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% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: marread.m,v $
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%
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% $Revision: 1.1 $ $Date: 2008/07/17 16:55:40 $
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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 TIFF files written by a MAR CCD
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%
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% Note:
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% MAR data are TIFF and can be read by forcing the type to tif.
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% The advantage of forcing the type to mar is, that additional header
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% fields like the exposure time are read.
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% This follows the MarCCD header documentaion by Blum and Doyle
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% marccd v0.17.1
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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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% - 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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% July 17th 2008: 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] = marread(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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% 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,'mar');
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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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% 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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% the MAR header has a fixed length of 1024 bytes for the TIFF header plus
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% 3072 bytes for the MAR specific part
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end_of_header_pos = 4096;
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if (length(fdat) < end_of_header_pos)
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error([ num2str(length(fdat)) ' bytes read, which is less than the constant header length' ]);
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end
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% check little/big endian, also to recognize MAR files
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if (typecast(fdat(1025+32:1025+35),'uint32') ~= 1234)
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error([ filename ' is not a MAR file or has big endian byte order' ]);
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end
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% get image dimensions
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nfast = typecast(fdat(1025+80:1025+83),'uint32');
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nslow = typecast(fdat(1025+84:1025+87),'uint32');
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bytes_per_pixel = typecast(fdat(1025+88:1025+91),'uint32');
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if ((bytes_per_pixel ~= 2) && (bytes_per_pixel ~= 4))
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error( [ 'unforseen no. of bytes per pixel of ' num2str(bytes_per_pixel) ] );
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end
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bytes_expected = end_of_header_pos + nfast*nslow*bytes_per_pixel;
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if (bytes_expected ~= length(fdat))
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error([ num2str(bytes_expected) ' bytes expected, ' num2str(length(fdat)) ' read' ]);
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end
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% return some selected header fields as lines of a cell array
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frame.header = cell(7,1);
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frame.header{1} = sprintf('IntegrationTime_ms %d',...
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typecast(fdat(1025+640+12:1025+640+15),'uint32'));
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frame.header{2} = sprintf('ExposureTime_ms %d',...
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typecast(fdat(1025+640+16:1025+640+19),'uint32'));
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frame.header{3} = sprintf('ReadoutTime_ms %d',...
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typecast(fdat(1025+640+20:1025+640+23),'uint32'));
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frame.header{4} = sprintf('nReads %d',...
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typecast(fdat(1025+640+24:1025+640+27),'uint32'));
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frame.header{5} = sprintf('DateTime %s %s %s:%s%s %s',...
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char(fdat(2369:2370)'),...
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char(fdat(2371:2372)'),...
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char(fdat(2373:2374)'),...
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char(fdat(2375:2376)'),...
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char(fdat(2381:2383)'),...
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char(fdat(2377:2380)'));
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frame.header{6} = sprintf('PixelSizeX_nm %d',...
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typecast(fdat(1025+768+4:1025+768+7),'uint32'));
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frame.header{7} = sprintf('PixelSizeY_nm %d',...
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typecast(fdat(1025+768+8:1025+768+11),'uint32'));
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% store data
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switch bytes_per_pixel
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case 2
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frame.data = typecast(fdat(4097:end),'uint16');
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case 4
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frame.data = typecast(fdat(4097:end),'uint32');
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otherwise
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error( [ 'unforseen no. of bytes per pixel of ' num2str(bytes_per_pixel) ] );
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end
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frame.data = reshape(frame.data,nfast,nslow);
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