ljsNProcs, patch updates

matlab/+Batch/batchSegment.m

@@ -5,7 +5,11 @@ if ~exist('bTrack','var')
 end
 
 if ~exist('nProcessors','var') || isempty(nProcessors)
-    nProcessors=feature('numcores');
+    nProcessors=ljsNProcs();
+% c=parcluster('local')
+% c.NumWorkers=nProcessors
+
+% saveProfile(c)
 end
 % batch segmentation
 d0=tic();

matlab/+Batch/processMovie.m

@@ -11,7 +11,8 @@ tProcess.tTrack1=toc(tx);
 
 [conn,CONSTANTS]=openDB(strDB);
 tx=tic();
-Smooth.Patch.patch(conn);
+Smooth.Patch.patch11(conn);
+Smooth.Patch.patch12(conn);
 tProcess.tPatch=toc(tx);
 
 tx=tic();
@@ -20,6 +21,6 @@ Smooth.extFamily(conn);
 tProcess.tClassify=toc(tx);
 tx=tic();
 Batch.batchFeatures(conn,CONSTANTS);
-tProcess.tFeatures=toc();
+tProcess.tFeatures=toc(tx);
 
 close(conn)

matlab/+Distance/movieDistance.m

@@ -14,7 +14,7 @@ updateDistance= conn.handle.prepareStatement(cmd);
 conn.AutoCommit='off';
 
 if ~exist('nProcessors','var') || isempty(nProcessors)
-    nProcessors=feature('numcores');
+    nProcessors=ljsNProcs();
 end
 p=gcp('nocreate');
 if isempty(p) || p.NumWorkers~=nProcessors

matlab/+Smooth/+Patch/patch.m

 function patch(conn)
 
-cmd='select cellID_child1 as cellID from tblFamilies union select cellID_child2 as cellID from tblFamilies';
-qChildren=fetch(conn,cmd);
-cidChildren=qChildren.cellID;
 
-cmd='select cellID_parent from tblFamilies';
-qParents=fetch(conn,cmd);
-cidParents=qParents.cellID_parent;
+Smooth.Patch.patch11(conn);
 
-Smooth.Patch.patch11(conn,cidChildren);
-Smooth.Patch.patch12(conn,cidParents,cidChildren);

matlab/+Smooth/+Patch/patch11.m

@@ -2,7 +2,7 @@
 % sometimes the tracker makes decisions based on longer time projections
 % if those fail, we fall back on the original single frame true love
 % (1st choice ccDistance <-> 1st choice ccDistance)
-function patch11(conn,cidChildren)
+function patch11(conn)
 
 cmd=['select cellID,trackID,max(time) as tmax from tblCells  '...
     ' where trackID not in (select trackID from tblCells inner join tblFamilies'...
@@ -17,16 +17,12 @@ cmd=['select cellID_src,cellID_dst,min(cost) from tblDistCC where cellID_src in
     cidList ' group by cellID_src'];
 qSrcCosts=fetch(conn,cmd);
 
-cmd=['select cellID_src,cellID_dst,trackID as trackID_dst,min(cost),time as time_dst '...
-    '  from tblCells inner join tblDistCC on cellID=cellID_dst where cellID_src in '...
-    cidList ' group by cellID_dst'];
+cmd=['select * from (select cellID_src,cellID_dst,trackID as trackID_dst,min(cost),time as time_dst '...
+    '  from tblCells inner join tblDistCC on cellID=cellID_dst group by cellID_dst)'...
+    ' where cellID_src in ' cidList];
 qPatch=fetch(conn,cmd);
 qPatch(qPatch.cellID_dst~=qPatch.trackID_dst,:)=[];
 for i=1:length(qPatch.cellID_src)       
-    if ~isempty(intersect(cidChildren,qPatch.cellID_dst(i)))
-        % can't patch to a mitotic child
-        continue;
-    end
     % check src costs. true love?
     idxSrcCosts=find(qSrcCosts.cellID_src==qPatch.cellID_src(i));
     if qSrcCosts.cellID_dst(idxSrcCosts)~=qPatch.cellID_dst(i)

matlab/+Smooth/+Patch/patch12.m

 % the second chance patcher
 % here, eligible tracks can get assigned their 1st choice, even if  they
 % are the corresponding 2nd choice
-function patch12(conn,cidParents,cidChildren)
+function patch12(conn)
+
+cmd='select cellID_child1 as cellID from tblFamilies union select cellID_child2 as cellID from tblFamilies';
+qChildren=fetch(conn,cmd);
+cidChildren=qChildren.cellID;
+
+cmd='select cellID_parent from tblFamilies';
+qParents=fetch(conn,cmd);
+cidParents=qParents.cellID_parent;
 
 % patch src's are leaf nodes on the tree
 % patch dst's are parent nodes on the tree
@@ -19,6 +27,21 @@ for i=1:length(qSrc.cellID_dst)
     if isempty(qTarget)
         continue;
     end    
+    
+    if qTarget.min_cost_(1)<qSrc.min_cost_(i)
+        % src(1:dst.tmin-1)->dst(1:end)
+        % reset src(dst.tmin:end) 
+        cmd=['update tblCells set trackID=cellID' ...
+            ' where trackID=' num2str(qTarget.trackID_src(1)) ...
+            ' and time>=' num2str(qTarget.time_dst(1))];
+        exec(conn,cmd);
+        % set src(dst.tmin:end)->dst
+        cmd=['update tblCells set trackID=' num2str(qTarget.trackID_src(1))...
+            ' where trackID=' num2str(qTarget.trackID_dst(1)) ...
+            ' and time>=' num2str(qTarget.time_dst(1))];
+        exec(conn,cmd);        
+    else
+        % src(1:end)->target(src.tmax)+1:end
         cmd=['update tblCells set trackID=(select trackID from tblCells where '...
             ' cellID=' num2str(qSrc.cellID_src(i)) ') where trackID= '...
             ' (select trackID from tblCells where cellID=' ...
@@ -26,7 +49,7 @@ for i=1:length(qSrc.cellID_dst)
             ' tblCells where trackID=(select trackID from tblCells where cellID='...
             num2str(qSrc.cellID_src(i)) '))'];        
         exec(conn,cmd);
-    
+    end    
 end
 
 function qTarget=getPatchTarget(conn,qSrc)

matlab/+Smooth/extFamily.m

 function extFamily(conn)
 
+exec(conn,'delete from uiExtFamilies');
 extParams=Read.getExtFamilyParams(conn);
 if extParams.firstFrame
     cmd=['insert or replace into uiExtFamilies select trackID from (select trackID from tblCells where time=1)'];
@@ -14,3 +15,10 @@ if extParams.nFrames>0
         ' where trackLength>' num2str(extParams.nFrames)];
     exec(conn,cmd);
 end
+% add mitotic events
+cmd=['insert or replace into uiExtFamilies(trackID) select trackID from '...
+    ' tblCells inner join tblFamilies on cellID=cellID_parent union select '...
+    ' trackID from tblCells inner join tblFamilies on cellID=cellID_child1 '...
+    ' union select trackID from tblCells inner join tblFamilies on cellID=cellID_child2'];
+exec(conn,cmd);
+    

matlab/ljsNProcs.m

+
+function nProcessors=ljsNProcs()
+
+nProcessors=floor(1.5*feature('numcores'));
\ No newline at end of file