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184 lines
7.5 KiB
Matlab
184 lines
7.5 KiB
Matlab
% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: integrate_range.m,v $
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%
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% $Revision: 1.7 $ $Date: 2012/09/02 15:13:04 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% azimuthal integration of a range of scans
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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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% The integration masks need to be prepared first using prep_integ_masks.m
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%
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% Dependencies:
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% - compile_x12sa_filename
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% - find_files
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% - radial_integ
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%
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% history:
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%
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% May 19th 2010: 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 [] = integrate_range(scan_no_from,scan_no_to,scan_no_step,varargin)
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import beamline.prep_integ_masks
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import beamline.radial_integ
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import utils.compile_x12sa_filename
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import utils.find_files
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% set default values for the variable input arguments:
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% select PILATUS 2M
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pilatus_det_no = 1;
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% writing cbf files
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file_extension = 'cbf';
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save_format = '-v6';
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if (nargin < 2)
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fprintf('\nUsage:\n');
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fprintf('%s(scan_no_from,scan_no_to,scan_no_step [[,<name>,<value>] ...]);\n',mfilename);
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fprintf('integrates the scans within the range [scan_no_from, scan_no_to].\n');
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fprintf('The optional <name>,<value> pairs are:\n');
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fprintf('''PilatusDetNo'',<number> Detector number, 1 for 2M, default is %d\n',pilatus_det_no);
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fprintf('''FileExtension'',<extension string> default is %s\n',file_extension);
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fprintf('''SaveFormat'',<format string> default is %s\n',save_format);
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fprintf('Example:\n');
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fprintf('%s(100,500);\n',mfilename);
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fprintf('Additional <name>,<value> pairs recognized by radial_integ can be specified.\n');
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error('At least the scan number range has to be specified as input argument.');
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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 == 4)
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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 = 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 'PilatusDetNo'
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pilatus_det_no = value;
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case 'SaveFormat'
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save_format = value;
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case 'FileExtension'
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file_extension = value;
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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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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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vararg_remain_x12sa_filename = vararg_remain;
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vararg_remain_x12sa_filename{end+1} = 'DetectorNumber';
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vararg_remain_x12sa_filename{end+1} = pilatus_det_no;
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vararg_remain_x12sa_filename_wildcard = vararg_remain_x12sa_filename;
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vararg_remain_x12sa_filename_wildcard{end+1} = 'PointWildcard';
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vararg_remain_x12sa_filename_wildcard{end+1} = 1;
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vararg_remain_x12sa_filename_wildcard{end+1} = 'SubExpWildcard';
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vararg_remain_x12sa_filename_wildcard{end+1} = 1;
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% highest number of an existing scan
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scan_no_exists = scan_no_from -1;
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scan_no_check = scan_no_from;
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for scan_no = scan_no_from:scan_no_step:scan_no_to
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% wait until the first file of the next scan is available
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while (scan_no >= scan_no_exists)
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scan_no_check = scan_no_check +1;
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if (scan_no_check > scan_no + 100)
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scan_no_check = scan_no +1;
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fprintf('Pausing for 1 minute.\n');
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pause(60);
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% check if the data directory and first file exists
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filename_mask = compile_x12sa_filename(scan_no,0,vararg_remain_x12sa_filename);
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[ddir fnames] = find_files(filename_mask);
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if (~isempty(fnames))
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% integrate all data available until now
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filename_mask = [ compile_x12sa_filename(scan_no,-1,vararg_remain_x12sa_filename) '*_' num2str(pilatus_det_no) '_' ['*' file_extension] ];
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radial_integ(filename_mask,vararg_remain);
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end
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end
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filename_next = compile_x12sa_filename(scan_no_check,0,vararg_remain_x12sa_filename);
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[ddir fnames] = find_files(filename_next);
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if (~isempty(fnames))
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scan_no_exists = scan_no_check;
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end
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end
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% integrate scan if a following scan has been started, i.e.,
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% if the current one must be finished
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if (scan_no < scan_no_exists)
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% check if the data directory and first file exists
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filename_mask = compile_x12sa_filename(scan_no,0,vararg_remain_x12sa_filename);
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[ddir fnames] = find_files(filename_mask);
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if (isempty(fnames))
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fprintf('Skipping scan no %d: no data found\n',scan_no);
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continue;
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end
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% integrate all data, i.e., all points and sub exposures
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filename_mask = [ compile_x12sa_filename(scan_no,0,vararg_remain_x12sa_filename_wildcard) ];
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radial_integ(filename_mask,vararg_remain);
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end
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end
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