cellDistance and resegComplete fixes

cellDistance - cull in and out edges separately

resegComplete - check for multiple splits on a hull before undoing
   (also ljsFetch->fetch)

thresholdImages - 2 levels for log on sensitivity>1

matlab/+Distance/cellDistance.m

@@ -3,20 +3,37 @@
 function cellDistance(conn,CONSTANTS,t0,t1Range,newCellIDs)
 
 srcCells=Distance.getRangeCells(conn,[],t0,CONSTANTS);
-t1Range=setdiff(t1Range,t0);
-dstCells=Distance.getRangeCells(conn,[],t1Range,CONSTANTS);
-if isempty(srcCells) || isempty(dstCells)
+% first, do from t1->t0
+t1_before=t1Range(t1Range<t0);
+beforeCells=Distance.getRangeCells(conn,[],t1_before,CONSTANTS);
+if isempty(srcCells) || isempty(beforeCells)
     return;
 end
 srcCells=[srcCells.rgCells];
-dstCells=[dstCells.rgCells];
-if isempty(srcCells) || isempty(dstCells)
+beforeCells=[beforeCells.rgCells];
+if isempty(srcCells) || isempty(beforeCells)
     return;
 end
 if ~exist('newCellIDs','var')
     newCellIDs=[];
 end
-dx=Distance.ccDistance(CONSTANTS,srcCells,dstCells,newCellIDs);
+dx=Distance.ccDistance(CONSTANTS,srcCells,beforeCells,newCellIDs);
+% now do from t0->t1 
+t1_after=t1Range(t1Range>t0);
+afterCells=Distance.getRangeCells(conn,[],t1_after,CONSTANTS);
+if isempty(afterCells)
+    return;
+end
+afterCells=[afterCells.rgCells];
+if isempty(afterCells)
+    return;
+end
+if ~exist('newCellIDs','var')
+    newCellIDs=[];
+end
+dx=[dx;Distance.ccDistance(CONSTANTS,srcCells,afterCells,newCellIDs)];
+
+
 
 cmd = ['INSERT OR REPLACE INTO tblDistCC(cellID_src,cellID_dst,cost) values (?, ?, ?)'];
 updateDistance= conn.handle.prepareStatement(cmd);

matlab/+Reseg/reSegmentComplete.m

@@ -11,23 +11,30 @@ function reSegmentComplete(conn,t,CONSTANTS)
 
 % ACK ACK note this also selects previous reseg edits...
 cmd=['SELECT * from tblEditList WHERE userID=0 AND imageFrame=' num2str(t)];
-editQ=ljsFetch(conn,cmd);
+editQ=fetch(conn,cmd);
 if ~isempty(editQ)
     
-    idxUndo = cellfun(@(x) strcmp(x,'undo'),editQ(:,5));
-    idxUndone = [editQ{idxUndo,1}]';
+    idxUndo = cellfun(@(x) strcmp(x,'undo'),editQ.operation);
+    if any(idxUndo)
+        idxUndone = cellfun(@str2double,editQ.arguments(idxUndo),'UniformOutput',false);
+        idxUndone=[idxUndone{:}];
+    else
+        idxUndone=[];
+    end
+    
     for i=1:size(editQ,1)
         if idxUndo(i)
             continue;
         end
-        if intersect(editQ{i,1},idxUndone)
+        if intersect(editQ.editID(i),idxUndone)
             continue
         end
-        cellIDs = editQ{i,6};
-        if ~ischar(cellIDs) || isempty(jsondecode(cellIDs))
+        
+        if ~iscell(editQ.arguments) || ~ischar(editQ.arguments{i}) || isempty(jsondecode(editQ.arguments{i}))
             fprintf('found bad entry in edit list, check database integrity. continuing\n');
             continue;
         end
+        cellIDs = editQ.arguments{i};
         
         % any cells that were the result of a split where cellID=trackID
         % mean those cells weren't tracked. 
@@ -36,14 +43,27 @@ if ~isempty(editQ)
         % then we can't undo the split
         cmd=['SELECT cellID,trackID FROM tblCells where cellID IN ('...
             cellIDs(2:end-1) ') AND cellID=trackID'];
-        mergeQ=ljsFetch(conn,cmd);
+        mergeQ=fetch(conn,cmd);        
         if ~isempty(mergeQ)
+            % make sure this is the last split for mergeQ
+            splitList=editQ.arguments;            
+            splitList=cellfun(@jsondecode,splitList,'UniformOutput',false);            
+            splitList(idxUndo)={0};
+            idSplit=cellfun(@(x) intersect(x,mergeQ.cellID),splitList,'UniformOutput',false);            
+            idSplit=find(cellfun(@length,idSplit));
+            if max(idSplit)>i
+                % this cell was split once (at operation i) and then again
+                % at max(idSplit). Don't undo this split...need to undo the
+                % last one...
+                continue;
+            end
+            
             % we have untracked cells in the split (cellID==trackID)
             % before undoing, check for any of the split cells are in a mitosis
             idSplitStr=['(' cellIDs(2:end-1) ')'];
             cmd=['select * from tblFamilies where cellID_parent in ' idSplitStr...
                 ' or cellID_child1 in ' idSplitStr '  or cellID_child2 in ' idSplitStr];
-            q=ljsFetch(conn,cmd);
+            q=fetch(conn,cmd);
             if ~isempty(q)
                 %  can't undo this split -- one of the splittees is a child
                 continue
@@ -51,7 +71,7 @@ if ~isempty(editQ)
             % ok -- we have untracked cells in the split, and none of the
             % splittees are involved in a mitosis. undo it.
             fprintf(1,'found untracked cells from reseg split -- merging\n');
-            Write.undoEdit(conn,editQ{i,1},0);
+            Write.undoEdit(conn,editQ.editID(i),0);
         end
     end
 

matlab/+Segment/thresholdImages.m

@@ -12,7 +12,7 @@ else
 end
 
 if sensitivity>1 && round(sensitivity)==sensitivity
-    lm=multithresh(imLog,sensitivity);
+    lm=multithresh(imLog,1);
     bwLog=logical(imLog>lm(end));
     bwLog=Segment.aiAreaOpen(bwLog,min_radius_pixels);
     lm=multithresh(im,sensitivity);