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180 lines
11 KiB
Matlab
180 lines
11 KiB
Matlab
% Evaluate registration error in an angle series. Returns the error between
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% subsequent images. The last image is evaluated against the first but
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% flipped in x. Recieves image FT with DC in (1,1), the image should have
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% had the center in center of array.
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% filt_stackFT FT of stack of images, previously filtered if needed
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% deltastack Estimates of positions
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% xmax Vector with positions of horizontal edges of rectangular
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% window for registration
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% ymax Same as xmax but vertical edges of window
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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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function [errorreg grad] = loopregerror(deltastack,filt_stackFT,xmask,ymask)
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import utils.dftregistration
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[nr, nc, nim] = size(filt_stackFT);
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errorreg = 0;
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% Compute shifted stack FT
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for ii = 1:nim-1,
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filt_stackFT(:,:,ii) = shiftpp3(filt_stackFT(:,:,ii),deltastack(1,ii),deltastack(2,ii));
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end
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filt_stack = ifft2(filt_stackFT); % Compute the stack
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filt_stack = filt_stack(ymask,xmask,:); % Registration window
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filt_stackp1 = filt_stack(:,:,2:end); % Slicing variable, takes more memory
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% necessary for parallelizaiton
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for ii = 1:nim-1 % Error of ii vs ii+1
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output = dftregistration(filt_stack(:,:,ii),filt_stackp1(:,:,ii),0);
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errorreg(ii) = output(1);
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end
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% Compute first vs last
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output = dftregistration(filt_stack(:,:,end),fliplr(filt_stackp1(:,:,1)),0);
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errorreg(nim) = output(1);
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if nargout == 2,
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grad = deltastack*0;
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stepe = 1e1; % For forward derivative
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Nr = ifftshift([-fix(nr/2):ceil(nr/2)-1]);
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Nc = ifftshift([-fix(nc/2):ceil(nc/2)-1]);
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[Nc,Nr] = meshgrid(Nc,Nr);
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expx = exp(1i*2*pi*(stepe*Nc/nc));
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expy = exp(1i*2*pi*(stepe*Nr/nr));
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for ii = 2:nim-1,
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auxim = filt_stackFT(:,:,ii).*expx; % FT{fn(x-(xn+eps))}
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auxim = ifft2(auxim); % fn(x-(xn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,filt_stackp1(:,:,ii),0);
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errorregepsx = output(1); % En(xn+eps)
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grad(2,ii) = grad(2,ii) + (errorregepsx - errorreg(ii))/stepe;
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output = dftregistration(auxim,filt_stack(:,:,ii-1),0);
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errorregepsx = output(1); % En-1(xn+eps)
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grad(2,ii) = grad(2,ii) + (errorregepsx - errorreg(ii))/stepe;
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auxim = filt_stackFT(:,:,ii).*expy; % FT{fn(y-(yn+eps))}
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auxim = ifft2(auxim); % fn(y-(yn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,filt_stackp1(:,:,ii),0);
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errorregepsy = output(1); % En(yn+eps)
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grad(1,ii) = grad(1,ii) + (errorregepsy - errorreg(ii))/stepe;
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output = dftregistration(auxim,filt_stack(:,:,ii-1),0);
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errorregepsy = output(1); % En-1(xn+eps)
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grad(1,ii) = grad(1,ii) + (errorregepsy - errorreg(ii))/stepe;
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end
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% grad(1)
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clear ii,
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auxim = filt_stackFT(:,:,1).*expx; % FT{fn(x-(xn+eps))}
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auxim = ifft2(auxim); % fn(x-(xn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,filt_stackp1(:,:,1),0);
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errorregepsx = output(1); % En(xn+eps)
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grad(2,1) = grad(2,1) + (errorregepsx - errorreg(1))/stepe;
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output = dftregistration(auxim,fliplr(filt_stack(:,:,nim)),0);
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errorregepsx = output(1); % En-1(xn+eps)
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grad(2,1) = grad(2,1) + (errorregepsx - errorreg(1))/stepe;
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auxim = filt_stackFT(:,:,1).*expy; % FT{fn(y-(yn+eps))}
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auxim = ifft2(auxim); % fn(y-(yn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,filt_stackp1(:,:,1),0);
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errorregepsy = output(1); % En(yn+eps)
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grad(1,1) = grad(1,1) + (errorregepsy - errorreg(1))/stepe;
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output = dftregistration(fliplr(auxim),filt_stack(:,:,nim),0);
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errorregepsy = output(1); % En-1(xn+eps)
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grad(1,1) = grad(1,1) + (errorregepsy - errorreg(1))/stepe;
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%grad(nim)
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auxim = filt_stackFT(:,:,nim).*expx; % FT{fn(x-(xn+eps))}
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auxim = ifft2(auxim); % fn(x-(xn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,fliplr(filt_stackp1(:,:,1)),0);
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errorregepsx = output(1); % En(xn+eps)
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grad(2,nim) = grad(2,nim) + (errorregepsx - errorreg(nim))/stepe;
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output = dftregistration(auxim,filt_stack(:,:,nim-1),0);
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errorregepsx = output(1); % En-1(xn+eps)
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grad(2,nim) = grad(2,nim) + (errorregepsx - errorreg(nim))/stepe;
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auxim = filt_stackFT(:,:,nim).*expy; % FT{fn(y-(yn+eps))}
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auxim = ifft2(auxim); % fn(y-(yn+eps)) Compute the image
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auxim = auxim(ymask,xmask,:); % Registration window
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output = dftregistration(auxim,fliplr(filt_stackp1(:,:,1)),0);
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errorregepsy = output(1); % En(yn+eps)
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grad(1,nim) = grad(1,nim) + (errorregepsy - errorreg(nim))/stepe;
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output = dftregistration(auxim,filt_stack(:,:,nim-1),0);
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errorregepsy = output(1); % En-1(xn+eps)
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grad(1,nim) = grad(1,nim) + (errorregepsy - errorreg(nim))/stepe;
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end
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errorreg = sum(errorreg),
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%
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% for ii = 1:nim-1,
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% aux1 = ifft2(shiftpp3(filt_stackFT(:,:,ii),deltastack(1,ii),deltastack(2,ii)));
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% aux2 = ifft2(shiftpp3(filt_stackFT(:,:,ii+1),deltastack(1,ii+1),deltastack(2,ii+1)));
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% aux1 = aux1(ymask,xmask);
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% aux2 = aux2(ymask,xmask);
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% output = dftregistration(aux1,aux2,0);
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% errorreg = errorreg + output(1);
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% end
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% INCLUDE THE LAST TO FIRST ERROR |