initial commit

+io/speread.m

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+% Call function without arguments for instructions on how to use it
+
+% Filename: $RCSfile: speread.m,v $
+%
+% $Revision: 1.1 $  $Date: 2008/06/10 17:05:14 $
+% $Author:  $
+% $Tag: $
+%
+% Description:
+% Macro for reading SPE CCD data files written by WinView from 
+% Roper Scientific / PI Acton
+%
+% Note:
+% Call without arguments for a brief help text.
+%
+% Dependencies:
+% - image_read_set_default
+% - fopen_until_exists
+% - get_hdr_val
+%
+%
+% history:
+%
+% May 9th 2008: 1st version
+%
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+function [frame,vararg_remain] = speread(filename,varargin)
+import io.*
+import utils.fopen_until_exists
+import utils.get_hdr_val
+
+% 0: no debug information
+% 1: some feedback
+% 2: a lot of information
+debug_level = 0;
+
+% initialize return argument
+frame = struct('header',[], 'data',[]);
+
+% check minimum number of input arguments
+if (nargin < 1)
+    image_read_sub_help(mfilename,'SPE');
+    error('At least the filename has to be specified as input parameter.');
+end
+
+% accept cell array with name/value pairs as well
+no_of_in_arg = nargin;
+if (nargin == 2)
+    if (isempty(varargin))
+        % ignore empty cell array
+        no_of_in_arg = no_of_in_arg -1;
+    else
+        if (iscell(varargin{1}))
+            % use a filled one given as first and only variable parameter
+            varargin = varargin{1};
+            no_of_in_arg = 1 + length(varargin);
+        end
+    end
+end
+
+% check number of input arguments
+if (rem(no_of_in_arg,2) ~= 1)
+    error('The optional parameters have to be specified as ''name'',''value'' pairs');
+end
+
+% set default values for the variable input arguments and parse the named
+% parameters: 
+vararg = cell(0,0);
+for ind = 1:2:length(varargin)
+    name = varargin{ind};
+    value = varargin{ind+1};
+    switch name
+        otherwise
+            % pass further arguments on to fopen_until_exists
+            vararg{end+1} = name;
+            vararg{end+1} = value;
+    end
+end
+
+
+% expected maximum length for the text header
+max_header_length = 4100;
+
+% try to open the data file
+if (debug_level >= 1)
+    fprintf('Opening %s.\n',filename);
+end
+[fid,vararg_remain] = fopen_until_exists(filename,vararg);
+if (fid < 0)
+    return;
+end
+
+% read all data at once
+[fdat,fcount] = fread(fid,'uint8=>uint8');
+
+% close input data file
+fclose(fid);
+if (debug_level >= 2)
+    fprintf('%d data bytes read\n',fcount);
+end
+
+% some sanity checks
+if (fdat(4099:4100) ~= [ 85; 85 ])
+    error('%s: no header end signature found',filename);
+    return;
+end
+
+
+% return some selected information from the header as lines of a cell array
+% and extract some variables needed for the data extraction
+% version 2.5 is assumed, otherwise some values may be wrong
+frame.header = cell(0,0);
+xdim = double(typecast(fdat(43:44),'uint16'));
+frame.header{end+1} = sprintf('xdim %.0f',xdim);
+
+ydim = double(typecast(fdat(657:658),'uint16'));
+frame.header{end+1} = sprintf('ydim %.0f',ydim);
+
+exposure_sec = double(typecast(fdat(11:14),'single'));
+frame.header{end+1} = sprintf('exposure %.3f',exposure_sec);
+
+frame.header{end+1} = sprintf('xDimDet %d',typecast(fdat(7:8),'uint16'));
+frame.header{end+1} = sprintf('yDimDet %d',typecast(fdat(19:20),'uint16'));
+
+frame.header{end+1} = sprintf('date %s',char(fdat(21:30)'));
+frame.header{end+1} = sprintf('ExperimentTimeLocal %s:%s:%s',...
+    char(fdat(173:174)'),char(fdat(175:176)'),char(fdat(177:178)'));
+
+data_type = fdat(109);
+frame.header{end+1} = sprintf('datatype %d',data_type);
+switch (data_type)
+    case 0
+        bytes_per_pixel = 4;
+        cast_type = 'single';
+    case 1
+        bytes_per_pixel = 4;
+        cast_type = 'int32';
+    case 2
+        bytes_per_pixel = 2;
+        cast_type = 'int16';
+    case 3
+        bytes_per_pixel = 2;
+        cast_type = 'uint16';
+    otherwise
+        error('unknown data type %d',data_type);
+end
+
+frame.header{end+1} = sprintf('BackGrndApplied %d',typecast(fdat(151:152),'uint16'));
+
+frame.header{end+1} = sprintf('gain %d',typecast(fdat(199:200),'uint16'));
+
+% frame.header{end+1} = sprintf('comments %s',char(fdat(201:600)'));
+
+% number of accumulations
+frame.header{end+1} = sprintf('lavgexp %ld',typecast(fdat(669:672),'uint32'));
+
+frame.header{end+1} = sprintf('ReadoutTime %f',typecast(fdat(673:676),'single'));
+
+frame.header{end+1} = sprintf('sw_version %s',char(fdat(689:703)'));
+
+frame.header{end+1} = sprintf('type %d',typecast(fdat(705:706),'uint16'));
+
+frame.header{end+1} = sprintf('flatFieldApplied %d',typecast(fdat(707:708),'uint16'));
+
+num_frames = double(typecast(fdat(1447:1450),'uint32'));
+frame.header{end+1} = sprintf('NumFrames %.0f',num_frames);
+
+file_header_ver = double(typecast(fdat(1993:1996),'single'));
+frame.header{end+1} = sprintf('file_header_ver %.2f',file_header_ver);
+
+
+% extract the data frames
+data_bytes = bytes_per_pixel * xdim * ydim * num_frames;
+if (fcount-4100 ~= data_bytes)
+    error('%d bytes expected, %d found',data_bytes,fcount-4100);
+end
+frame.data = reshape(typecast(fdat(4101:end),cast_type),...
+    xdim, ydim, num_frames );
+
+% conversion to standard view on PI-SCX4300 data at the SLS/cSAXS beamline
+% if (~original_orientation)
+%     frame.data = permute(frame.data,[2 1 3]);
+% end
+
+% return as double precision floating point
+frame.data = double(frame.data);
+
+