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% Call function without arguments for a detailed explanation of its use
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% Filename: $RCSfile: fliread.m,v $
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%
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% $Revision: 1.4 $ $Date: 2008/10/03 13:50:04 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% read a data file in the format stored by the program ccdfli.c
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%
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% Note:
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% The image files have the extension raw and the file format is home
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% defined.
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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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%
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%
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% history:
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%
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% Pctober 3rd 2008:
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% add new end-of-header signature search for version 1.20 files
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%
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% October 1st 2008: Exchange width and height in reshape command
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%
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% May 9th 2008: adapt to call from image_read
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%
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% November 3, 2005: include new fields of data format 1.1:
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% exposure time Spec, exposure time measured, monitor counts
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%
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% October 2005: include optional from-to line reading
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%
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% March 2005: 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] = fliread(filename, varargin)
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import io.*
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import utils.char_to_cellstr
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import utils.fopen_until_exists
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import utils.get_hdr_val
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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,'raw');
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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 = 1024;
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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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% return the complete header as lines of a cell array
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frame.header = char_to_cellstr( char(fdat(1:max_header_length)'),1 );
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version_no = get_hdr_val(frame.header,'% version','%f',1);
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if ((version_no ~= 1.00) && (version_no ~= 1.10) && (version_no ~= 1.20))
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fprintf('%s: File version number %.2f may not be supported\n',...
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mfilename,version_no);
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end
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[frameHeight,line_number] = get_hdr_val(frame.header,'% rows','%d',1);
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[frameWidth,line_number] = get_hdr_val(frame.header,'% columns','%d',1);
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if (version_no < 1.20)
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if (version_no == 1.10)
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[monCounts,line_number] = get_hdr_val(frame.header,'% monitorcounts','%d',1);
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end
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% cut off non-header lines
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frame.header = frame.header(1:line_number);
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% find start of data
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eol_ind = regexp(char(fdat(1:max_header_length)'),'\n');
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data_start = eol_ind(line_number) +1;
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else
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eoh_signature = sprintf('%% EOH%c%c',10,26);
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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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data_start = end_of_header_pos + length(eoh_signature);
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end
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% calculate end of data (should be end of file)
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data_end = data_start + frameWidth * frameHeight *2 -1;
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if (data_end > fcount)
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error('%d bytes read but %d are needed',fcount,data_end);
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end
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if (data_end ~= fcount)
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fprintf('%s warning: %d bytes read vs. %d needed\n',mfilename,...
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fcount,data_end);
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end
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% cut out frame data
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frame.data = double( reshape(typecast(fdat(data_start:data_end),'uint16'), ...
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frameWidth,frameHeight) );
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% conversion to standard view on FLI-CCD data at the SLS/cSAXS beamline
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% (to be determined)
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% if (~original_orientation)
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% % frame = flipud(frame');
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% frame.data = frame.data';
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% end
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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} = [ 'FileTimestamp ' dir_entry.date ];
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