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111 lines
4.3 KiB
Matlab
111 lines
4.3 KiB
Matlab
%im_output = remove_linear_phase_smart(im_input, [,<name>,<value>] ...])
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%
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% Receives a complex valued array, returns the complex array after removing
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% the linear and the constant phase offset. Different options are given for
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% defining a reference area on the sample
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%
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% im_input Input complex valued image
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%
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% The optional <name>,<value> pairs are:
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%
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% 'mask', maskarray Binary array with ones where the linear phase should be
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% removed. Alternatively the mask can be an array of
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% non unitary weights for the computation of average
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% phase ramp and average phase. For example, the
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% magnitude can be use to weight
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%
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% June 21,2016
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% Upcoming features
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% 'roi', []
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% method
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% upsamp Linear phase will be removed within 2*pi/upsamp peak to valley
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% in radians
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% errorm Optional ouput with all outputs from dftregistration
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%
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% Many lines taken from rmsphaseramp.m
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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 [im_output, ph_err] = remove_linear_phase_smart(im, varargin)
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import utils.auto_mask_find
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import utils.dftregistration
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% Defaults
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mask = ones(size(im));
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% parse the variable input arguments not handled by auto_mask_find
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vararg = cell(0,0);
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch lower(name)
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case 'mask'
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mask = value;
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otherwise
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vararg{end+1} = name;
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vararg{end+1} = value;
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end
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end
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if any(mask(:) == 1)
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ph = exp(1i*angle(im));
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[gx, gy] = gradient(ph);
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gx = -real(1i*gx./ph);
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gy = -real(1i*gy./ph);
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nrm = sum(sum(mask));
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agx = sum(sum(gx.*mask)) / nrm;
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agy = sum(sum(gy.*mask)) / nrm;
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sz = size(ph);
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[xx,yy] = meshgrid(1:sz(2),1:sz(1));
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ph_corr = ph.*exp(-1i*(agx*xx + agy*yy));
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ph_corr = ph_corr.*conj(sum(sum(ph_corr.*mask)) / nrm);
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im_output = abs(im).*ph_corr;
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if nargout > 1
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ph_err = sum(sum(angle(ph_corr).^2.*mask)) / nrm;
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end
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else
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warning('The mask provided has only zeros. Cannot remove ramp')
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im_output = im;
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ph_err = 0;
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end
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end |