diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..85223e81651b3b3988329852ccbfbf6f788e6c2a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,35 @@
+
+bin/*.c
+bin/*.log
+*.mat
+bin/*.prj
+bin/*.txt
+
+#ignore thumbnails created by windows
+Thumbs.db
+#Ignore files build by Visual Studio
+*.obj
+*.exe
+*.pdb
+*.user
+*.aps
+*.pch
+*.vspscc
+*_i.c
+*_p.c
+*.ncb
+*.suo
+*.tlb
+*.tlh
+*.bak
+*.cache
+*.ilk
+*.log
+src/c/[Bb]in
+src/c/[Dd]ebug*/
+*.lib
+*.sbr
+src/c/obj/
+src/c/[Rr]elease*/
+src/c/_ReSharper*/
+src/c/[Tt]est[Rr]esult*
\ No newline at end of file
diff --git a/bin/CompileLEVer.m b/bin/CompileLEVer.m
new file mode 100644
index 0000000000000000000000000000000000000000..fec620633231ae59caa46b9169a4ae779d5c8c9c
--- /dev/null
+++ b/bin/CompileLEVer.m
@@ -0,0 +1 @@
+mcc -m ../LEVer.m
\ No newline at end of file
diff --git a/src/MATLAB/AddHull.m b/src/MATLAB/AddHull.m
new file mode 100644
index 0000000000000000000000000000000000000000..090b6e82aa6f76b7997ccf65e267e9ff4a2eb24b
--- /dev/null
+++ b/src/MATLAB/AddHull.m
@@ -0,0 +1,57 @@
+function AddHull(num)
+global Figures CellHulls
+
+if(num>6)
+ msgbox('Please limit number of new cells to 6','Add Hull Limit','help');
+ return
+end
+
+[hullID trackID] = GetClosestCell(1);
+clickPt = get(gca,'CurrentPoint');
+
+if ( ~CHullContainsPoint(clickPt(1,1:2), CellHulls(hullID)) )
+ trackID = [];
+end
+
+if(~isempty(trackID))
+ % Try to split the existing hull
+ History('Push');
+ try
+ newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
+ if(isempty(newTracks))
+ msgbox(['Unable to split ' num2str(trackID) ' any further in this frame'],'Unable to Split','help','modal');
+ return
+ end
+ catch errorMessage
+ try
+ ErrorHandeling(['SplitHull(' num2str(hullID) ' ' num2str(num+1) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ LogAction('Split cell',trackID,[trackID newTracks]);
+elseif ( num<2 )
+ % Try to run local segmentation and find a hull we missed or place a
+ % point-hull at least
+ History('Push');
+ try
+ newTrack = AddNewSegmentHull(clickPt(1,1:2));
+ catch errorMessage
+ try
+ ErrorHandeling(['AddNewSegmentHull(clickPt(1,1:2)) -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ LogAction('Added cell',[],newTrack);
+else
+ return;
+end
+
+DrawTree(Figures.tree.familyID);
+DrawCells();
+end
\ No newline at end of file
diff --git a/src/MATLAB/AddNewSegmentHull.m b/src/MATLAB/AddNewSegmentHull.m
index c0533b1419c8bd2f138cffd9fd9cd2bde1871333..e75faa3ebdae598f79907bf249e750ab9e343620 100644
--- a/src/MATLAB/AddNewSegmentHull.m
+++ b/src/MATLAB/AddNewSegmentHull.m
@@ -14,7 +14,7 @@ function newTrackID = AddNewSegmentHull(clickPt)
newHull.time = Figures.time;
newHull.points = round(clickPt);
newHull.centerOfMass = [clickPt(2) clickPt(1)];
- newHull.indexPixels = sub2ind(size(img), clickPt(2), clickPt(1));
+ newHull.indexPixels = sub2ind(size(img), newHull.points(2), newHull.points(1));
else
newHull.time = Figures.time;
newHull.points = newObj.points;
diff --git a/src/MATLAB/CHullContainsPoint.m b/src/MATLAB/CHullContainsPoint.m
index 7292d5cbf87edf195d64f18ee7af20f95b452f2d..45b31b9d014983e26ab194b6576b1033a36b46d0 100644
--- a/src/MATLAB/CHullContainsPoint.m
+++ b/src/MATLAB/CHullContainsPoint.m
@@ -1,5 +1,5 @@
function bInHull = CHullContainsPoint(pt, hulls)
- bInHull = boolean(zeros(length(hulls),1));
+ bInHull = false(length(hulls),1);
for i=1:length(hulls)
@@ -7,17 +7,19 @@ function bInHull = CHullContainsPoint(pt, hulls)
continue;
end
- cvpts = hulls(i).points;
- hullvec = diff(cvpts);
-
- outnrm = [-hullvec(:,2) hullvec(:,1)];
- %outnrm = outnrm ./ sqrt(sum(outnrm.^2,2));
-
- ptvec = cvpts(1:end-1,:) - ones(size(outnrm,1),1)*pt;
- %ptvec = ptvec ./ sqrt(sum(ptvec.^2,2));
-
- chkIn = sign(sum(outnrm .* ptvec,2));
-
- bInHull(i) = all(chkIn >= 0);
+% cvpts = hulls(i).points;
+% hullvec = diff(cvpts);
+%
+% outnrm = [-hullvec(:,2) hullvec(:,1)];
+% %outnrm = outnrm ./ sqrt(sum(outnrm.^2,2));
+%
+% ptvec = cvpts(1:end-1,:) - ones(size(outnrm,1),1)*pt;
+% %ptvec = ptvec ./ sqrt(sum(ptvec.^2,2));
+%
+% chkIn = sign(sum(outnrm .* ptvec,2));
+%
+% bInHull(i) = all(chkIn >= 0);
+
+ bInHull(i) = inpolygon(pt(1), pt(2), hulls(i).points(:,1), hulls(i).points(:,2));
end
end
\ No newline at end of file
diff --git a/src/MATLAB/ChangeTrackParent.m b/src/MATLAB/ChangeTrackParent.m
index 0685e1a3186781ded8ab35df49c24e374ded0371..736aef8c5d811f043b44fd94fc5ae5614e232b77 100644
--- a/src/MATLAB/ChangeTrackParent.m
+++ b/src/MATLAB/ChangeTrackParent.m
@@ -1,9 +1,10 @@
function ChangeTrackParent(parentTrackID,time,childTrackID)
-%This will take the childTrack and connect it to the parent track. It also
-%takes the hulls that exist in the parent track that are come after the
-%childTrack root and makes a new track with said hulls. When finished
-%there should be a new track and the child track that are siblings with the
-%parent track being the parent.
+%ChangeTrackParent(parentTrackID,time,childTrackID) will take the
+%childTrack and connect it to the parent track. It also takes the hulls
+%that exist in the parent track that are come after the childTrack root and
+%makes a new track with said hulls. When finished there should be a new
+%track and the child track that are siblings with the parent track being
+%the parent.
%--Eric Wait
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index 42380afded85939b9e5fc8e628ffcd81696cf81f..5e0f8143ac17dd50ffc14871587cabfbc00bdb05 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -19,7 +19,18 @@ elseif(length(CellTracks)<newTrackID || isempty(CellTracks(newTrackID).hulls))
switch choice
case 'Continue'
newLabel = length(CellTracks) + 1;
- ContextRemoveFromTree(time,trackID);
+ History('Push');
+ try
+ ContextRemoveFromTree(time,trackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['ContextRemoveFromTree(' num2str(time) ' ' num2str(trackID) ' ) -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
msgbox(['The new cell label is ' num2str(newLabel)],'Remove From Tree','help');
return
case 'Cancel'
@@ -37,6 +48,7 @@ elseif(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
catch errorMessage
try
ErrorHandeling(['RemoveFromTree(' num2str(time) ' ' num2str(trackID) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -48,27 +60,38 @@ elseif(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
return
end
elseif(~isempty(find([HashedCells{time}.trackID]==newTrackID,1)))
- choice = questdlg(['Label ' num2str(newTrackID) ' exist on this frame. Would you like these labels to swap from here forward or just this frame?'],...
- 'Swap Labels?','Forward','This Frame','Cancel','Cancel');
- switch choice
- case 'Forward'
+% choice = questdlg(['Label ' num2str(newTrackID) ' exist on this frame. Would you like these labels to swap from here forward or just this frame?'],...
+% 'Swap Labels?','Forward','This Frame','Cancel','Cancel');
+% switch choice
+% case 'Forward'
History('Push');
try
SwapTrackLabels(time,trackID,newTrackID);
catch errorMessage
try
ErrorHandeling(['SwapTrackLabels(' num2str(time) ' ' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
end
end
LogAction('Swapped Labels',trackID,newTrackID);
- case 'This Frame'
- SwapHulls(time,trackID,newTrackID);
- case 'Cancel'
- return
- end
+% case 'This Frame'
+% History('Push');
+% try
+% SwapHulls(time,trackID,newTrackID);
+% catch errorMessage
+% try
+% ErrorHandeling(['SwapHulls(' num2str(time) ' ' num2str(trackID) num2str(newTrackID) ') -- ' errorMessage.message]);
+% catch errorMessage2
+% fprintf(errorMessage2.message);
+% return
+% end
+% end
+% case 'Cancel'
+% return
+% end
elseif(isempty(CellTracks(trackID).parentTrack) && isempty(CellTracks(trackID).childrenTracks) && 1==length(CellTracks(trackID).hulls))
hullID = CellTracks(trackID).hulls(1);
History('Push');
@@ -77,6 +100,7 @@ elseif(isempty(CellTracks(trackID).parentTrack) && isempty(CellTracks(trackID).c
catch errorMessage
try
ErrorHandeling(['AddSingleHullToTrack(' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -90,6 +114,7 @@ elseif(~isempty(CellTracks(trackID).parentTrack) && CellTracks(trackID).parentTr
catch errorMessage
try
ErrorHandeling(['MoveMitosisUp(' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -103,6 +128,7 @@ elseif(~isempty(CellTracks(newTrackID).parentTrack) && CellTracks(newTrackID).pa
catch errorMessage
try
ErrorHandeling(['MoveMitosisUp(' num2str(time) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -116,6 +142,7 @@ else
catch errorMessage
try
ErrorHandeling(['ChangeLabel(' num2str(time) ' ' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
diff --git a/src/MATLAB/ContextChangeParent.m b/src/MATLAB/ContextChangeParent.m
index 3648ed93cef73b22f4d2f58aa1387a3008436a2a..83c0db2da38f8978e8e3d7180e19c23c28ec8c3f 100644
--- a/src/MATLAB/ContextChangeParent.m
+++ b/src/MATLAB/ContextChangeParent.m
@@ -29,6 +29,7 @@ try
catch errorMessage
try
ErrorHandeling(['ChangeTrackParent(' num2str(newParentID) ' ' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
diff --git a/src/MATLAB/ContextRemoveFromTree.m b/src/MATLAB/ContextRemoveFromTree.m
index ce6726cea646da81621b9519c43cf02cc8581e8b..e81d3b85b6e43cec16263f75201ae62932bde64e 100644
--- a/src/MATLAB/ContextRemoveFromTree.m
+++ b/src/MATLAB/ContextRemoveFromTree.m
@@ -12,6 +12,7 @@ try
catch errorMessage
try
ErrorHandeling(['RemoveFromTree(' num2str(time) ' ' num2str(trackID) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
diff --git a/src/MATLAB/ConvertTrackingData.m b/src/MATLAB/ConvertTrackingData.m
index f4890427f47646fb2b711282172640216b125d2b..78f1f72eebab7be8becc23b82f6f5581c0089d90 100644
--- a/src/MATLAB/ConvertTrackingData.m
+++ b/src/MATLAB/ConvertTrackingData.m
@@ -17,6 +17,7 @@ CONSTANTS.minFamilyTimeFrame = 5;
CONSTANTS.maxFrameDifference = 5;
CONSTANTS.historySize = 50;
CONSTANTS.clickMargin = 500;
+CONSTANTS.timeResolution = 10; %in frames per min
Costs = gConnect;
%Initialize Structures
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 1faefc483ce227ef44c1a66eda7f3d4752ad9c19..426a271c4ac5c7ab4b58896ed61dded67b995175 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -103,6 +103,7 @@ switch choice
try
ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).siblingTrack).startTime)...
num2str(CellTracks(object.UserData).siblingTrack) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -115,7 +116,9 @@ switch choice
newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
catch errorMessage
try
- ErrorHandeling(['RemoveFromTree(CellTracks(' num2str(CellTracks(object.UserData).startTime) ' ' num2str(object.UserData) ' yes) -- ' errorMessage.message]);
+ ErrorHandeling(['RemoveFromTree(CellTracks(' num2str(CellTracks(object.UserData).startTime) ' '...
+ num2str(object.UserData) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -130,9 +133,9 @@ DrawCells();
end
function addMitosis(src,evnt)
-global CellTracks Figures
+global CellTracks Figures HashedCells
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
% answer = inputdlg({['Enter new sibling of ' num2str(trackID)],'Enter Time of Mitosis'},...
@@ -146,29 +149,115 @@ if(isempty(answer)),return,end
siblingTrack = str2double(answer(1));
time = Figures.time;
-if(isempty(CellTracks(siblingTrack).hulls))
- msgbox([answer(2) ' is not a valid cell'],'Not a valid cell','error');
+if(siblingTrack>length(CellTracks) || isempty(CellTracks(siblingTrack).hulls))
+ msgbox([answer(1) ' is not a valid cell'],'Not a valid cell','error');
+ return
+end
+if(CellTracks(siblingTrack).endTime<time || siblingTrack==trackID)
+ msgbox([answer(1) ' is not a valid sibling'],'Not a valid sibling','error');
return
end
if(CellTracks(trackID).startTime>time)
msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid child','error');
return
end
+if(~isempty(CellTracks(siblingTrack).timeOfDeath) && CellTracks(siblingTrack).timeOfDeath<=time)
+ msgbox(['Cannot attach a cell to cell ' num2str(siblingTrack) ' beacuse it is dead at this time'],'Dead Cell','help');
+ return
+end
+if(~isempty(CellTracks(trackID).timeOfDeath) && CellTracks(trackID).timeOfDeath<=time)
+ msgbox(['Cannot attach a cell to cell ' num2str(trackID) ' beacuse it is dead at this time'],'Dead Cell','help');
+ return
+end
-oldParent = CellTracks(siblingTrack).parentTrack;
-
-if(CellTracks(trackID).startTime==time)
+if(CellTracks(trackID).startTime==time && CellTracks(siblingTrack).startTime<time)
History('Push');
try
ChangeTrackParent(siblingTrack,time,trackID);
catch errorMessage
try
ErrorHandeling(['ChangeTrackParent(' num2str(siblingTrack) ' ' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ Figures.tree.familyID = CellTracks(siblingTrack).familyID;
+elseif(CellTracks(siblingTrack).startTime==time && CellTracks(trackID).startTime<time)
+ History('Push');
+ try
+ ChangeTrackParent(trackID,time,siblingTrack);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
end
end
+ Figures.tree.familyID = CellTracks(trackID).familyID;
+elseif(CellTracks(siblingTrack).startTime==time && CellTracks(trackID).startTime==time)
+ valid = 0;
+ while(~valid)
+ answer = inputdlg({'Enter parent of these siblings '},'Parent',1,{''});
+ if(isempty(answer)),return,end
+ parentTrack = str2double(answer(1));
+
+ if(CellTracks(parentTrack).startTime>=time || isempty(CellTracks(parentTrack).hulls) ||...
+ (~isempty(CellTracks(parentTrack).timeOfDeath) && CellTracks(parentTrack).timeOfDeath<=time))
+ choice = questdlg([num2str(parentTrack) ' is an invalid parent for these cells, please choose another'],...
+ 'Not a valid parent','Enter a different parent','Cancel','Cancel');
+ switch choice
+ case 'Cancel'
+ return
+ end
+ else
+ valid = 1;
+ end
+ end
+
+ History('Push');
+ if(~isempty(find([HashedCells{time}.trackID]==parentTrack,1)))
+ try
+ SwapTrackLabels(time,trackID,parentTrack);
+ catch errorMessage
+ try
+ ErrorHandeling(['SwapTrackLabels(' num2str(time) ' ' num2str(trackID) ' ' num2str(parentTrack) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ LogAction('Swapped Labels',trackID,parentTrack);
+ else
+ try
+ ChangeLabel(time,trackID,parentTrack);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeLabel(' num2str(time) ' ' num2str(trackID) ' ' num2str(parentTrack) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ end
+
+ try
+ ChangeTrackParent(parentTrack,time,siblingTrack);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(parentTrack) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+ Figures.tree.familyID = CellTracks(parentTrack).familyID;
else
History('Push');
try
@@ -176,23 +265,25 @@ else
catch errorMessage
try
ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
end
end
+ Figures.tree.familyID = CellTracks(trackID).familyID;
end
-LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
+LogAction(['Changed parent of ' num2str(trackID) ' and ' num2str(siblingTrack)],[],[]);
-DrawTree(CellTracks(trackID).familyID);
+DrawTree(Figures.tree.familyID);
DrawCells();
end
function changeLabel(src,evnt)
global Figures
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
ContextChangeLabel(Figures.time,trackID);
@@ -200,39 +291,39 @@ end
function changeParent(src,evnt)
global Figures
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
ContextChangeParent(trackID,Figures.time);
end
function addHull1(src,evnt)
-addHull(1);
+AddHull(1);
end
function addHull2(src,evnt)
-addHull(2);
+AddHull(2);
end
function addHull3(src,evnt)
-addHull(3);
+AddHull(3);
end
function addHull4(src,evnt)
-addHull(4);
+AddHull(4);
end
function addHullOther(src,evnt)
-num = inputdlg('Enter Number of Hulls to Add','Add Hulls',1,{1});
+num = inputdlg('Enter Number of Hulls to Add','Add Hulls',1,{'1'});
if(isempty(num)),return,end;
num = str2double(num(1));
-addHull(num);
+AddHull(num);
end
function removeHull(src,evnt)
global Figures CellFamilies
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
History('Push');
@@ -241,6 +332,7 @@ try
catch errorMessage
try
ErrorHandeling(['RemoveHull(' num2str(hullID) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -271,7 +363,7 @@ end
function markDeath(src,evnt)
global Figures CellTracks
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
CellTracks(trackID).timeOfDeath = Figures.time;
@@ -284,6 +376,7 @@ if(~isempty(CellTracks(trackID).childrenTracks))
catch errorMessage
try
ErrorHandeling(['ProcessNewborns(StraightenTrack(' num2str(trackID) ')-- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -300,78 +393,17 @@ end
function removeFromTree(src,evnt)
global Figures
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
ContextRemoveFromTree(Figures.time,trackID);
end
function properties(src,evnt)
-[hullID trackID] = getClosestCell();
+[hullID trackID] = GetClosestCell(0);
if(isempty(trackID)),return,end
ContextProperties(hullID,trackID);
end
%% Helper functions
-function addHull(num)
-global Figures CellHulls
-
-[hullID trackID] = getClosestCell(num<2);
-clickPt = get(gca,'CurrentPoint');
-
-if ( ~CHullContainsPoint(clickPt(1,1:2), CellHulls(hullID)) )
- trackID = [];
-end
-
-if(~isempty(trackID))
- % Try to split the existing hull
- History('Push');
- try
- newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
- catch errorMessage
- try
- ErrorHandeling(['SplitHull(' num2str(hullID) ' ' num2str(num+1) ') -- ' errorMessage.message]);
- catch errorMessage2
- fprintf(errorMessage2.message);
- return
- end
- end
- LogAction('Split cell',trackID,[trackID newTracks]);
-elseif ( num<2 )
- % Try to run local segmentation and find a hull we missed or place a
- % point-hull at least
- History('Push');
- try
- newTrack = AddNewSegmentHull(clickPt(1,1:2));
- catch errorMessage
- try
- ErrorHandeling(['AddNewSegmentHull(clickPt(1,1:2)) -- ' errorMessage.message]);
- catch errorMessage2
- fprintf(errorMessage2.message);
- return
- end
- end
- LogAction('Added cell',[],newTrack);
-else
- return;
-end
-
-DrawTree(Figures.tree.familyID);
-DrawCells();
-end
-
-function [hullID trackID] = getClosestCell(allowEmpty)
-hullID = FindHull(get(gca,'CurrentPoint'));
-if(0>=hullID)
- if (allowEmpty )
- hullID = [];
- else
- warndlg('Please click closer to the center of the desired cell','Unknown Cell');
- end
- trackID = [];
- return
-end
-trackID = GetTrackID(hullID);
-
-end
diff --git a/src/MATLAB/CreateContextMenuTree.m b/src/MATLAB/CreateContextMenuTree.m
index 63019c70106b5a27f564b1529710396f22d0deb2..25cb6f83cf9a4287d1e0a7bf4e839c1b333b5757 100644
--- a/src/MATLAB/CreateContextMenuTree.m
+++ b/src/MATLAB/CreateContextMenuTree.m
@@ -58,7 +58,10 @@ else
msgbox('Please Click on the Node or the Vertical Edge to Remove Mitosis','Unable to Remove Mitosis','warn');
return
end
+
switch choice
+ case 'Cancel'
+ return
case num2str(object.UserData)
remove = CellTracks(object.UserData).siblingTrack;
History('Push');
@@ -69,6 +72,7 @@ switch choice
try
ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).siblingTrack).startTime) ' '...
num2str(CellTracks(object.UserData).siblingTrack) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -81,7 +85,9 @@ switch choice
newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
catch errorMessage
try
- ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(object.UserData).startTime) ' ' num2str(object.UserData) ' yes) -- ' errorMessage.message]);
+ ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(object.UserData).startTime) ' '...
+ num2str(object.UserData) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -97,6 +103,7 @@ switch choice
try
ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).childrenTracks(2)).startTime) ' '...
num2str(CellTracks(object.UserData).childrenTracks(2)) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -112,6 +119,7 @@ switch choice
try
ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).childrenTracks(1)).startTime) ' '...
num2str(CellTracks(object.UserData).childrenTracks(1)) ' yes) -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
@@ -140,7 +148,7 @@ if(isempty(answer)),return,end
time = str2double(answer(1));
siblingTrack = str2double(answer(2));
-if(isempty(CellTracks(siblingTrack).hulls))
+if(siblingTrack>length(CellTracks) || isempty(CellTracks(siblingTrack).hulls))
msgbox([answer(2) ' is not a valid cell'],'Not a valid cell','error');
return
end
@@ -156,7 +164,9 @@ try
ChangeTrackParent(trackID,time,siblingTrack);
catch errorMessage
try
- ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' '...
+ num2str(siblingTrack) ') -- ' errorMessage.message]);
+ return
catch errorMessage2
fprintf(errorMessage2.message);
return
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index 167fe30bbd09c2a945ee4b001e93fb7ec233dc77..6996080838151aee3b9fa140e56cf3fe2482c91a 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -37,6 +37,7 @@ uimenu(...
saveMenu = uimenu(...
'Parent', fileMenu,...
'Label', 'Save',...
+ 'Separator', 'on',...
'HandleVisibility', 'callback', ...
'Callback', @saveFile,...
'Enable', 'off',...
@@ -53,14 +54,23 @@ uimenu(...
'Label', 'Export Image',...
'Separator', 'on',...
'HandleVisibility', 'callback', ...
- 'Callback', @exportImage);
+ 'Callback', @exportImage,...
+ 'Visible', 'off');
uimenu(...
'Parent', fileMenu,...
'Label', 'Print',...
+ 'Separator', 'on',...
'HandleVisibility', 'callback', ...
'Callback', @printFigure);
+uimenu(...
+ 'Parent', fileMenu,...
+ 'Label', 'Export Movie Tiffs',...
+ 'Separator', 'on',...
+ 'HandleVisibility', 'callback', ...
+ 'Callback', @makeMovie);
+
undoMenu = uimenu(...
'Parent', editMenu,...
'Label', 'Undo',...
@@ -170,8 +180,29 @@ function printFigure(src,evnt)
printdlg;
end
+function makeMovie(src,evnt)
+global CONSTANTS Figures
+choice = questdlg('Please set the zoom that you would like for the duration of the movie. Click OK when accomplished.','Set Zoom','OK','Cancel','OK');
+switch choice
+ case 'Cancel'
+ return
+end
+xLim = get(get(Figures.cells.handle, 'CurrentAxes'),'XLim');
+yLim = get(get(Figures.cells.handle, 'CurrentAxes'),'YLim');
+dim = [floor(xLim(2)-xLim(1)) floor(yLim(2)-yLim(1))];
+answer = inputdlg({'Enter the prefix for the exported files:','Enter Frames Per Second:','Enter X Dimension:','Enter Y Dimension'},...
+ 'Movie Options',1,{CONSTANTS.datasetName,'1',num2str(1024),num2str(384)});%num2str(CONSTANTS.imageSize(2)),num2str(CONSTANTS.imageSize(1))
+if(isempty(answer)),return,end
+
+filename = answer(1);
+try
+ MakeMovie(filename{1},str2double(answer(2)),[str2double(answer(3)) str2double(answer(4))]);
+catch errorMessage
+ disp(errorMessage);
+end
+end
+
function undo(src,evnt)
-History('Push');%put the current state on the stack then go to the previous
History('Pop');
end
diff --git a/src/MATLAB/DrawTree.m b/src/MATLAB/DrawTree.m
index 9afd693de35fa164300d2bb552b28683d12af661..7aca6f234f3e2dab161e66224a0dd1a274743406 100644
--- a/src/MATLAB/DrawTree.m
+++ b/src/MATLAB/DrawTree.m
@@ -3,7 +3,11 @@ function DrawTree(familyID)
%--Eric Wait
-global CellFamilies HashedCells Figures
+global CellFamilies HashedCells Figures CONSTANTS
+
+if(~isfield(CONSTANTS,'timeResolution'))
+ CONSTANTS.timeResolution = 10;
+end
if(isempty(CellFamilies(familyID).tracks)),return,end
@@ -17,20 +21,42 @@ trackID = CellFamilies(familyID).tracks(1);
figure(Figures.tree.handle);
delete(gca);
+% delete(gca);
+% hold off
+%
+% underAxes = axes;
+%
+% set(underAxes,...
+% 'YDir', 'reverse',...
+% 'YLim', [0 length(HashedCells)],...
+% 'Position', [.07 .06 .80 .90],...
+% 'YAxisLocation', 'right',...
+% 'YLim', [0 length(HashedCells)*CONSTANTS.timeResolution/60],...
+% 'XColor', 'w',...
+% 'XTick', [],...
+% 'Box', 'off');
+% ylabel('Time (Hours)');
+% axis off
+
+overAxes = axes;
-set(gca,...
+set(overAxes,...
'YDir', 'reverse',...
'YLim', [0 length(HashedCells)],...
'Position', [.06 .06 .90 .90],...
'XColor', 'w',...
- 'XTick', []);
+ 'XTick', [],...
+ 'Box', 'off');
+% ylabel('Time (Frames)');
hold on
[xMin xCenter xMax] = traverseTree(trackID,0);
-set(gca,...
+% set(underAxes,...
+% 'XLim', [xMin-1 xMax+1]);
+set(overAxes,...
'XLim', [xMin-1 xMax+1]);
-Figures.tree.axesHandle = gca;
+Figures.tree.axesHandle = overAxes;
hold off
UpdateTimeIndicatorLine();
diff --git a/src/MATLAB/ErrorHandeling.m b/src/MATLAB/ErrorHandeling.m
index 8b665bcad77813aec1278ecd72870ab3c8a9cd2a..35b41df9859e979febc29b87067452463aeba082 100644
--- a/src/MATLAB/ErrorHandeling.m
+++ b/src/MATLAB/ErrorHandeling.m
@@ -12,7 +12,7 @@ History('Pop');
History('Redo');%this is to get to the state just before the error, it was on the top of the stack
msgboxHandle = msgbox('Attempting to fix database. Will take some time depending on the size of the database. This window will close when done',...
- 'Fixing Database','help','modal');
+ 'Fixing Database','warn','modal');
LogAction(errorMessage,[],[]);
%let the user know that this might take a while
diff --git a/src/MATLAB/GetClosestCell.m b/src/MATLAB/GetClosestCell.m
new file mode 100644
index 0000000000000000000000000000000000000000..340f2cd403a0a175e4f8fd16c6e827cd47f71559
--- /dev/null
+++ b/src/MATLAB/GetClosestCell.m
@@ -0,0 +1,14 @@
+function [hullID trackID] = GetClosestCell(allowEmpty)
+hullID = FindHull(get(gca,'CurrentPoint'));
+if(0>=hullID)
+ if (allowEmpty )
+ hullID = [];
+ else
+ warndlg('Please click closer to the center of the desired cell','Unknown Cell');
+ end
+ trackID = [];
+ return
+end
+trackID = GetTrackID(hullID);
+
+end
\ No newline at end of file
diff --git a/src/MATLAB/GetPixelSize.m b/src/MATLAB/GetPixelSize.m
new file mode 100644
index 0000000000000000000000000000000000000000..eb6c6618eac217fc36c73de2667c01549475e77b
--- /dev/null
+++ b/src/MATLAB/GetPixelSize.m
@@ -0,0 +1,12 @@
+function pixSz = GetPixelSize(axisHandle)
+
+%--Mark Winter
+
+ oldUnits = get(axisHandle, 'Units');
+ set(axisHandle, 'Units','pixels');
+
+ pos = get(axisHandle, 'Position');
+ set(axisHandle, 'Units',oldUnits);
+
+ pixSz = pos(3:4);
+end
\ No newline at end of file
diff --git a/src/MATLAB/InitializeFigures.m b/src/MATLAB/InitializeFigures.m
index 64d28f9e90d811eb8b29300623f23d2dcd47573e..835b86ed5ccb3e0e2be2bb3855f5fe2092996c53 100644
--- a/src/MATLAB/InitializeFigures.m
+++ b/src/MATLAB/InitializeFigures.m
@@ -127,6 +127,8 @@ if(strcmp(get(Figures.cells.handle,'SelectionType'),'normal'))
return
end
set(Figures.cells.handle,'WindowButtonUpFcn',@figureCellUp);
+elseif(strcmp(get(Figures.cells.handle,'SelectionType'),'extend'))
+ AddHull(1);
end
if(strcmp(Figures.advanceTimerHandle.Running,'on'))
TogglePlay(src,evnt);
@@ -134,17 +136,36 @@ end
end
function figureCellUp(src,evnt)
-global Figures HashedCells CellTracks
+global Figures CellTracks
+
+set(Figures.cells.handle,'WindowButtonUpFcn','');
if(Figures.cells.currentHullID == -1)
return
end
-trackID = [HashedCells{Figures.time}(:).hullID]==Figures.cells.currentHullID;
-trackID = HashedCells{Figures.time}(trackID).trackID;
-if(CellTracks(trackID).familyID~=Figures.tree.familyID)
- DrawTree(CellTracks(trackID).familyID);
- DrawCells();
+
+currentHullID = FindHull(get(gca,'CurrentPoint'));
+previousTrackID = GetTrackID(Figures.cells.currentHullID);
+
+if(currentHullID~=Figures.cells.currentHullID)
+ History('Push')
+ try
+ SwapTrackLabels(Figures.time,GetTrackID(currentHullID),previousTrackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['SwapTrackLabels(' num2str(Figures.time) ' ' num2str(GetTrackID(currentHullID))...
+ ' ' num2str(previousTrackID) ') -- ' errorMessage.message]);
+ return
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+elseif(CellTracks(previousTrackID).familyID==Figures.tree.familyID)
+ %no change and the current tree contains the cell clicked on
+ return
end
-set(Figures.cells.handle,'WindowButtonUpFcn','');
+DrawTree(CellTracks(previousTrackID).familyID);
+DrawCells();
end
function figureTreeDown(src,evnt)
diff --git a/src/MATLAB/LEVer.m b/src/MATLAB/LEVer.m
index 64cc06cfc088fee13def8d3b9f0f8af219650957..7a9767a52fe34ac44131354cc6206fa8dc219df6 100644
--- a/src/MATLAB/LEVer.m
+++ b/src/MATLAB/LEVer.m
@@ -8,13 +8,17 @@ global Figures
%if LEVer is already opened, save state just in case the User cancels the
%open
if(~isempty(Figures))
+ saveEnabled = strcmp(get(Figures.cells.menuHandles.saveMenu,'Enable'),'on');
History('Push');
+ if(~saveEnabled)
+ set(Figures.cells.menuHandles.saveMenu,'Enable','off');
+ end
end
if(OpenData())
InitializeFigures();
History('Init');
-else %if(~isempty(Figures))
+elseif(~isempty(Figures))
History('Pop');
DrawTree(Figures.tree.familyID);
DrawCells();
diff --git a/src/MATLAB/MakeMovie.m b/src/MATLAB/MakeMovie.m
new file mode 100644
index 0000000000000000000000000000000000000000..3f91c97452b40e339750cf700ebcf0c643320867
--- /dev/null
+++ b/src/MATLAB/MakeMovie.m
@@ -0,0 +1,70 @@
+function MakeMovie(filename, fps, outRes)
+
+%--Mark Winter
+
+global CONSTANTS Figures HashedCells;
+
+axHandles = [get(Figures.cells.handle, 'CurrentAxes') get(Figures.tree.handle, 'CurrentAxes')];
+
+lims.cells = [get(axHandles(1), 'XLim'); get(axHandles(1), 'YLim')];
+lims.tree = [get(axHandles(2), 'XLim'); get(axHandles(2), 'YLim')];
+
+figpos.cells = get(Figures.cells.handle, 'Position');
+figpos.tree = get(Figures.tree.handle, 'Position');
+
+spc = 10;
+set(axHandles(2), 'YLim', [lims.tree(2,1)-spc lims.tree(2,2)+spc]);
+
+cellSz = GetPixelSize(axHandles(1));
+cellApsect = cellSz(1) / cellSz(2);
+
+treeSz = GetPixelSize(axHandles(2));
+treeApsect = treeSz(1) / treeSz(2);
+
+outCellSz = floor([outRes(2)*cellApsect outRes(2)]);
+outTreeSz = [outRes(1)-outCellSz(1) outRes(2)];
+
+oldtime = Figures.time;
+
+% movfile = avifile(fname, 'Compression','cinepak', 'fps',fps);
+
+if ( ~exist(filename,'dir') )
+ mkdir(filename);
+end
+
+save(fullfile(filename,'params.mat'), 'outRes', 'lims');
+
+% set(axHandles(1), 'XLim', [1 );
+
+for t=1:length(HashedCells)
+ Figures.time = t;
+
+ set(Figures.cells.timeLabel,'String',['Time: ' num2str(Figures.time)]);
+ set(Figures.tree.timeLabel,'String',['Time: ' num2str(Figures.time)]);
+ UpdateTimeIndicatorLine();
+ SetPixelSize(axHandles(2), outTreeSz);
+ treeFrm = getframe(axHandles(2));
+
+ DrawCells();
+ SetPixelSize(axHandles(1), outCellSz);
+ cellFrm = getframe(axHandles(1));
+
+ fullFrm = cellFrm;
+ fullFrm.cdata = [cellFrm.cdata(1:outCellSz(2),1:outCellSz(1),:) treeFrm.cdata(1:outTreeSz(2),1:outTreeSz(1),:)];
+
+ imwrite(fullFrm.cdata, fullfile(filename,[filename '_' num2str(t,'%04d') '.tif']), 'tif');
+
+ % movfile = addframe(movfile,fullFrame);
+end
+
+% movfile = close(movfile);
+
+Figures.time = oldtime;
+set(Figures.cells.timeLabel,'String',['Time: ' num2str(Figures.time)]);
+set(Figures.tree.timeLabel,'String',['Time: ' num2str(Figures.time)]);
+
+set(Figures.cells.handle, 'Position',figpos.cells);
+set(Figures.tree.handle, 'Position',figpos.tree);
+UpdateTimeIndicatorLine();
+DrawCells();
+end
\ No newline at end of file
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index 7b4f4082cf3ef6071f5b38c2f2e8106514ddceb8..e25f185e07d77748b9e636859e7d61d5508d3e9e 100644
--- a/src/MATLAB/OpenData.m
+++ b/src/MATLAB/OpenData.m
@@ -7,7 +7,7 @@ function opened = OpenData()
global Figures Colors CONSTANTS CellFamilies CellHulls HashedCells Costs CellTracks
if(isempty(Figures))
- fprintf('LEVer ver 3.6\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 3.7\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
@@ -38,6 +38,24 @@ imageDataset = [];
goodLoad = 0;
opened = 0;
+if(~isempty(Figures))
+ if(strcmp(get(Figures.cells.menuHandles.saveMenu,'Enable'),'on'))
+ choice = questdlg('Save current edits before opening new data?','Closing','Yes','No','Cancel','Cancel');
+ switch choice
+ case 'Yes'
+ SaveData();
+ set(Figures.cells.menuHandles.saveMenu,'Enable','off');
+ case 'Cancel'
+ return
+ case 'No'
+ set(Figures.cells.menuHandles.saveMenu,'Enable','off');
+ otherwise
+ return
+ end
+ end
+end
+
+oldCONSTANTS = CONSTANTS;
% .mat file handling
while(~goodLoad)
fprintf('Select .mat data file...\n');
@@ -92,7 +110,10 @@ imageFilter = [settings.imagePath '*' CONSTANTS.datasetName '*.TIF'];
while (filterIndexImage==0)
fprintf('\nSelect first .TIF image...\n\n');
[imageFile,imagePath,filterIndexImage] = uigetfile(imageFilter,['Open First Image in dataset: ' CONSTANTS.datasetName]);
- if (filterIndexImage==0),return,end
+ if (filterIndexImage==0)
+ CONSTANTS = oldCONSTANTS;
+ return
+ end
end
index = strfind(imageFile,'t');
@@ -106,7 +127,10 @@ end
while (isempty(index) || ~exist(fileName,'file'))
fprintf(['Image file name not in correct format: ' CONSTANTS.datasetName '_t001.TIF\nPlease choose another...\n']);
[imageFile,imagePath,filterIndexImage] = uigetfile(settings.imagePath,'Open First Image');
- if(filterIndexImage==0),return,end
+ if(filterIndexImage==0)
+ CONSTANTS = oldCONSTANTS;
+ return
+ end
index = strfind(imageFile,'t');
CONSTANTS.rootImageFolder = [imgPath '\'];
imageDataset = imageFile(1:(index(length(index))-2));
diff --git a/src/MATLAB/PartialImageSegment.m b/src/MATLAB/PartialImageSegment.m
index 010ad7970ae4562f38bc6297e11b2b8486ff033f..73838a4e6351f3c2f19193ab3e2bf33e56574fe8 100644
--- a/src/MATLAB/PartialImageSegment.m
+++ b/src/MATLAB/PartialImageSegment.m
@@ -172,6 +172,46 @@ function hull = PartialImageSegment(img, centerPt, subSize, alpha)
no.Eccentricity=stats(idx(i)).Eccentricity;
objs = [objs no];
end
+
+ % bright interiors
+ igm=bwig|bwHalo;
+ se=strel('square',5);
+ igm=imclose(igm,se);
+ igm=imfill(igm,'holes');
+ igm(logical(bwCellFG))=0;
+ se=strel('square',13);
+ igm=imerode(igm,se);
+
+ CC = bwconncomp(igm,8);
+ Ligm = labelmatrix(CC);
+ stats = regionprops(CC, 'Area','Eccentricity');
+ idx = find( [stats.Area] >25 & [stats.Area] <1000 & [stats.Eccentricity]<.95 ) ;
+ for i=1:length(idx)
+ pix = find(Ligm==idx(i));
+ [r c] = ind2sub(size(subImg),pix);
+ ch = convhull(r,c);
+
+ bwPoly = poly2mask(c(ch),r(ch),size(subImg,1),size(subImg,2));
+ if length(find(bwCellFG & bwPoly))
+ continue;
+ end
+
+ glc = c + coordMin(1);
+ glr = r + coordMin(2);
+
+ no=[];
+
+ no.points=[glc(ch),glr(ch)];
+ no.centerOfMass = mean([glr glc]);
+
+ no.indexPixels = sub2ind(imSize,[glr glc]);
+ no.imagePixels=img(no.indexPixels);
+
+ no.ID=-1;
+ no.BrightInterior=1;
+ no.Eccentricity=stats(idx(i)).Eccentricity;
+ objs=[objs no];
+ end
bInHull = CHullContainsPoint(centerPt, objs);
diff --git a/src/MATLAB/ProcessNewborns.m b/src/MATLAB/ProcessNewborns.m
index 74c253f737e373eb0de0e86721f338543b69141e..86fecd5b7438745ecb83eb49dc93e36095d771d6 100644
--- a/src/MATLAB/ProcessNewborns.m
+++ b/src/MATLAB/ProcessNewborns.m
@@ -54,6 +54,7 @@ for i=1:size
if(isempty(parentTrackID))
try
ErrorHandeling(['GetTrackID(' num2str(parentHullID) ') -- while in ProcessNewborns']);
+ return
catch errorMessage2
fprintf(errorMessage2);
return
diff --git a/src/MATLAB/RemoveChildren.m b/src/MATLAB/RemoveChildren.m
index 43e6be64c13fe2bbdf710a2e18aed48cbad74ab2..99ee3985cf2acf83d5e4d492d47136000f7702c4 100644
--- a/src/MATLAB/RemoveChildren.m
+++ b/src/MATLAB/RemoveChildren.m
@@ -14,5 +14,5 @@ end
CellTracks(trackID).childrenTracks = [];
%run processNewborns on them
-ProcessNewborns(familyIDs);
+% ProcessNewborns(familyIDs);
end
diff --git a/src/MATLAB/SetPixelSize.m b/src/MATLAB/SetPixelSize.m
new file mode 100644
index 0000000000000000000000000000000000000000..addcca60659e096262123a1aa3ec4a0244307bd6
--- /dev/null
+++ b/src/MATLAB/SetPixelSize.m
@@ -0,0 +1,23 @@
+function SetPixelSize(axisHandle, pixSz)
+
+%--Mark Winter
+
+ parentHandle = get(axisHandle, 'Parent');
+ if ( ~ishandle(parentHandle) )
+ return
+ end
+
+ oldUnits = get(axisHandle, 'Units');
+ set(axisHandle, 'Units','pixels');
+
+ curPos = get(axisHandle, 'Position');
+ newPos = [curPos(1:2) pixSz];
+
+ %figPos = get(parentHandle, 'Position');
+ figPos = [1 1 (2*newPos(1:2)+newPos(3:4))];
+
+ set(parentHandle, 'Position',figPos);
+ set(axisHandle, 'Position',newPos);
+
+ set(axisHandle, 'Units',oldUnits);
+end
\ No newline at end of file
diff --git a/src/MATLAB/SplitHull.m b/src/MATLAB/SplitHull.m
index b2586ef4a2bb8ddc00fe54a243fe0679ab232ca5..1d01f1aa269bfe2dae916da674dbcb5c080e026b 100644
--- a/src/MATLAB/SplitHull.m
+++ b/src/MATLAB/SplitHull.m
@@ -9,6 +9,7 @@ global CellHulls CellFamilies
newHulls = ResegmentHull(CellHulls(hullID), k);
if ( isempty(newHulls) )
+ newTrackIDs = [];
return;
end
diff --git a/src/MATLAB/TestDataIntegrity.m b/src/MATLAB/TestDataIntegrity.m
index 4d5d189d87737d0ab1f1cd8f2b5be4f3156a096c..2f73721a3f61f9e97d2d1da8eee7bdc10ba6b24d 100644
--- a/src/MATLAB/TestDataIntegrity.m
+++ b/src/MATLAB/TestDataIntegrity.m
@@ -123,4 +123,6 @@ if(~isempty(missingHulls))
end
error('HullsList ~= CellHulls');
end
+
+fprintf('\n');
end