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+io/image_orient.m

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+% Call function without arguments for instructions on how to use it
+
+% Filename: $RCSfile: image_orient.m,v $
+%
+% $Revision: 1.5 $  $Date: 2014/04/11 12:47:09 $
+% $Author:  $
+% $Tag: $
+%
+% Description:
+% Macro for mirroring or rotating images or stacks of images. 
+%
+% Note:
+% Call without arguments for a brief help text.
+% In case of image stacks the first two dimensions are treated as the image
+% dimensions. 
+%
+% Dependencies: 
+% ---
+%
+% history:
+%
+% January 16th 2009:
+% return the complete structure rather than just the data array
+%
+% June 19th 2008:
+% change call to complete frame rather than data only
+%
+% May 27th 2008: 
+% 1st version based on orientm.m by Tilman Donath
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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_out,vararg_remain] = image_orient(frame, varargin)
+import io.*
+import utils.default_parameter_value
+
+% check minimum number of input arguments
+if (nargin < 1)
+    image_orient_help(mfilename);
+    error('At least one input parameter has to be specified.');
+end
+
+if (ndims(frame.data) < 2)
+    error('The input data array must have at least two dimensions.');
+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:
+orient_extension = frame.extension{1};
+do_transpose = default_parameter_value(mfilename,'Transpose');
+do_fliplr = default_parameter_value(mfilename,'FlipLR');
+do_flipud = default_parameter_value(mfilename,'FlipUD');
+invert_orientation = 0;
+
+% parse the variable input arguments
+vararg_remain = cell(0,0);
+for ind = 1:2:length(varargin)
+    name = varargin{ind};
+    value = varargin{ind+1};
+    switch name
+        case 'Transpose' 
+            do_transpose = value;
+        case 'FlipLR' 
+            do_fliplr = value;
+        case 'FlipUD' 
+            do_flipud = value;
+        case 'Orientation' 
+            if (length(value) ~= 3)
+                error('Invalid Orientation parameter of length %d',length(value));
+            end
+            do_transpose = value(1);
+            do_fliplr = value(2);
+            do_flipud = value(3);
+        case 'OrientExtension' 
+            orient_extension = value;
+        case 'OrientByExtension' 
+            if (value)
+                orient_vec = image_default_orientation(frame.header,orient_extension);
+                do_transpose = orient_vec(1);
+                do_fliplr = orient_vec(2);
+                do_flipud = orient_vec(3);
+            end
+        case 'InvertOrientation'
+            invert_orientation = value;
+        otherwise
+            vararg_remain{end+1} = name;
+            vararg_remain{end+1} = value;
+    end
+end
+
+
+% initialize return arguments
+frame_out = frame;
+
+if (invert_orientation)
+    % apply orientation modifications in inverse order, e.g., to revert the
+    % original orientation prior to writing a file
+    if (do_flipud)
+        frame_out.data = flip(frame_out.data,1);
+    end
+    
+    if (do_fliplr)
+        frame_out.data = flip(frame_out.data,2);
+    end
+end
+
+if (do_transpose)
+    dim_order = 1:ndims(frame_out.data);
+    dim_order(1) = 2;
+    dim_order(2) = 1;
+    frame_out.data = permute(frame_out.data,dim_order);
+end
+
+if (~invert_orientation)
+    if (do_fliplr)
+        frame_out.data = flip(frame_out.data,2);
+    end
+
+    if (do_flipud)
+        frame_out.data = flip(frame_out.data,1);
+    end
+end