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2026-09-17 20:39:08 +09:00 · 2026-08-07 15:56:42 +09:00
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+% Integrates frames from a loopscan
+%
+% Syntax:
+% [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfilename,masktype)
+% Needed parameters: base_path (e.g. '~/Data10/')
+%                    scan_num   (scan number)
+% Optional parameters: plotfigure (figure number for final 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)
+%                      masktype (type of valid mask file name: 'bin' for binary or 'Oliver')
+% 14-11-2012
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfile,masktype)
+import beamline.pilatus_valid_pixel_roi
+import io.image_read
+import io.spec_read
+import utils.compile_x12sa_filename
+
+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
+if exist('masktype') == 0
+   plotfigure ='Oliver';
+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)
+    switch lower(masktype)
+        case 'oliver'
+            load(maskfile)
+            valid_mask = pilatus_valid_pixel_roi(valid_mask,'RoiSize',size(img0));
+            mask = zeros(size(img0));
+            mask(valid_mask.indices) = 1;
+        case 'bin'
+            load(maskfile)
+        otherwise
+            disp('masktype unknown')
+    end
+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