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% [delta_stack_prealign, obj_interf_pos_x, obj_interf_pos_y ] = get_auto_tomo(param_autotomo,surface_calib_file, omnyposfile)
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%
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% Description:
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%
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% The function (1) loads the omnyposfile file and determine the scanning
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% positions if get_auto_calibration or auto_alignment is 1 and
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% (2) loads the surface_calib_file to give an initial guess for
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% the alignemnt array (deltastack) if auto_alignment is 1
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%
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% Input:
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%
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% par. auto_alignment: 0 or 1 (default)
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% par. get_auto_calibration: 0 or 1 (default)
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% surface_calib_file (mandatory if auto_alignment=1)
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% omnyposfile (mandatory if auto_alignment=1 or get_auto_calibration=1)
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%
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% Output:
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%
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% delta_stack_prealign: used as initial guess for the alignment
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% obj_interf_pos_x and obj_interf_pos_y: Object maximum position based on interferometry
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%
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [delta_stack_prealign, obj_interf_pos_x, obj_interf_pos_y ] = ...
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get_auto_tomo(par,surface_calib_file, omnyposfile, theta, scanstomo)
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import beamline.read_omny_pos
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import utils.*
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import ptycho.*
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import beamline.*
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obj_interf_pos_x = [];
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obj_interf_pos_y = [];
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flag_plot = 1;
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delta_stack_prealign = [];
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%%% To improve: Shifts of the probe are not yet considered here, see
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%%% /cSAXS_sxdm_2013_06_omny/matlab/tomo/autotomo_calibration_porous_S00506_S00930.m
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if par.auto_alignment ||par.get_auto_calibration
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%% Determine position of first pixel in the reconstructions %%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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disp('Loading omny_pos for autoalignment')
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for ii = 1:max(size(scanstomo))
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progressbar(ii, max(size(scanstomo)))
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out_orch = read_omny_pos(sprintf(omnyposfile,scanstomo(ii)));
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positions_real = [out_orch.Average_y_st_fzp*1e-6 out_orch.Average_x_st_fzp*1e-6];
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% clear positions
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% positions = positions_real./par.pixel_size;
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%
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% % Change from object to probe positions
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% positions = -positions;
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%
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% positions(:,1) = positions(:,1) - min(positions(:,1));
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% positions(:,2) = positions(:,2) - min(positions(:,2));
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% positions = round(positions);
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%%% Object maximum position based on interferometry - sample motion
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%%% Corresponds to pos to coordinates of (1,1) pixel
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%%% increasing number means the sample was higher
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obj_interf_pos_y(ii) = max(positions_real(:,1));
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obj_interf_pos_x(ii) = max(positions_real(:,2));
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end
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end
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if par.auto_alignment && exist(surface_calib_file, 'file')
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%%% Read calibration file and interpolate correction to these angles
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pos_cal = load(surface_calib_file);
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delta_stack_corr_y_filt = spline(pos_cal.thetasort,pos_cal.delta_stack_corr_y_filt,theta);
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delta_stack_corr_x_filt = spline(pos_cal.thetasort,pos_cal.delta_stack_corr_x_filt,theta);
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%%% Interferometer alignment with mirror surface corrections
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delta_stack_prealign(1,:) = delta_stack_corr_y_filt+obj_interf_pos_y;
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delta_stack_prealign(2,:) = delta_stack_corr_x_filt+obj_interf_pos_x;
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%%% Remove constant term from y alignment
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delta_stack_prealign(1,:) = delta_stack_prealign(1,:)-mean(delta_stack_prealign(1,:));
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%%% Remove sin term from correction in x
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[~,indsort] = sort(theta);
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auxfunc = delta_stack_prealign(2,indsort);
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auxfunc = [auxfunc -auxfunc+auxfunc(end)+auxfunc(1)];
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auxfuncft = fft(auxfunc);
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auxfuncft(3:end-1) = 0;
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auxfunc2 = ifft(auxfuncft);
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auxfunc3 = auxfunc2(1:end/2);
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delta_stack_prealign(2,indsort) = delta_stack_prealign(2,indsort) - auxfunc3;
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delta_stack_prealign = delta_stack_prealign/par.pixel_size;
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if flag_plot
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figure(1);
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clf;
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subplot(2,1,1)
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plot(theta,obj_interf_pos_y,'.')
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title('Interferometer y position [microns]')
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subplot(2,1,2)
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plot(theta,obj_interf_pos_x,'.')
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title('Interferometer x position [microns]')
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figure(2);
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clf;
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subplot(2,1,1)
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plot(theta,delta_stack_prealign(1,:),'.')
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title('Correction in y [pixels]')
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subplot(2,1,2)
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plot(theta,delta_stack_prealign(2,:),'.')
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title('Correction in x [pixels]')
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end
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elseif ~exist(surface_calib_file, 'file')
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warning('Missing surface calibration file %s', surface_calib_file)
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end
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end
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