Added read/write code samples from LEVer.

samples/TestReadTrackData.m

+% [objTracks gConnect] = SampleReadTrackData(DatasetDir, DatasetName) - Sample LEVer track data writer.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%    Copyright 2013 Andrew Cohen, Eric Wait and Mark Winter
+% 
+%    This file is part of LEVer - the tool for stem cell lineaging. See
+%    http://bioimage.coe.drexel.edu for details
+% 
+%    LEVer 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.
+% 
+%    LEVer 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 LEVer in file "gnu gpl v3.txt".  If not, see 
+%    <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function [objTracks gConnect] = SampleReadTrackData(DatasetDir, DatasetName)
+global CellHulls
+
+bValidCell = ~[CellHulls.deleted];
+backMap = find(bValidCell);
+
+objTracks = struct('Label',cell(1,length(CellHulls)), 'ccc',cell(1,length(CellHulls)),...
+                   'outID',{0}, 'inID',{0});
+
+fname = fullfile(DatasetDir,['Tracked_' DatasetName '.txt']);
+fid=fopen(fname,'rt');
+bDone=0;
+TrackList=[];
+
+while ~bDone
+    dd=fscanf(fid,'%d,%d,%d\n',3);
+    if -1==dd(1)
+       bDone=1;
+       break
+    end
+    TrackList=[TrackList;dd'];
+end
+
+bDone=0;
+InList=[];
+dd=textscan(fid,'%f,%f,%f');
+InList=[dd{1},dd{2},dd{3}];
+
+fclose(fid);
+
+for i=1:size(TrackList,1)
+    o1 = backMap(TrackList(i,2));
+    o2 = backMap(TrackList(i,3));
+    
+    objTracks(o1).Label=TrackList(i,1);
+    objTracks(o2).Label=TrackList(i,1);
+    objTracks(o1).outID=o2;
+    objTracks(o2).inID=o1;
+end
+
+nLabel=max([objTracks.Label])+1;
+for n=1:length(objTracks)
+    if (objTracks(n).Label>0)
+        continue;
+    end
+    
+    objTracks(n).Label = nLabel;
+    nLabel=nLabel+1;
+end
+
+gConnect=sparse(InList(:,2),InList(:,1),InList(:,3),length(CellHulls),length(CellHulls));
+end
\ No newline at end of file

samples/TestWriteSegData.m

+% SampleWriteSegData(DatasetDir, DatasetName) - Sample LEVer segmentation data writer.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%    Copyright 2013 Andrew Cohen, Eric Wait and Mark Winter
+% 
+%    This file is part of LEVer - the tool for stem cell lineaging. See
+%    http://bioimage.coe.drexel.edu for details
+% 
+%    LEVer 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.
+% 
+%    LEVer 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 LEVer in file "gnu gpl v3.txt".  If not, see 
+%    <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function SampleWriteSegData(DatasetDir, DatasetName)
+global CONSTANTS CellHulls
+
+sz = CONSTANTS.imageSize;
+
+th = max([CellHulls.time]);
+hashedHulls = cell(th,1);
+
+% reset tracking info
+for n=1:length(CellHulls)
+    hashedHulls{CellHulls(n).time} = [hashedHulls{CellHulls(n).time}; n];
+end
+
+fname = fullfile(DatasetDir, ['SegObjs_Test_' DatasetName '.txt']);
+fid=fopen(fname,'wt');
+
+fprintf(fid, '%d %d\n', sz(2), sz(1));
+fprintf(fid, '%d %d\n\n', th, length(CellHulls));
+
+for t=1:length(hashedHulls)
+    fprintf(fid, '%d\n', length(hashedHulls{t}));
+    
+    for i=1:length(hashedHulls{t})
+        [r c]=ind2sub(sz,CellHulls(hashedHulls{t}(i)).indexPixels);
+        
+        COM = mean([c r], 1);
+        fprintf(fid, '%f %f %d:', COM(1), COM(2), length(r));
+        
+        for k=1:length(r)
+            fprintf(fid, ' (%d,%d)', c(k), r(k));
+        end
+        
+        fprintf(fid,'\n');
+    end
+end
+
+fclose(fid);
+end
\ No newline at end of file