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https://github.com/c-sooyoung/fold_slice.git
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119 lines
7.8 KiB
Matlab
119 lines
7.8 KiB
Matlab
%% Data path info
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asize = [128 128];
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a2 = prod(asize);
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%% Physical parameters for this dataset
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% all lengths in meter
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energy = 6.2; % Energy (in keV)
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lambda = 1.2398e-9/energy; % wavelength
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dr = 0.5e-6; % shell step size
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lx = 10e-6; % field of view (x)
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ly = 10e-6; % field of view (y)
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nth = 5 ; % theta intervals in first shell
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dwell_time = 0.4; % Counts per diffraction pattern in seconds
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projections = 1; % Number of scans to be run
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z = 7.2; % Distance from object to screen
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ds = 172e-6; % Camera pixel size
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dx_spec = lambda*z ./ (asize*ds); % resolution in the specimen plane
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theta_offset = 0; % Offset the whole scan by this number of degrees
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%% Prepare field of view
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rmax = sqrt((lx/2)^2 + (ly/2)^2);
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nr = 1 + floor(rmax/dr);
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real_positions = [];
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positions = [];
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for ir=1:nr+1
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rr = ir*dr;
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dth = 2*pi / (nth*ir);
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for ith=0:nth*ir-1
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th = ith*dth + (theta_offset*pi/180);
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x2 = rr * cos(th);
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x1 = rr * sin(th);
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if( abs(x1) >= ly/2 || (abs(x2) > lx/2) )
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continue
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end
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real_positions(end+1,:) = [x1 x2]; %#ok<AGROW>
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end
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end
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numpts = size(real_positions,1);
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% For now: round this up
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positions(:,1) = (real_positions(:,1) - min(real_positions(:,1)))./dx_spec(1);
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positions(:,2) = (real_positions(:,2) - min(real_positions(:,2)))./dx_spec(2);
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positions = round(positions);
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object_size = asize + max(positions,[],1);
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fprintf('\nNumber of points: %d\n',numpts)
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fprintf('Estimated time for %d projections at %g sec per point: %g hours\n',projections,dwell_time,numpts*dwell_time*projections/3600);
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fprintf('Estimated time for %d projections at %g sec per point: %g minutes\n',projections,dwell_time,numpts*dwell_time*projections/60);
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%%
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figure(1)
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plot((positions(:,2)-max(positions(:,2))/2).*dx_spec(2).*1e6, ...
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(positions(:,1)-max(positions(:,1))/2).*dx_spec(1).*1e6, 'o-')
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axis xy image
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title('Round\_ROI Ptychography Scan Positions(x,y) in scan plane')
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xlabel('X-position (micron)'); ylabel('Y-position (micron)')
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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 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 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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% 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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