.modes{ll}.probe_positions(:,2),'.'); axis image
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if ~isempty(jumps)
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% expected step continuation
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self.modes{ll}.probe_positions(jumps,:) = bsxfun(@plus, self.modes{ll}.probe_positions(jumps-1,:),step);
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end
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end
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%% PSI code
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%{
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if length(jumps) < par.Nscans
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% assume that smooth path is used
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%% ADVANCED FLY SCAN - SPIRAL
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for ii = 1:par.Nscans
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assert(~any(isfinite(par.probe_position_search)), 'Position refinement and fly scans not suported')
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ind = self.reconstruct_ind{ii};
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pos = self.probe_positions_0(ind,:);
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[ang, rad] = cart2pol(pos(:,1)-pos(1,1), pos(:,2)-pos(1,2));
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ang = unwrap(ang);
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% get interpolate d positions of the sub probes
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ang_all = ang + (par.flyscan_offset -0.5+linspace(0,par.flyscan_dutycycle*(par.Nmodes-1)/par.Nmodes, par.Nmodes) ).*[diff(ang);0];
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rad_all = interp1(ang, rad, ang_all, 'pchip');
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[X,Y] = pol2cart(ang_all, rad_all);
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for ll = 1:par.Nmodes
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self.modes{ll}.probe_positions(ind,:) = pos(1,1:2) + [X(:,ll), Y(:,ll)];
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%if iter == 1; self.probe{ll} = self.probe{1}; end
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%%deleted by YJ. seems a bug
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end
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end
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else
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%% ADVANCED FLY SCAN - LINE SCAN
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% interpolate the other modes into new positions
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pos = self.modes{1}.probe_positions;
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for ll = 1:par.Nmodes
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ratio = par.flyscan_dutycycle*(ll-1)/par.Nmodes;
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self.modes{ll}.probe_positions = pos(min((1:self.Npos)+1,self.Npos),:)*ratio + (1-ratio)*pos;
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if ~isempty(jumps)
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% expected step continuation
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self.modes{ll}.probe_positions(jumps,:) = bsxfun(@plus, self.modes{ll}.probe_positions(jumps-1,:),step);
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end
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end
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end
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%}
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end |