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+io/edfread.m

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+% Call function without arguments for a detailed explanation of its use
+
+% Filename: $RCSfile: edfread.m,v $
+%
+% $Revision: 1.1 $  $Date: 2008/06/10 17:05:14 $
+% $Author:  $
+% $Tag: $
+%
+% Description:
+% Macro for reading ESRF Data Format (EDF) files written by the
+% Pilatus detector control program camserver. 
+%
+% Note:
+% Currently this routine supports only the subset of EDF features needed to
+% read the Pilatus detector data. 
+% Call without arguments for a brief help text.
+%
+% Dependencies:
+% - fopen_until_exists
+% - get_hdr_val
+% - image_read_set_default
+%
+%
+% history:
+%
+% May 9th 2008: 1st version after redesign
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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] = edfread(filename,varargin)
+import io.*
+import utils.char_to_cellstr
+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,'edf');
+    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 = 4096;
+
+
+% 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
+
+% search for end of header signature within the expected maximum length of
+% a header
+end_of_header_pos = 1024;
+max_pos = min( max_header_length,length(fdat) );
+
+while ((end_of_header_pos < max_pos) && (fdat(end_of_header_pos-1) ~= '}'))
+    end_of_header_pos = end_of_header_pos +1024;
+end
+if (end_of_header_pos >= max_pos)
+    error('no header end signature found');
+end
+if (debug_level >= 2)
+    fprintf('Header length is %d bytes.\n',end_of_header_pos);
+end
+data_length = fcount - end_of_header_pos;
+
+% convert the header to lines of a cell array
+frame.header = char_to_cellstr( char(fdat(1:(end_of_header_pos-1))') );
+
+% check for opening parenthesis
+if (frame.header{1} ~= '{')
+    error([filename ': EDF start ,''{'' not found in first line ''' ...
+        frame.header{1} '''' ]);
+end
+
+
+% extract the mandatory information for data extraction from the header:
+byte_order = get_hdr_val(frame.header,'ByteOrder',' = %s',1);
+dim1 = get_hdr_val(frame.header,'Dim_1',' = %d',1);
+dim2 = get_hdr_val(frame.header,'Dim_2',' = %d',1);
+data_type = get_hdr_val(frame.header,'DataType',' = %s',1);
+if (debug_level >= 2)
+    fprintf('Byte order is %s\n',byte_order);
+    fprintf('Frame dimensions are %d x %d.\n',dim2,dim1);
+    fprintf('Data type is %s\n',data_type);
+end
+
+% determine number of bytes per pixel
+switch data_type
+    case 'UnsignedByte',
+        bytes_per_pixel = 1;
+        data_class = 'uint8';
+    case 'UnsignedShort',
+        bytes_per_pixel = 2;
+        data_class = 'uint16';
+    case {'SignedInteger','UnsignedInteger','UnsignedInt','UnsignedLong'}
+        bytes_per_pixel = 4;
+        data_class = 'uint32';
+    case {'Float','FloatValue','Real'}
+        bytes_per_pixel = 4;
+        data_class = 'single';
+    case 'DoubleValue'
+        bytes_per_pixel = 8;
+        data_class = 'double';
+    otherwise
+        error('unsupported data type %s',data_type);
+end
+no_of_bytes = bytes_per_pixel * dim1 * dim2;
+if (debug_level >= 2)
+    fprintf('%d bytes per pixel, %d in total expected, %d available\n',...
+        bytes_per_pixel,no_of_bytes,data_length);
+end
+
+% check length of available data
+if (no_of_bytes > data_length)
+    error('%d data bytes expected, %d are available',...
+        no_of_bytes,data_length);
+end
+
+% compare file with machine byte order, swap if necessary
+[str,maxsize,endian] = computer;
+if (((strcmp(byte_order,'HighByteFirst')) && (endian == 'L')) || ...
+    ((strcmp(byte_order,'LowByteFirst')) && (endian == 'H')))
+    if (debug_level >= 2)
+        fprintf('Machine byte order is %s: swapping data bytes\n',...
+            endian,bytes_per_pixel);
+    end
+    dat = fdat(end_of_header_pos+1:end_of_header_pos+no_of_bytes);
+    dat = reshape(dat,bytes_per_pixel,[]);
+    dat = flipud(dat);
+    fdat(end_of_header_pos+1:end_of_header_pos+no_of_bytes) = dat(:);
+end
+
+% extract the frame from the binary data
+[frame.data] = ...
+    double(reshape(typecast(fdat(end_of_header_pos+1:end_of_header_pos+no_of_bytes),...
+                            data_class),...
+                   dim1,dim2));
+
+    
+% conversion to standard view on Pilatus 2M data at the SLS/cSAXS beamline
+% if (~original_orientation)
+%     % this is slow, even slower is fliplr(flipud(frame.'))
+%     frame.data = frame.data(end:-1:1,end:-1:1)';
+% end