% 14-11-2012
% Integrates frames from a loopscan
%
% Syntax:
% [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfilename)
% Needed parameters: base_path (e.g. '~/Data10/')
%                    scan_num   (scan number)
% Optional parameters: plotfigure (figure number for fial plot, 0 for no plotting, by default is 0)
%                      det_num (detector number, default 1)
%                      savedata (=1 to save data in 'analysis/integrated_frames/', default 0)
%                      maskfilename (valid mask file name. If empty [], no mask used)

% 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 
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% 2.	LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements 
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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 
%       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.
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%       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 [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfile)
import beamline.pilatus_valid_pixel_roi
import io.image_read
import io.spec_read
import plotting.integrate_frames

if exist('det_num') == 0
   det_num=1;
end
if exist('savedata') == 0
   savedata=0;
end
if exist('maskfile') == 0
   maskfile=[];
end
if exist('plotfigure') == 0
   plotfigure = 0;
end

%maskfile=[];
if savedata
   savefolder=[base_path 'analysis/integrated_frames/'];
   if savefolder ~= 7
      mkdir(savefolder)
   end
end

path=sprintf('%spilatus_%01d',base_path,det_num);
filename0=compile_x12sa_filename(scan_num,0);
data0=image_read(filename0);
img0=data0.data;
dims=size(img0);
S=spec_read(base_path,'ScanNr',scan_num);
num=size(S.bpm4i,1);

if ~isempty(maskfile)
    load(maskfile)
    valid_mask = pilatus_valid_pixel_roi(valid_mask,'RoiSize',size(img0));
    mask = zeros(size(img0));
    mask(valid_mask.indices) = 1;
else
    mask = ones(size(img0));
end

int=img0*0;
stack=zeros(dims(1),dims(2),num);

for jj=1:num
    filename=compile_x12sa_filename(scan_num,jj-1);
    data1=image_read(filename);
    img=data1.data.*mask;
    int=int+img;
    stack(:,:,jj)=img;
end

if plotfigure ~= 0
  figure(plotfigure)
  figure_position=[187   295   817   650];
  set(gcf,'Position',figure_position);
  imagesc(log10(int)); axis xy equal tight; colorbar; colormap jet
  title(sprintf('integrated frames S%05d',scan_num))
end
if savedata
  savefilename=sprintf('%s/S%05d_%01d_integrated_frames',savefolder,scan_num,det_num);
  save([savefilename '.mat'],'int')
  print('-f2','-djpeg','-r300',[ savefilename '.jpg'] );
  print('-f2','-depsc','-r1200',[savefilename '.eps'] );
end