check_stim_dirs

 Creates a directory structure for jlmt_proc_series calculations 

 new_stimlist = check_stim_dirs(stimlist);

 Given a list of paths to stimuli, checks to make sure that there are
 corresponding directories in the destination tree.  At the level of the
 specific stimulus file, a directory is created with the stimulus name.  A
 subdirectory is placed in that directory with the extension for the
 filetype. Within that directory, a symlink is optionally created to the
 original stimulus file. 

 Returns a list of files with the new target path.

 Subsequent analysis directories will be placed at this same level.

 INPUTS
 stimlist - relative paths from srcroot to individual stimuli, passed as a cell array of strings
 srcroot  - (optional) passed in as tag/value pair. Directory where stimuli are stored.
 destroot - (optional) passed in as tag/value pair. Directory where subdirectories for each stim will be created

 OUTPUTS
 new_stimlist - list of symlinks to original stimuli.

 Copyright (c) 2006-2012 The Regents of the University of California
 All Rights Reserved

 December 29, 2006 Petr Janata
 April 30,2008 - Added escaping of irregular directory name
                 characters(space, parenthesis, etc.)
 08Jul2019 - added ability to copy source file from atonal via rsync

0001 function new_stimlist = check_stim_dirs(stimlist,varargin)
0002 % Creates a directory structure for jlmt_proc_series calculations
0003 %
0004 % new_stimlist = check_stim_dirs(stimlist);
0005 %
0006 % Given a list of paths to stimuli, checks to make sure that there are
0007 % corresponding directories in the destination tree.  At the level of the
0008 % specific stimulus file, a directory is created with the stimulus name.  A
0009 % subdirectory is placed in that directory with the extension for the
0010 % filetype. Within that directory, a symlink is optionally created to the
0011 % original stimulus file.
0012 %
0013 % Returns a list of files with the new target path.
0014 %
0015 % Subsequent analysis directories will be placed at this same level.
0016 %
0017 % INPUTS
0018 % stimlist - relative paths from srcroot to individual stimuli, passed as a cell array of strings
0019 % srcroot  - (optional) passed in as tag/value pair. Directory where stimuli are stored.
0020 % destroot - (optional) passed in as tag/value pair. Directory where subdirectories for each stim will be created
0021 %
0022 % OUTPUTS
0023 % new_stimlist - list of symlinks to original stimuli.
0024 %
0025 % Copyright (c) 2006-2012 The Regents of the University of California
0026 % All Rights Reserved
0027 %
0028 % December 29, 2006 Petr Janata
0029 % April 30,2008 - Added escaping of irregular directory name
0030 %                 characters(space, parenthesis, etc.)
0031 % 08Jul2019 - added ability to copy source file from atonal via rsync
0032 
0033 destroot = '';
0034 srcroot = '';
0035 MAKE_SYMLINK = false;
0036 RSYNC = false;
0037 VERBOSE = false;
0038 new_stimlist = {};
0039 
0040 % Process the input arguments
0041 narg = length(varargin);
0042 for iarg = 1:2:narg
0043   switch varargin{iarg}
0044     case {'destroot'}
0045       destroot = varargin{iarg+1};
0046     case {'srcroot'}
0047       srcroot = varargin{iarg+1};
0048       
0049       % Check whether the source is something we need to make an rsync copy
0050       % from. This check is a bit of a hack right now, and should be made
0051       % less machine-specific.
0052       if ~isempty(regexp(srcroot,'atonal.ucdavis.edu','once'))
0053         RSYNC = true;
0054       else
0055         MAKE_SYMLINK = true;
0056       end
0057       
0058       
0059     case {'verbose'}
0060       VERBOSE = varargin{iarg+1};
0061     otherwise
0062       fprintf('check_stim_dirs: Unknown input argument: %s\n', varargin{iarg});
0063   end
0064 end
0065 
0066 if ~iscell(stimlist)
0067   stimlist = {stimlist};
0068 end
0069 
0070 
0071 if(VERBOSE)
0072   fprintf('\nChecking stimulus directories...\n');
0073 end
0074 
0075 check_dir(destroot);
0076 
0077 nstims = length(stimlist);
0078 for istim = 1:nstims
0079   if VERBOSE
0080     fprintf('Stim %d/%d\n', istim,nstims);
0081   end
0082   curr_dir = destroot;
0083   
0084   res = stimlist{istim};
0085   while ~isempty(res)
0086     [tok,res] = strtok(res,filesep);
0087     if ~isempty(res)
0088       curr_dir = fullfile(curr_dir,tok);
0089       check_dir(curr_dir, VERBOSE);
0090     else
0091       [dummy,fname,fext] = fileparts(tok);
0092       curr_dir = fullfile(curr_dir,fname);
0093       check_dir(curr_dir, VERBOSE);  % directory named after the stimulus
0094       
0095       curr_dir = fullfile(curr_dir,fext(2:end));
0096       check_dir(curr_dir, VERBOSE);
0097       
0098       if MAKE_SYMLINK || RSYNC
0099         srcfile = fullfile(srcroot,stimlist{istim});
0100         linkname = fullfile(curr_dir,tok);
0101         if ~exist(linkname) 
0102           srcfile = regexprep(srcfile,'[()'',& ]','\\$0');
0103           linkname_escaped = regexprep(linkname,'[()'',& ]','\\$0');
0104           if MAKE_SYMLINK
0105             unix_str = sprintf('ln -s %s %s >& /dev/null', srcfile, linkname_escaped);
0106           else
0107             unix_str = sprintf('rsync -a "%s" "%s" >& /dev/null', srcfile, linkname);
0108           end
0109           
0110           if VERBOSE
0111             fprintf('%s\n', unix_str);
0112           end
0113           status = unix(unix_str);
0114           
0115         end
0116         new_stimlist(end+1) = {linkname};
0117       end
0118     end
0119   end
0120 end % for istim=