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% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: scan_movie.m,v $
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%
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% $Revision: 1.4 $ $Date: 2010/11/12 15:26:15 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% plot a sequence of 2D data frames, optionally save them as .avi file
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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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% - image_read
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%
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% history:
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%
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% June 10th 2008: 1st documented 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 [vararg_remain] = scan_movie(filenames,varargin)
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import io.image_info
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import io.image_read
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import plotting.image_show
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import utils.find_files
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% set default values
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% figure number for display
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fig_no = 2;
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% do not display time in title
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display_time = 0;
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% do not write AVI files
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write_avi = 0;
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% avi filename
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avi_filename = '~/Data10/scan_movie.avi';
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% AVI frames per second
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avi_fps = 5;
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% capture the full figure
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capture_figure = 1;
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% screen frames per second, 0 for no wait
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screen_fps = 0;
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% search masks rather than filenames are specified
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is_fmask = 1;
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% use Linux/Unix find command to interprete filename mask
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use_find = 1;
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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('[vararg_remain]=%s(<filenames> [[,<name>,<value>] ...]);\n',...
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mfilename);
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fprintf('The optional <name>,<value> pairs are:\n');
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fprintf('''FigNo'',<integer value> figure number for data display, default is %d\n',fig_no);
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fprintf('''WriteAVI'',<0-no, 1-yes> write the image frames as AVI file, default is %d\n',write_avi);
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fprintf('''AVIfilename'',<filename> default is %s\n',avi_filename);
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fprintf('''AVI_fps'',<value in Hz> default is %.1f\n',avi_fps);
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fprintf('''CaptureFigure'',<0-axes,1-figure> capture image or full figure, default is %d\n',capture_figure);
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fprintf('''Screen_fps'',<value in Hz> pause if update is faster than this rate / 0 for no pause, default is %.1f\n',screen_fps);
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fprintf('''IsFmask'',<0-no,1-yes> interprete the filename(s) as search mask that may include wildcards, default %d',is_fmask);
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fprintf('''UseFind'',<0-no, 1-yes> use Linux/Unix command find to interprete the filename mask, default is %d\n',use_find);
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fprintf('Additional <name>,<value> pairs recognized by image_show can be specified. Please call image_show for an overview\n');
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fprintf('\n');
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fprintf('Examples:\n');
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fprintf('%s({''file1.cbf'',''file2.cbf''});\n',mfilename);
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fprintf('%s(''dir/*.cbf'');\n',mfilename);
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fprintf('%s(''dir/*.cbf'', ''WriteAVI'',1);\n',mfilename);
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fprintf('%s(''dir/*.cbf'',''ColumnFrom'',700,''ColumnTo'',1100,''RowFrom'',500,''RowTo'',1000,''Screen_fps'',0.5,''LogScale'',0,''AxisMax'',1e3);\n',mfilename);
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fprintf('%s(''dir/*.cbf'',''WriteAVI'',1,''AVIfilename'',''test.avi'');\n',mfilename);
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error('At least the filenames have 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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% parse the variable input arguments
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vararg = cell(1,2);
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% do not display current time by default, can be overruled with parameters
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vararg{1} = 'DisplayTime';
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vararg{2} = 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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case 'FigNo'
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fig_no = value;
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case 'WriteAVI'
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write_avi = value;
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case 'AVIfilename'
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avi_filename = value;
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case 'AVI_fps'
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avi_fps = value;
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case 'Screen_fps'
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screen_fps = value;
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case 'IsFmask'
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is_fmask = value;
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case 'UseFind'
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use_find = value;
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case 'CaptureFigure'
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capture_figure = value;
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otherwise
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vararg{end+1} = name; %#ok<AGROW>
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vararg{end+1} = value; %#ok<AGROW>
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end
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end
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% pass some parameters to image_show
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vararg{end+1} = 'FigNo';
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vararg{end+1} = fig_no;
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image_handle = 0;
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vararg{end+1} = 'ImageHandle';
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vararg{end+1} = image_handle;
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% initialize the list of unhandled parameters
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vararg_remain = cell(0,0);
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% convert the filename to a cell array to use the same loop for single and
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% multiple file names
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if (~iscell(filenames))
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filenames = { filenames };
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end
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% convert single filename to cell array to ease handling
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if (~is_fmask)
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fnames = struct('name',cell(1,1),'isdir',cell(1,1));
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fnames.isdir = false;
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end
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% loop over all filenames or filename masks
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frame_no = 0;
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tic;
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previous_time = toc;
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file_ind_max = length(filenames);
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figure(fig_no);
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hold off;
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clf;
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avi_obj = [];
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for (file_ind = 1:file_ind_max)
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filename = filenames{file_ind};
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if (is_fmask)
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[data_dir,fnames,vararg_remain] = find_files( filename, 'UseFind',use_find );
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if (length(fnames) < 1)
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fprintf('No matching files found for %s.\n',filename);
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continue;
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end
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else
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fnames.name = filename;
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end
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for (fname_ind =1:length(fnames))
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if (~fnames(fname_ind).isdir)
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frame_no = frame_no +1;
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% initialize avi object in case this is the first frame
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if ((write_avi) && (isempty(avi_obj)))
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fprintf('Opening video output file %s, %.1f fps\n',...
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avi_filename,avi_fps);
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avi_obj=VideoWriter(avi_filename);
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avi_obj.FrameRate=avi_fps;
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open(avi_obj);
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end
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% this does currently not work in case of several frames per
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% file
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vararg{end} = image_handle;
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filename = [data_dir fnames(fname_ind).name];
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fi = image_info(filename);
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for (frame_ind = 1:fi.no_of_frames)
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if (frame_ind == 1)
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vararg_mod = vararg;
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vararg_mod{length(vararg_mod)+1} = 'FrameNumber';
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frame_ind_pos = length(vararg_mod)+1;
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vararg_mod{frame_ind_pos} = frame_ind;
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[frame,image_handle] = image_show(filename,vararg_mod);
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% hand over the already read data to image_show for the
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% display of the following frames
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vararg_mod{length(vararg_mod)+1} = 'Frame';
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vararg_mod{length(vararg_mod)+1} = frame;
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else
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vararg_mod{frame_ind_pos} = frame_ind;
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image_show(filename,vararg_mod);
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end
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drawnow;
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% add frame to avi file
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if (write_avi)
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if (capture_figure)
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avi_frame = getframe(fig_no);
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else
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avi_frame = getframe(gca);
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end
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writeVideo(avi_obj,avi_frame);
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end
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% pause in the unlikely case that the screen update is too fast
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if ((~isempty(screen_fps)) && (screen_fps > 0))
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time_now = toc;
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time_remain = 1.0/screen_fps - time_now + previous_time;
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if (time_remain > 0)
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pause(time_remain);
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previous_time = 1.0/screen_fps + previous_time;
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else
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previous_time = time_now;
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end
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end
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end
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end
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end
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end
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% close avi file, if necessary
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if (write_avi)
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close(avi_obj); %#ok<NASGU>
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end
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