Make Tree-Inference run on the currently selected tree only.

src/MATLAB/+Editor/TreeInference.m

@@ -3,8 +3,8 @@
 % 
 % Applies inference to attempt to improve tree structure.
 
-function historyAction = TreeInference()
-    [iters totalTime] = Families.LinkFirstFrameTrees();
+function historyAction = TreeInference(families)
+    [iters totalTime] = Families.LinkTrees(families);
     
     Helper.SweepDeleted();
     

src/MATLAB/+Families/LinkTrees.m

+function [iterations totalTime] = LinkTrees(families)
+    global CellFamilies
+    
+    iterations = 0;
+    
+    rootTrackIDs = [CellFamilies(families).rootTrackID];
+    
+    % Try to Push/reseg
+    totalTime = 0;
+    maxPushCount = 10;
+    for i=1:maxPushCount
+    	[assignExt findTime extTime] = Families.LinkTreesForward(rootTrackIDs);
+%         LogAction(['Tree inference step ' num2str(i)],[assignExt findTime extTime],[]);
+        totalTime = totalTime + findTime + extTime;
+        
+        iterations = i;
+        
+        if ( assignExt == 0 )
+            break;
+        end
+    end
+    
+%     LogAction('Completed Tree Inference', [i totalTime],[]);
+end
\ No newline at end of file

src/MATLAB/+Families/LinkTreesForward.m

 function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
-    global CellHulls HashedCells Costs
+    global CellHulls CellTracks HashedCells Costs
 
     assignedExtensions = 0;
     foundExtensions = 0;
@@ -7,6 +7,20 @@ function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
     findTime = 0;
     extTime = 0;
     
+    rootTracks = unique(getRootTracks(rootTracks));
+    
+    % Initialize mex routine with current cost-graph
+    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);
@@ -16,11 +30,6 @@ function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
 	extGraph = sparse([],[],[], size(Costs,1),size(Costs,1), round(0.01*size(Costs,1)));
     extEnds = sparse([],[],[], size(Costs,1),size(Costs,1), round(0.01*size(Costs,1)));
     
-    costMatrix = Tracker.GetCostMatrix();
-    
-    % Initialize mex routine with current cost-graph
-    mexDijkstra('initGraph', costMatrix);
-    
     chkFindTime = tic();
     UI.Progressbar(0);
     i = 1;
@@ -50,7 +59,6 @@ function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks)
                 for l = 1:length(nextLeaves)
                     trackCost = calcTrackCost(costMatrix, extHulls(j),nextLeaves(l), maxFrameExt);
                     
-                    
                     extendCost = trackCost + pathCost(extIdx(k));
                     extGraph(checkExtHulls(i),nextLeaves(l)) = extendCost;
                     extEnds(checkExtHulls(i),nextLeaves(l)) = pathExt{extIdx(k)}(end);
@@ -121,6 +129,28 @@ 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
     
@@ -324,3 +354,17 @@ function [paths pathCosts] = dijkstraSearch(startHull, costGraph, acceptFunc, ma
         pathCosts(i) = bestCosts(termHulls(i));
     end
 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

src/MATLAB/+UI/CreateMenuBar.m

@@ -355,7 +355,7 @@ function treeInference(src, evt)
     
     currentHull = CellTracks(CellFamilies(Figures.tree.familyID).rootTrackID).hulls(1);
     
-    bErr = Editor.ReplayableEditAction(@Editor.TreeInference);
+    bErr = Editor.ReplayableEditAction(@Editor.TreeInference, Figures.tree.familyID);
     if ( bErr )
         return;
     end