% [frame_unwrapped, frame_replaced_from_lowcount] = unwrap_pilatus(frame_low, frame_high, numbad, slope)
%
% unwraps the pilatus pixels that had too high intensity.
% slope and numbad are optional.
% slope should be (high exposure time / low exposure time), but can be
% evaluated from the data.
% numbad is the rough number of bad pixels - it should be greater than the actual
% value. It is used only if the slope needs to be evaluated.
%
% The first output is the result of unwrapping the high intensity counts.
% The second is equal to the high intensity frame with all wrapped values
% replaced with scaled counts from the low exposure frame. These two should
% be equal, but the first output is biased by the intensity correction done
% by the pilatus. 

% 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").
%
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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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% 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 
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%       © 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.
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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, 
%       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. 

function varargout = unwrap_pilatus_weird(frame_low, frame_high, varargin)

ratio = .95;
max_counts = 2^20;

sz = size(frame_low);
N = numel(frame_low);

if nargin >= 3 && ~isempty(varargin{1})
    ratio = varargin{1} / N;
end

slope = -1;
if nargin == 4
    slope = varargin{2};
end

Nr = round(N*ratio);

% Flatten the frames
I_low = reshape(frame_low, [1 N]);
I_high = reshape(frame_high, [1 N]);

% sort
%[dum, ind] = sort(I_low);

% fit the lowest values
%if slope == -1
%    slope = I_low(ind(1:Nr))'\I_high(ind(1:Nr))';
%end

%figure(10); plot(I_low(ind), I_high(ind), 'k.', [0 max_counts], [0, max_counts*slope], 'b-'); pause;

% Here we find all the out liers.
bad_guys = (I_low - I_high/slope) > 1e-1 * max_counts / slope;


%[dum, ind] = sort(I_low);
%figure(5); plot(I_low(ind), I_high(ind), 'k.', [0 max_counts], [0, max_counts*slope], 'b-', I_low(ind), I_high(ind) .* (double(bad_guys(ind)) ./ bad_guys(ind)), 'ro');
%idcut = find(bad_guys(ind),1);
%axis(2*[0 I_low(ind(idcut)) 0 slope*I_low(ind(idcut))]);
%pause;

I_high_replaced = I_high;
I_high_replaced(bad_guys) = slope*I_low(bad_guys);

varargout{1} = reshape(I_high_replaced, sz);

%figure(1); plot(I_low(ind), I_high(ind), 'k.', [0 I_low(ind(end))], [0, I_low(ind(end))*slope], 'b-', I_low(ind), I_high_unwrapped(ind),'r.', I_low(ind), I_high_replaced(ind),'m.');

return;