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+utils/remove_linear_phase_smart.m

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+%im_output = remove_linear_phase_smart(im_input, [,<name>,<value>] ...])
+%
+% Receives a complex valued array, returns the complex array after removing
+% the linear and the constant phase offset. Different options are given for
+% defining a reference area on the sample
+%
+% im_input  Input complex valued image
+% 
+% The optional <name>,<value> pairs are:
+%
+% 'mask', maskarray     Binary array with ones where the linear phase should be
+%                       removed. Alternatively the mask can be an array of
+%                       non unitary weights for the computation of average
+%                       phase ramp and average phase. For example, the
+%                       magnitude can be use to weight 
+%
+% June 21,2016
+
+
+% Upcoming features
+% 'roi', []             
+% method
+% upsamp    Linear phase will be removed within 2*pi/upsamp peak to valley
+%           in radians
+% errorm    Optional ouput with all outputs from dftregistration
+%
+% Many lines taken from rmsphaseramp.m
+%
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+function [im_output, ph_err] = remove_linear_phase_smart(im, varargin)
+import utils.auto_mask_find
+import utils.dftregistration
+
+% Defaults
+mask = ones(size(im));
+
+% parse the variable input arguments not handled by auto_mask_find
+vararg = cell(0,0);                    
+for ind = 1:2:length(varargin)
+    name = varargin{ind};
+    value = varargin{ind+1};
+    switch lower(name)
+        case 'mask'
+            mask = value;
+        otherwise
+            vararg{end+1} = name;
+            vararg{end+1} = value;
+    end
+end
+
+if any(mask(:) == 1)
+    ph = exp(1i*angle(im));
+    [gx, gy] = gradient(ph);
+    gx = -real(1i*gx./ph);
+    gy = -real(1i*gy./ph);
+    
+    nrm = sum(sum(mask));
+    agx = sum(sum(gx.*mask)) / nrm;
+    agy = sum(sum(gy.*mask)) / nrm;
+    
+    sz = size(ph);
+    [xx,yy] = meshgrid(1:sz(2),1:sz(1));
+    ph_corr = ph.*exp(-1i*(agx*xx + agy*yy));
+    ph_corr = ph_corr.*conj(sum(sum(ph_corr.*mask)) / nrm);
+    
+    im_output = abs(im).*ph_corr;
+    
+    if nargout > 1
+        ph_err = sum(sum(angle(ph_corr).^2.*mask)) / nrm;
+    end
+else
+    warning('The mask provided has only zeros. Cannot remove ramp')
+    im_output = im;
+    ph_err = 0;
+end
+
+end