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124 lines
4.9 KiB
Matlab
124 lines
4.9 KiB
Matlab
% Integrates frames from a loopscan
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%
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% Syntax:
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% [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfilename,masktype)
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% Needed parameters: base_path (e.g. '~/Data10/')
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% scan_num (scan number)
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% Optional parameters: plotfigure (figure number for final plot, 0 for no plotting, by default is 0)
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% det_num (detector number, default 1)
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% savedata (=1 to save data in 'analysis/integrated_frames/', default 0)
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% maskfilename (valid mask file name. If empty [], no mask used)
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% masktype (type of valid mask file name: 'bin' for binary or 'Oliver')
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% 14-11-2012
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfile,masktype)
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import beamline.pilatus_valid_pixel_roi
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import io.image_read
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import io.spec_read
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import utils.compile_x12sa_filename
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if exist('det_num') == 0
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det_num=1;
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end
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if exist('savedata') == 0
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savedata=0;
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end
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if exist('maskfile') == 0
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maskfile=[];
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end
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if exist('plotfigure') == 0
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plotfigure = 0;
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end
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if exist('masktype') == 0
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plotfigure ='Oliver';
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end
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%maskfile=[];
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if savedata
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savefolder=[base_path 'analysis/integrated_frames/'];
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if savefolder ~= 7
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mkdir(savefolder)
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end
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end
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path=sprintf('%spilatus_%01d',base_path,det_num);
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filename0=compile_x12sa_filename(scan_num,0);
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data0=image_read(filename0);
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img0=data0.data;
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dims=size(img0);
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S=spec_read(base_path,'ScanNr',scan_num);
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num=size(S.bpm4i,1);
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if ~isempty(maskfile)
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switch lower(masktype)
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case 'oliver'
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load(maskfile)
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valid_mask = pilatus_valid_pixel_roi(valid_mask,'RoiSize',size(img0));
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mask = zeros(size(img0));
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mask(valid_mask.indices) = 1;
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case 'bin'
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load(maskfile)
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otherwise
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disp('masktype unknown')
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end
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else
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mask = ones(size(img0));
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end
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int=img0*0;
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stack=zeros(dims(1),dims(2),num);
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for jj=1:num
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filename=compile_x12sa_filename(scan_num,jj-1);
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data1=image_read(filename);
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img=data1.data.*mask;
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int=int+img;
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stack(:,:,jj)=img;
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end
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if plotfigure ~= 0
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figure(plotfigure)
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figure_position=[187 295 817 650];
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set(gcf,'Position',figure_position);
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imagesc(log10(int)); axis xy equal tight; colorbar; colormap jet
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title(sprintf('integrated frames S%05d',scan_num))
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end
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if savedata
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savefilename=sprintf('%s/S%05d_%01d_integrated_frames',savefolder,scan_num,det_num);
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save([savefilename '.mat'],'int')
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print('-f2','-djpeg','-r300',[ savefilename '.jpg'] );
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print('-f2','-depsc','-r1200',[savefilename '.eps'] );
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end |