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% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: prep_valid_mask.m,v $
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%
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% $Revision: 1.8 $ $Date: 2016/01/21 15:07:41 $
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% $Author: guizar_m $
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% $Tag: $
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%
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% Description:
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% prepare a list of the linear indices for the valid pixels
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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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% May 15th 2010, Oliver Bunk:
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% add command line argument for ThresholdMedian
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%
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% September 4th 2009, Oliver Bunk:
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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, Oliver Bunk: 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 [valid_mask] = prep_valid_mask(data_dir, varargin)
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import io.image_read
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import plotting.display_valid_mask
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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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% use all cbf files
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filename_mask = '*.cbf';
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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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% below this threshold intensity a pixel is considered to be dark
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threshold_dark = 1;
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% above this threshold intensity a pixel is considered to be hot
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threshold_hot = 20;
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% this value times the square root of the intensity is used as hot pixel
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% threshold
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threshold_median = 5.0;
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% replace the existing mask
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extend = 'no';
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% save the mask
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save_data = 1;
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% display result in this figure
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fig_no = 200;
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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('[valid_mask]=%s(data_dir [[,<name>,<value>]...]);\n',mfilename);
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fprintf('Prepare a list of the linear indices for the valid pixels.\n');
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fprintf('To get reliable data a series of at least 10 frames should be analyzed.\n');
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fprintf('The direct beam region will be regarded as invalid since it is out of the\n');
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fprintf('range for valid pixels. To ''repair'' this one should take a second series of\n');
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fprintf('exposures at a different detector position and call this macro with the ''Extend'',''or''\n');
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fprintf('option.\n');
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fprintf('\n');
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fprintf('The optional <name>,<value> pairs are:\n');
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fprintf('''FilenameMask'',<file specifier> specify the files to be used from the data directory, empty string for all, default is ''%s''\n',...
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filename_mask);
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fprintf('''ThresholdDark'',<float> pixels permanently below this value are considered to be dark, default is %d\n',...
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threshold_dark);
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fprintf('''ThresholdHot'',<float> pixels at least once above this value are considered to be hot, default is %d\n',...
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threshold_hot);
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fprintf('''ThresholdMedian'',<float> pixels of intensity I above the constant ThresholdHot and above\n');
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fprintf(' ThresholdMedian times (I+sqrt(I)) are considered to be hot, 0 to deactivate this additional threshold,\n');
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fprintf(' default is %.1f\n',...
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threshold_median);
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fprintf('''SaveData'',<0-no,1-yes> save the valid pixel mask, default is %d\n',save_data);
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fprintf('''FilenameValidMask'',<path and filename> Matlab file with the valid pixel indices,\n');
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fprintf(' default is %s\n',filename_valid_mask);
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fprintf('''Extend'',<''and'', ''or'' or ''no''> update an existing mask using the specified conjunction, default is %s\n',...
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extend);
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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('[valid_mask]=%s(''~/Data10/pilatus/air_scattering/'');\n',...
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mfilename);
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fprintf('[valid_mask]=%s(''~/Data10/pilatus/air_scattering_det_pos_2/'',''Extend'',''or'');\n',...
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mfilename);
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error('At least the data directory 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 'ThresholdDark'
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threshold_dark = value;
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case 'ThresholdHot'
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threshold_hot = value;
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case 'ThresholdMedian'
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threshold_median = value;
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case 'FilenameMask'
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filename_mask = value;
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case 'FilenameValidMask'
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filename_valid_mask = value;
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case 'SaveData'
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save_data = value;
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case 'FigNo'
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fig_no = value;
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case 'Extend'
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extend = 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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% check extend parameter
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if ((~strcmp(extend,'no')) && ...
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(~strcmp(extend,'and')) && (~strcmp(extend,'or')))
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error('extend must be ''and'', ''or'' or ''no''\n');
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end
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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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if (data_dir(end) ~= '/')
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data_dir(end+1) = '/';
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end
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[data_dir,fnames,vararg_remain] = ...
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find_files( [ data_dir filename_mask ], vararg_remain );
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if (length(fnames) < 1)
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error('No matching files found for %s%s.\n',data_dir,filename_mask);
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end
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if (~strcmp(extend,'no'))
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if exist(filename_valid_mask,'file')
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fprintf('loading the existing valid mask %s\n', ...
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filename_valid_mask);
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load(filename_valid_mask);
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ind_existing_valid = valid_mask.indices;
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else
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fprintf('no prior valid mask %s found\n', ...
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filename_valid_mask);
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ind_existing_valid = '';
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end
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end
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% process the frames
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ind_hot = [];
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ind_dark = [];
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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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frame.data = double(frame.data);
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for (frame_ind = 1:size(frame.data,3))
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% median filtered data for comparison
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if (threshold_median ~= 0)
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data_med = frame.data(:,:,frame_ind);
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% add pixels at the module boundary to ease median filtering
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ind = find(data_med == 0);
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data_med_shift = circshift(data_med,[2 2]);
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data_med(ind) = data_med_shift(ind);
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ind = find(data_med == 0);
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data_med_shift = circshift(data_med,[-2 -2]);
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data_med(ind) = data_med_shift(ind);
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ind = find(data_med == 0);
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data_med_shift = circshift(data_med,[-2 2]);
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data_med(ind) = data_med_shift(ind);
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ind = find(data_med == 0);
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data_med_shift = circshift(data_med,[2 -2]);
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data_med(ind) = data_med_shift(ind);
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% median filter the data
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data_med = medfilt2(data_med,[5 5]);
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% the square root of the intensity estimates the standard deviation
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data_med_sqrt = data_med.^0.5;
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end
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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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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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% pixels are considered to be dark if the intensity is below the
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% constant threshold
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ind = find(frame.data(:,:,frame_ind) < threshold_dark);
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fprintf('%6d dark pixels below %10.3e counts, ', ...
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length(ind),threshold_dark);
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if (f_ind == 1)
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ind_dark = ind;
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else
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% dark pixels must be dark in all frames
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ind_dark = intersect(ind_dark,ind);
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end
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% hot pixels are hot if they are above the threshold
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ind = find(frame.data(:,:,frame_ind) > threshold_hot);
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% and, if active, above the intensity plus a threshold times the square
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% root of the intensity as an estimation of the countin statistics
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% error
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if (threshold_median ~= 0.0)
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ind = intersect(ind,find((frame.data(:,:,frame_ind) > data_med+threshold_median*data_med_sqrt)));
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fprintf('%4d hot pixels above %d and %.1f * sqrt(intensity) counts\n', ...
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length(ind),threshold_hot,threshold_median);
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else
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fprintf('%4d hot pixels above %d counts\n', ...
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length(ind),threshold_hot);
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end
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% for hot pixels it is enough to be above the threshold in one frame
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ind_hot = union(ind_hot,ind);
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end
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end
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% calculate the complementary masks of the valid pixels
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valid_mask.indices = setdiff(1:framesize,union(ind_dark,ind_hot));
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fprintf('In total %d dark and %d hot pixels found.\n',...
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length(ind_dark),length(ind_hot));
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fprintf('%d valid pixels remain.\n',length(valid_mask.indices));
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if (~strcmp(extend,'no'))
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fprintf('Extending the existing valid pixel mask of %d pixels\n',...
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length(ind_existing_valid));
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if (strcmp(extend,'and'))
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fprintf('using the and conjugation\n');
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valid_mask.indices = ...
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intersect(valid_mask.indices,ind_existing_valid);
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else
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fprintf('using the or conjugation\n');
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if ~isempty(ind_existing_valid)
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valid_mask.indices = ...
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union(valid_mask.indices,ind_existing_valid);
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end
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end
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fprintf('The combined mask has %d valid pixels.\n',...
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length(valid_mask.indices));
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end
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% store the frame size in the return data
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valid_mask.framesize = [framesize1 framesize2];
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if (save_data)
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% create a backup of the mask
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if (exist(filename_valid_mask,'file'))
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filename_mask_backup = [ filename_valid_mask '.bak' ];
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fprintf('Copying the current mask %s to %s\n',filename_valid_mask,...
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filename_mask_backup);
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copyfile(filename_valid_mask,filename_mask_backup);
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end
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% save the masks
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fprintf('Saving valid_mask to %s\n',filename_valid_mask);
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save(filename_valid_mask,'valid_mask');
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end
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% plot new valid pixel mask
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if (fig_no > 0)
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display_valid_mask('FilenameValidMask',filename_valid_mask,...
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'NoHelp',1,'FigNo',fig_no);
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end
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