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% Call function without arguments for a detailed explanation of its use
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% Filename: $RCSfile: datread.m,v $
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%
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% $Revision: 1.2 $ $Date: 2009/02/20 19:33:01 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% Macro for reading .dat files in self-defined data formats
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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_set_default
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% - fopen_until_exists
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% - get_hdr_val
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% - compiling cbf_uncompress.c increases speed but is not mandatory
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%
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%
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% history:
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%
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% February 18th 2009: 1st 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 [frame,vararg_remain] = datread(filename,varargin)
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import io.*
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import utils.fopen_until_exists
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import utils.get_hdr_val
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import utils.char_to_cellstr
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% 0: no debug information
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% 1: some feedback
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% 2: a lot of information
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debug_level = 0;
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% initialize return argument
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frame = struct('header',[], 'data',[]);
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% check minimum number of input arguments
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if (nargin < 1)
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image_read_sub_help(mfilename,'cbf');
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error('At least the filename 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 = 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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% set default values for the variable input arguments and parse the named
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% parameters:
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vararg = 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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otherwise
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% pass further arguments on to fopen_until_exists
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vararg{end+1} = name;
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vararg{end+1} = value;
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end
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end
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% expected maximum length for the text header
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max_header_length = 4096;
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% end-of-header signature
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eoh_signature = [ '# end-of-header' char(10) ];
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% try to open the data file
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if (debug_level >= 1)
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fprintf('Opening %s.\n',filename);
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end
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[fid,vararg_remain] = fopen_until_exists(filename,vararg);
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if (fid < 0)
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return;
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end
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% read all data at once
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[fdat,fcount] = fread(fid,'uint8=>uint8');
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% close input data file
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fclose(fid);
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if (debug_level >= 2)
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fprintf('%d data bytes read\n',fcount);
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end
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% files with header start with a has sign, otherwise just a series of
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% numbers is expected
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if (~strcmp(fdat(1),'#'))
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% convert the array to cell strings
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cell_values = char_to_cellstr( char(fdat)' );
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% convert the strings to double precision values
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frame.data = zeros(length(cell_values),1);
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for (ind = 1:length(cell_values))
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frame.data(ind) = str2double(cell_values{ind});
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end
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% No header information are available.
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% Fake exposure time information to avoid problems in other
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% macros.
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frame.header{end+1} = 'Exposure_time 1.0';
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% add the file modification date to the header
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dir_entry = dir(filename);
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frame.header{end+1} = [ 'DateTime ' dir_entry.date ];
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end
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% search for end of header signature within the expected maximum length of
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% a header
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end_of_header_pos = ...
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strfind( fdat(1:min(max_header_length,length(fdat)))',...
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eoh_signature );
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if (length(end_of_header_pos) < 1)
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error( [ filename,': no header end signature found' ] );
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return;
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end
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if (debug_level >= 2)
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fprintf('Header length is %d bytes.\n',end_of_header_pos -1);
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end
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% return the complete header as lines of a cell array
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frame.header = char_to_cellstr( char(fdat(1:(end_of_header_pos-1))') );
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% increase the index to the first data byte
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end_of_header_pos = end_of_header_pos + length(eoh_signature);
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% check for information on the various dimensions in ascending speed order
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dim1 = get_hdr_val(frame.header,'dim2','%d',1);
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dim2 = get_hdr_val(frame.header,'dim1','%d',1);
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dim3 = get_hdr_val(frame.header,'number-of-exposures','%d',1);
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dim4 = get_hdr_val(frame.header,'channels','%d',1);
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if (debug_level >= 2)
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fprintf('Frame dimensions are %d x %d % %d x %d.\n', ...
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dim4,dim3,dim2,dim1);
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end
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% store the numbers in the array, fastest axis first
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frame.data = zeros(dim4,dim3,dim2,dim1);
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% convert the strings to double precision values
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data_1d = sscanf(char(fdat(end_of_header_pos:end))','%f');
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frame.no_of_el_read = length(data_1d);
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if (length(data_1d) > numel(frame.data))
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frame.data = zeros(dim4,dim3,dim2,ceil(length(data_1d)/(dim4*dim3*dim2)));
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end
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frame.data(1:frame.no_of_el_read) = data_1d;
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