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+%  SAVE_MOVIE Function to save stack of images as a movie 
+%
+%  save_movie(img_stack, movie_filename, theta, par, varargin)
+% 
+%  ** img_stack    stack of input images, real or complex 
+%  ** movie_filename   name of the movie to be saved 
+% *optional*
+%  ** theta   angles of the projections, default = []
+%  ** par     structure with tomo parameters, default = [] 
+%  ** varargin   other parameters, see the code for more details 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 pareters, 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 save_movie(img_stack, movie_filename, theta, par, varargin)
+
+    import math.*
+
+    parser = inputParser;
+    parser.addParameter('pixel_size',  nan , @isnumeric )
+    parser.addParameter('colormap',  bone , @isnumeric )
+    parser.addParameter('output_folder',  '' , @isstr )
+    parser.addParameter('fps',  10 , @isnumeric )
+    parser.addParameter('quality',  100 , @isnumeric ) % 100 is maximal 
+    parser.addParameter('baraxis','auto') 
+    parser.addParameter('windowautopos',false) 
+
+    parser.parse(varargin{:})
+    r = parser.Results;
+
+    if nargin < 4
+        par = struct(); 
+    end
+    
+    % load all to the param structure 
+    for name = fieldnames(r)'
+        if ~isfield(par, name{1}) || ~ismember(name, parser.UsingDefaults) % prefer values in param structure 
+            par.(name{1}) = r.(name{1});
+        end
+    end
+    
+    movie_path = [par.output_folder, movie_filename]; 
+    
+    if exist(movie_path,'file')
+        disp(['File ' movie_path ' exists,' ])
+        userans = input(['Do you want to overwrite (Y/n)? '],'s');
+        if strcmpi(userans,'n')
+            disp(['Did not save ' par.saveprojfile])
+            return
+        end
+    else
+        delete(movie_path);
+    end
+
+    Nslices = size(img_stack,3);
+
+    
+    frames = 1:Nslices;
+    if ~isempty(theta) && par.showsorted 
+        [~, ind] = sort(theta);
+        frames = ind(frames);
+    end
+    
+    
+    clf()
+    if isfield(par, 'baraxis') && strcmpi(par.baraxis,'auto') && isreal(img_stack)
+        % set the same range for all the frames using quantile range
+        range = gather(sp_quantile(img_stack, [1e-3, 1-1e-3], 10));
+    end
+    
+     
+    
+    
+    
+    disp(['Saving movie to  ' movie_path]);
+    writeobj = VideoWriter(movie_path);
+    writeobj.Quality=par.quality;
+    writeobj.FrameRate=par.fps;
+    
+    open(writeobj); 
+
+    % Create an animation.
+    plotting.imagesc3D(img_stack(:,:,1))
+    axis off image 
+    colormap(par.colormap)
+
+    set(gca,'nextplot','replacechildren');
+
+    if  par.windowautopos
+        screensize = get( groot, 'Screensize' );
+        win_size = [1060 767]; 
+        set(gcf,'Outerposition',[141 min(257,screensize(2)-win_size(2)) 1060 767]);
+    end
+
+    
+    
+    disp('Creating movie')
+    for kk = 1:Nslices
+       utils.progressbar(kk, Nslices)
+       % use imagesc3D to image also complex valued images 
+       plotting.imagesc3D(img_stack(:,:,frames(kk)))
+       if isreal(img_stack) && isfield(par, 'baraxis') 
+           if ~strcmpi(par.baraxis,'auto')
+               caxis(par.baraxis)
+           else
+               caxis(range)
+           end
+       end
+       axis xy
+       % Write each frame to the file.
+       currFrame = getframe;
+       writeVideo(writeobj,currFrame);
+    end
+    
+    close(writeobj); 
+    
+    disp('Movie finished')
+
+
+
+end