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% [orient_vec] = image_default_orientation(header, extension, varargin)
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% Determine default orientation for an image_orient.m call based on the
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% file extension
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% Filename: $RCSfile: image_default_orientation.m,v $
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%
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% $Revision: 1.11 $ $Date: 2013/03/23 15:01:09 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% Determine default orientation for an image_orient.m call based on the
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% file extension
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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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% ---
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%
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% history:
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%
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% September 30th 2010:
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% add orientation for HDF5 files
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%
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% November 19th 2008:
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% add .mat files
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%
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% August 28th 2008:
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% add orientation for extension .dat
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%
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% July 17th 2008:
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% add mar extension, raw default orientation changed before
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%
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% June 19th 2008:
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% add header to call parameters
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%
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% June 10th 2008:
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% 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 [orient_vec] = ...
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image_default_orientation(header, extension, varargin)
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import io.*
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% check minimum number of input arguments
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if (nargin < 1)
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fprintf('Usage:\n')
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fprintf('[orientation_vector]=%s(extension);\n',...
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m_file_name);
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fprintf('The vector contains three values which can be 0 or 1 for transpose, flip-left-right, flip-up-down\n');
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error('At least one input parameter has to be specified.');
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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 == 3)
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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 = 2 + 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) ~= 0)
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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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% parse the variable input arguments
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% vararg_remain = 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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error('Do not know how to handle parameter %s\n',name);
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% vararg_remain{end+1} = name;
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% vararg_remain{end+1} = value;
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end
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end
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% image_read calls this function prior to converting the single frame
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% to a cell array of frames
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if (~iscell(header))
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fprintf('Warning (%s): header is not a cell array\n',mfilename);
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fprintf('If this is an image_spec call then please report to Oliver:\n')
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whos header
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header
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else
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if ((~isempty(header)) && (iscell(header{1})))
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header = header{1};
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end
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end
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% set the default orientation as a function of the filename extension
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switch extension
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case 'dat'
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orient_vec = [ 0 0 0 ];
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case 'edf'
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orient_vec = [ 1 1 1 ];
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case 'cbf'
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orient_vec = [ 1 1 1 ];
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case {'h5', 'hdf5', 'nxs', 'cxs'}
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orient_vec = [ 0 0 1 ];
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case {'tif', 'tiff'}
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if (strcmp(header{1}(1:5),'Andor'))
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orient_vec = [ 1 0 0 ];
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else
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orient_vec = [ 0 0 0 ];
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end
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case {'mar','mccd'}
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orient_vec = [ 1 0 1 ];
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case 'mat'
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orient_vec = [ 0 0 0 ];
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case 'raw'
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% FLI CCD at ICON
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% orient_vec = [ 0 1 0 ];
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% FLI CCD at laser setup
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orient_vec = [ 1 0 1 ];
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case 'spe'
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orient_vec = [ 0 0 0 ];
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otherwise
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error([ 'unknown extension ''' extension '''' ]);
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end
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