trackOptiListNeighbor

 trackOptiListNeighbor : creates a neighbors list for each cell.

 INPUT :
       dirname : seg folder eg. maindirectory/xy1/seg
       CONST : segmentation constants.
       header : string displayed with information
 OUTPUT :
       clist_temp : contains list of neighbors

 Copyright (C) 2016 Wiggins Lab 
 Written by Paul Wiggins.
 University of Washington, 2016
 This file is part of SuperSegger.
 
 SuperSegger is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
 SuperSegger is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
 along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.

0001 function [clist_tmp] = trackOptiListNeighbor(dirname,CONST,header)
0002 % trackOptiListNeighbor : creates a neighbors list for each cell.
0003 %
0004 % INPUT :
0005 %       dirname : seg folder eg. maindirectory/xy1/seg
0006 %       CONST : segmentation constants.
0007 %       header : string displayed with information
0008 % OUTPUT :
0009 %       clist_temp : contains list of neighbors
0010 %
0011 % Copyright (C) 2016 Wiggins Lab
0012 % Written by Paul Wiggins.
0013 % University of Washington, 2016
0014 % This file is part of SuperSegger.
0015 %
0016 % SuperSegger is free software: you can redistribute it and/or modify
0017 % it under the terms of the GNU General Public License as published by
0018 % the Free Software Foundation, either version 3 of the License, or
0019 % (at your option) any later version.
0020 %
0021 % SuperSegger is distributed in the hope that it will be useful,
0022 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0023 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0024 % GNU General Public License for more details.
0025 %
0026 % You should have received a copy of the GNU General Public License
0027 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0028 
0029 if ~exist('header','var')
0030     header = [];
0031 end
0032 
0033 if(nargin<1 || isempty(dirname))
0034     dirname = '.';
0035 end
0036 dirname = fixDir(dirname);
0037 
0038 % Get the track file names...
0039 contents=dir([dirname '*_err.mat']);
0040 if isempty(contents)
0041     disp('trackOptiListNeighbor : No files found');
0042     clist_tmp.data = [];
0043     clist_tmp.def={};
0044     clist_tmp.gate=[];
0045 else
0046     data_c = loaderInternal([dirname,contents(end).name]);
0047     MAX_CELL = max(data_c.regs.ID) + 100;
0048     num_im = numel(contents);
0049     
0050     if CONST.parallel.show_status
0051         h = waitbar( 0, 'Make Neighbor List.');
0052         cleanup = onCleanup( @()( delete( h ) ) );
0053     else
0054         h = [];
0055     end
0056     
0057     clist_tmp = cell( 1, MAX_CELL );
0058     
0059     % loop through all the cells.
0060     for i = 1:num_im
0061         data_c = loaderInternal([dirname,contents(i  ).name]);            
0062         if CONST.parallel.show_status
0063             waitbar(i/num_im,h,['Make Neighbor List--Frame: ',num2str(i),'/',num2str(num_im)]);
0064         else
0065             disp([header, 'Make Neighbor List. frame: ',num2str(i),' of ',num2str(num_im)]);
0066         end
0067 
0068         for j = 1:data_c.regs.num_regs
0069            ID = data_c.regs.ID(j);      
0070            if ID
0071                neigh = data_c.regs.ID( makenat(data_c.regs.neighbors{j}) );
0072                neigh = neigh(logical(neigh));
0073                if ID > MAX_CELL
0074                    clist_tmp{ ID } = [neigh];
0075                else
0076                     clist_tmp{ ID } = [clist_tmp{ID}, neigh];
0077                end
0078            end
0079         end
0080         
0081         
0082     end
0083     
0084     % save the updated err files.
0085     if CONST.parallel.show_status
0086         close(h);
0087     end
0088     
0089    
0090 end
0091 end
0092 
0093 function data = loaderInternal( filename )
0094 data = load( filename );
0095 end