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ptycho/utils/obsolete/unwrap_pilatus_weird.m
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% [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").
%
% Terms and Conditions of the LICENSE
% 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
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% 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
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 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
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% 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
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% 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
% 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
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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
% 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.
% 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
% 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
% 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:
% © 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.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% 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;