initial commit

ptycho/utils/obsolete/calculate_round_roi.m

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