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% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: integrated_intensity.m,v $
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%
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% $Revision: 1.1 $ $Date: 2009/04/08 16:46:40 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% sum the intensity of frames
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%
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% Note:
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% Call without arguments for a brief help text.
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%
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% Dependencies:
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% - image_read
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%
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% history:
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%
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% September 4th 2009:
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% use find_files rather than dir to find the files
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%
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% May 9th 2008: 1st documented version
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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_int] = integrated_intensity(filename_mask, varargin)
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import beamline.pilatus_valid_pixel_roi
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import io.image_read
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import utils.find_files
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% initialize return arguments
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valid_mask = struct('indices',[], 'framesize',[]);
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% set default values for the variable input arguments:
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% filename for loading and saving the valid pixel mask
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filename_valid_mask = '~/Data10/analysis/data/pilatus_valid_mask.mat';
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% display result in this figure
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fig_no = 2;
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% check minimum number of input arguments
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if (nargin < 1)
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fprintf('\nUsage:\n');
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fprintf('[int_int]=%s(filename_mask [[,<name>,<value>]...]);\n',mfilename);
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fprintf('''FigNo'',<integer> number of the figure in which the result is displayed, default is %d\n',...
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fig_no);
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fprintf('\n');
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fprintf('Examples:\n');
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fprintf('[int_int]=%s(''~/Data10/pilatus/air_scattering/*.cbf'');\n',...
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mfilename);
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error('At least the filename mask has to be specified as input parameter.');
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end
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% accept cell array with name/value pairs as well
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no_of_in_arg = nargin;
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if (nargin == 2)
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if (isempty(varargin))
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% ignore empty cell array
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no_of_in_arg = no_of_in_arg -1;
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else
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if (iscell(varargin{1}))
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% use a filled one given as first and only variable parameter
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varargin = varargin{1};
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no_of_in_arg = no_of_in_arg -1 + length(varargin);
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end
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end
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end
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% check number of input arguments
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if (rem(no_of_in_arg,2) ~= 1)
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error('The optional parameters have to be specified as ''name'',''value'' pairs');
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end
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% parse the variable input arguments:
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% initialize the list of unhandled parameters
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vararg_remain = cell(0,0);
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch name
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case 'FigNo'
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fig_no = value;
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otherwise
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vararg_remain{end+1} = name; %#ok<AGROW>
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vararg_remain{end+1} = value; %#ok<AGROW>
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end
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end
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vararg_remain{end+1} = 'UnhandledParError';
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vararg_remain{end+1} = 0;
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% set some default values for the plot window
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set(0, 'DefaultAxesfontsize', 12);
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set(0, 'DefaultAxeslinewidth', 1, 'DefaultAxesfontsize', 12);
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set(0, 'DefaultLinelinewidth', 1);
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% get all matching filenames
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[data_dir,fnames,vararg_remain] = ...
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find_files( filename_mask, vararg_remain );
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if (length(fnames) < 1)
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error('No matching files found for %s.\n',search_mask);
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end
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fprintf('loading the valid pixel mask %s\n',filename_valid_mask);
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load(filename_valid_mask);
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% process the frames
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int_int = zeros(1,length(fnames));
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fprintf('data directory is %s\n',data_dir);
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for (f_ind=1:length(fnames))
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fprintf('%3d/%3d: reading %s%s\n',f_ind,length(fnames),...
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data_dir,fnames(f_ind).name);
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[frame] = image_read([data_dir fnames(f_ind).name ],vararg_remain);
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if (f_ind == 1)
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framesize1 = size(frame.data,1);
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framesize2 = size(frame.data,2);
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framesize = framesize1 * framesize2;
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ind_valid = 1:numel(frame.data);
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if (isstruct(valid_mask))
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% cut out the region of interest from the valid pixel mask
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valid_mask_cut = pilatus_valid_pixel_roi(valid_mask,...
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'RoiSize',frame.img_full_size{1});
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% from this cut out the region of interest,
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% if specified
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valid_mask_cut = pilatus_valid_pixel_roi(valid_mask_cut,vararg_remain);
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ind_valid = valid_mask_cut.indices;
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end
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end
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% check that the file have identical dimensions
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if ((framesize1 ~= size(frame.data,1)) || ...
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(framesize2 ~= size(frame.data,2)))
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error('The previous file(s) had %d x %d pixels, this frame has %d x %d pixels',...
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framesize1,framesize2,size(frame.data,1),size(frame.data,2));
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end
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% sum the valid pixels
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int_int(f_ind) = sum(frame.data(ind_valid));
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end
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% plot the result
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if (fig_no > 0)
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figure(fig_no);
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plot(int_int);
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title_str = [ strrep(filename_mask,'_','\_') ': average int. int. = ' ...
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num2str(mean(int_int),'%.4e') ];
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title(title_str);
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end
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