Tree inference fixes, relink back once before the inference loop.

src/MATLAB/+Families/LinkTrees.m

 function [iterations totalTime] = LinkTrees(families)
-    global CellFamilies
+    global CellFamilies CellTracks
     
     iterations = 0;
     
     rootTrackIDs = [CellFamilies(families).rootTrackID];
     
+    % Use changelabel to try and extend tracks back to first frame
+    newRootTracks = [];
+    backTracks = rootTrackIDs([CellTracks(rootTrackIDs).startTime] ~= 1);
+    for i=1:length(backTracks)
+        newRootTracks = [newRootTracks linkTreeBack(backTracks(i))];
+    end
+    
+    rootTrackIDs = unique(getRootTracks(union(rootTrackIDs,newRootTracks)));
+    
     % Try to Push/reseg
     totalTime = 0;
     maxPushCount = 10;
@@ -22,3 +31,41 @@ function [iterations totalTime] = LinkTrees(families)
     
 %     LogAction('Completed Tree Inference', [i totalTime],[]);
 end
+
+function newroot = linkTreeBack(rootTrack)
+    global CellTracks
+    
+    costMatrix = Tracker.GetCostMatrix();
+    
+    curTrack = rootTrack;
+    while ( CellTracks(curTrack).startTime > 1 )
+        curHull = CellTracks(curTrack).hulls(1);
+        prevHulls = find(costMatrix(:,curHull) > 0);
+        
+        if ( isempty(prevHulls) )
+            break;
+        end
+        
+        [bestCost bestIdx] = min(costMatrix(prevHulls,curHull));
+        prevTrack = Hulls.GetTrackID(prevHulls(bestIdx));
+        
+        Tracks.ChangeLabel(curTrack, prevTrack);
+        curTrack = getRootTracks(prevTrack);
+    end
+    
+    newroot = curTrack;
+end
+
+function rootTracks = getRootTracks(tracks)
+    global CellTracks CellFamilies
+    
+    rootTracks = [];
+    for i=1:length(tracks)
+        if ( isempty(CellTracks(tracks(i)).startTime) )
+            continue;
+        end
+        
+        familyID = CellTracks(tracks(i)).familyID;
+        rootTracks = [rootTracks CellFamilies(familyID).rootTrackID];
+    end
+end
\ No newline at end of file

src/MATLAB/+Families/LinkTreesForward.m

@@ -13,14 +13,6 @@ function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
     costMatrix = Tracker.GetCostMatrix();
     mexDijkstra('initGraph', costMatrix);
     
-    % Use changelabel to try and extend tracks back to first frame
-    backTracks = rootTracks([CellTracks(rootTracks).startTime] ~= 1);
-    for i=1:length(backTracks)
-        linkTreeBack(backTracks(i));
-    end
-    
-    rootTracks = unique(getRootTracks(rootTracks));
-    
     leafHulls = getLeafHulls(rootTracks);
     tStart = CellHulls(leafHulls(1)).time;
     tEnd = length(HashedCells);
@@ -129,28 +121,6 @@ function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
     extTime = toc(chkExtendTime);
 end
 
-function linkTreeBack(rootTrack)
-    global CellTracks
-    
-    costMatrix = Tracker.GetCostMatrix();
-    
-    curTrack = rootTrack;
-    while ( CellTracks(curTrack).startTime > 1 )
-        curHull = CellTracks(curTrack).hulls(1);
-        prevHulls = find(costMatrix(:,curHull) > 0);
-        
-        if ( isempty(prevHulls) )
-            break;
-        end
-        
-        [bestCost bestIdx] = min(costMatrix(prevHulls,curHull));
-        prevTrack = Hulls.GetTrackID(prevHulls(bestIdx));
-        
-        Tracks.ChangeLabel(curTrack, prevTrack);
-        curTrack = getRootTracks(prevTrack);
-    end
-end
-
 function cost = calcTrackCost(costMatrix, startHull, endHull, maxFrameExt)
     global CellHulls CellTracks