diff --git a/src/MATLAB/AddHashedCell.m b/src/MATLAB/AddHashedCell.m
index a0260fd928c5fe297bc978558d7f9f6216064eb5..d0d3065de4f274c7d4aff2bccaadf9eb8220a4c2 100644
--- a/src/MATLAB/AddHashedCell.m
+++ b/src/MATLAB/AddHashedCell.m
@@ -14,9 +14,13 @@ else
HashedCells{t}(1).trackID = cellTrackID;
else
%if the hullID exists update it, otherwise create the entry
- index = find([HashedCells{t}(:).hullID] == cellHullID);
- if(isempty(index))
- index = length(HashedCells{t}) + 1;
+ if(t>length(HashedCells) || isempty(HashedCells{t}))
+ index = 1;
+ else
+ index = find([HashedCells{t}(:).hullID] == cellHullID);
+ if(isempty(index))
+ index = length(HashedCells{t}) + 1;
+ end
end
HashedCells{t}(index).hullID = cellHullID;
HashedCells{t}(index).trackID = cellTrackID;
diff --git a/src/MATLAB/CombineTrackWithParent.m b/src/MATLAB/CombineTrackWithParent.m
index b55598dfff7ae4be0b025c25c49754c9d0a13ad0..6d1e60707a4eed08f2063825813320520e8da01d 100644
--- a/src/MATLAB/CombineTrackWithParent.m
+++ b/src/MATLAB/CombineTrackWithParent.m
@@ -30,6 +30,9 @@ end
%inherit grandchildren
CellTracks(parentID).childrenTracks = CellTracks(trackID).childrenTracks;
+for i=1:length(CellTracks(parentID).childrenTracks)
+ CellTracks(CellTracks(parentID).childrenTracks(i)).parentTrack = parentID;
+end
%update the endTime of the parent
CellTracks(parentID).endTime = CellTracks(trackID).endTime;
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index 5ce3f1451cc29b296ed0aa1347f188cebc60bf96..8af1d7d45dcb0531292e6039aaa22297a2906951 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -9,8 +9,25 @@ newTrackID = inputdlg('Enter New Label','New Label',1,{num2str(trackID)});
if(isempty(newTrackID)),return,end;
newTrackID = str2double(newTrackID(1));
-if(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
- choice = questdlg('New label does not exist. Do you want this cell and its children dropped from its tree?','Drop Cell?','Yes','Cancel','Cancel');
+%error checking
+if(0>=newTrackID)
+ msgbox(['New label of ' num2str(newTrackID) ' is not a valid number'],'Change Label','warn');
+ return
+elseif(length(CellTracks)<newTrackID || isempty(CellTracks(newTrackID).hulls))
+ choice = questdlg(['Changing ' num2str(trackID) ' to ' num2str(newTrackID) ' will have the same effect as Remove From Tree'],...
+ 'Remove From Tree?','Continue','Cancel','Cancel');
+ switch choice
+ case 'Continue'
+ newLabel = length(CellTracks) + 1;
+ ContextRemoveFromTree(time,trackID);
+ msgbox(['The new cell label is ' num2str(newLabel)],'Remove From Tree','help');
+ return
+ case 'Cancel'
+ return
+ end
+elseif(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
+ choice = questdlg('New label does not exist. Do you want this cell and its children dropped from its tree?',...
+ 'Drop Cell?','Yes','Cancel','Cancel');
switch choice
case 'Yes'
oldFamily = CellTracks(trackID).familyID;
@@ -21,13 +38,15 @@ if(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?'],...
- 'Swap Labels?','Yes','Cancel','Cancel');
+ 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 'Yes'
+ case 'Forward'
SwapTrackLabels(time,trackID,newTrackID);
History('Push');
LogAction('Swapped Labels',trackID,newTrackID);
+ case 'This Frame'
+ SwapHulls(time,trackID,newTrackID);
case 'Cancel'
return
end
diff --git a/src/MATLAB/ContextChangeParent.m b/src/MATLAB/ContextChangeParent.m
index 2172cf5f96957ffc1045a9db0dfd3fc2a94a8e61..6eaf77b9b08d73067947a1b06fdebdb0a8911855 100644
--- a/src/MATLAB/ContextChangeParent.m
+++ b/src/MATLAB/ContextChangeParent.m
@@ -9,6 +9,11 @@ newParentID = inputdlg('Enter New Parent','New Parent',1,{num2str(CellTracks(tra
if(isempty(newParentID)),return,end;
newParentID = str2double(newParentID(1));
+%error checking
+if(0>=newParentID || length(CellTracks)<newParentID || isempty(CellTracks(newParentID).hulls))
+ msgbox(['Parent ' num2str(newParentID) ' is not a valid cell'],'Parent Change','warn');
+ return
+end
if(CellTracks(newParentID).startTime > time)
msgbox(['Parent ' num2str(newParentID) ' comes after ' num2str(trackID) ' consider a different edit.'],'Parent Change','warn');
return
diff --git a/src/MATLAB/ConvertTrackingData.m b/src/MATLAB/ConvertTrackingData.m
index bad774e2072d58db887b1df21f56c50c646ab35d..6ec6b58e3f8161ce8c4b46853be7257f4603511d 100644
--- a/src/MATLAB/ConvertTrackingData.m
+++ b/src/MATLAB/ConvertTrackingData.m
@@ -15,7 +15,7 @@ CONSTANTS.minParentHistoryTimeFrame = 5;
CONSTANTS.minParentFuture = 5;
CONSTANTS.minFamilyTimeFrame = 5;
CONSTANTS.maxFrameDifference = 5;
-CONSTANTS.historySize = 5;
+CONSTANTS.historySize = 50;
CONSTANTS.clickMargin = 500;
Costs = gConnect;
@@ -36,19 +36,48 @@ end
%loop through the data
for i=2:length(objHulls)
- CellHulls(i).time = objHulls(i).t;
- CellHulls(i).points = objHulls(i).pts;
- CellHulls(i).centerOfMass = objHulls(i).COM;
- CellHulls(i).indexPixels = objHulls(i).indPixels;
- CellHulls(i).deleted = 0;
-
- if objHulls(i).inID == 0
- NewCellFamily(i,objHulls(i).t);
- else
- AddHullToTrack(i,[],objHulls(i).inID);
+ if(i<=length(CellHulls)+1 || ~isempty(CellHulls(i).time))
+ addHull(i);
end
+% CellHulls(i).time = objHulls(i).t;
+% CellHulls(i).points = objHulls(i).pts;
+% CellHulls(i).centerOfMass = objHulls(i).COM;
+% CellHulls(i).indexPixels = objHulls(i).indPixels;
+% CellHulls(i).deleted = 0;
+%
+% if objHulls(i).inID == 0
+% NewCellFamily(i,objHulls(i).t);
+% else
+% AddHullToTrack(i,[],objHulls(i).inID);
+% end
end
%create the family trees
ProcessNewborns(1:length(CellFamilies));
+
+ function addHull(num)
+ CellHulls(num).time = objHulls(num).t;
+ CellHulls(num).points = objHulls(num).pts;
+ CellHulls(num).centerOfMass = objHulls(num).COM;
+ CellHulls(num).indexPixels = objHulls(num).indPixels;
+ CellHulls(num).deleted = 0;
+
+ if objHulls(num).inID > length(CellHulls)+1
+ if objHulls(objHulls(num).inID).inID == 0
+ NewCellFamily(num,objHulls(objHulls(num).inID).t);
+ else
+ addHull(objHulls(num).inID);
+ end
+ end
+
+ if objHulls(num).inID == 0
+ NewCellFamily(num,objHulls(num).t);
+ else
+ AddHullToTrack(num,[],objHulls(num).inID);
+ end
+
+ if objHulls(num).outID > length(CellHulls)+1
+ addHull(objHulls(num).outID);
+ end
+ end
end
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 544d213a0434f257c27f8f9a32f4e7cd93161a24..2be7ab2dabf4bfeb38c3cd94d937a1dc39c236b5 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -9,9 +9,23 @@ global Figures
figure(Figures.cells.handle);
Figures.cells.contextMenuHandle = uicontextmenu;
+% Figures.cells.contextMenuLabelHandle = uimenu(Figures.cells.contextMenuHandle,...
+% 'Label', 'Click to Show Which Cell Is Selected',...
+% 'CallBack', @cellSelected);
+
+Figures.cells.removeMenu = uimenu(Figures.cells.contextMenuHandle,...
+ 'Label', 'Remove Mitosis',...
+ 'CallBack', @removeMitosis,...
+ 'Visible', 'off');
+
+uimenu(Figures.cells.contextMenuHandle,...
+ 'Label', 'Add Mitosis',...
+ 'CallBack', @addMitosis);
+
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Change Label',...
- 'CallBack', @changeLabel);
+ 'CallBack', @changeLabel,...
+ 'Separator', 'on');
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Change Parent',...
@@ -66,6 +80,80 @@ uimenu(Figures.cells.contextMenuHandle,...
end
%% Callback functions
+% function cellSelected(src,evnt)
+% %doesn't work, closes context menu
+% global Figures
+% [hullID trackID] = getClosestCell();
+%
+% if(isempty(trackID))
+% set(Figures.cells.contextMenuLabelHandle,'Label','No Cell Selected, Click Closer');
+% else
+% set(Figures.cells.contextMenuLabelHandle,'Label',['Cell: ' num2str(trackID)]);
+% end
+% end
+
+function removeMitosis(src,evnt)
+global CellTracks Figures
+object = get(gco);
+
+if(~strcmp(object.Tag,'SiblingRelationship'))
+ msgbox('Please click on a Relationship line to remove','Not on line','warn');
+ return
+end
+
+choice = questdlg('Which Side to Keep?','Merge With Parent',object.UserData,...
+ num2str(CellTracks(object.UserData).siblingTrack),'Cancel','Cancel');
+switch choice
+ case num2str(object.UserData)
+ remove = CellTracks(object.UserData).siblingTrack;
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).siblingTrack).startTime,...
+ CellTracks(object.UserData).siblingTrack,'yes');
+ case num2str(CellTracks(object.UserData).siblingTrack)
+ remove = object.UserData;
+ newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
+ otherwise
+ return
+end
+History('Push');
+LogAction(['Removed ' num2str(remove) ' from tree'],Figures.tree.familyID,newTree);
+DrawTree(Figures.tree.familyID);
+DrawCells();
+end
+
+function addMitosis(src,evnt)
+global CellTracks Figures
+
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
+
+answer = inputdlg({'Enter Time of Mitosis',['Enter new sibling of ' num2str(trackID)]},...
+ 'Add Mitosis',1,{num2str(Figures.time),''});
+
+if(isempty(answer)),return,end
+
+time = str2double(answer(1));
+siblingTrack = str2double(answer(2));
+
+if(isempty(CellTracks(siblingTrack).hulls))
+ msgbox([answer(2) ' is not a valid cell'],'Not a valid cell','error');
+ return
+end
+if(CellTracks(trackID).startTime>time)
+ msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid child','error');
+ return
+end
+
+oldParent = CellTracks(siblingTrack).parentTrack;
+
+ChangeTrackParent(trackID,time,siblingTrack);
+
+History('Push');
+LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
+
+DrawTree(CellTracks(trackID).familyID);
+DrawCells();
+end
+
function changeLabel(src,evnt)
global Figures
@@ -107,7 +195,7 @@ addHull(num);
end
function removeHull(src,evnt)
-global Figures
+global Figures CellFamilies
[hullID trackID] = getClosestCell();
if(isempty(trackID)),return,end
@@ -115,6 +203,22 @@ if(isempty(trackID)),return,end
RemoveHull(hullID);
History('Push');
LogAction(['Removed hull from track ' num2str(trackID)],hullID,[]);
+
+%if the whole family disapears with this change, pick a diffrent family to
+%display
+if(isempty(CellFamilies(Figures.tree.familyID).tracks))
+ for i=1:length(CellFamilies)
+ if(~isempty(CellFamilies(i).tracks))
+ Figures.tree.familyID = i;
+ break
+ end
+ end
+ DrawTree(Figures.tree.familyID);
+ DrawCells();
+ msgbox(['By removing this hull, the complete tree is no more. Displaying tree rooted at ' num2str(CellFamilies(i).rootTrackID) ' instead'],'Displaying Tree','help');
+ return
+end
+
DrawTree(Figures.tree.familyID);
DrawCells();
end
diff --git a/src/MATLAB/CreateContextMenuTree.m b/src/MATLAB/CreateContextMenuTree.m
index ac1a048c7cc3b43540572c7ad109517a5e35f018..079861618dd11a0875a8dad4729c8cb58e6a1b12 100644
--- a/src/MATLAB/CreateContextMenuTree.m
+++ b/src/MATLAB/CreateContextMenuTree.m
@@ -9,9 +9,18 @@ global Figures
figure(Figures.tree.handle);
Figures.tree.contextMenuHandle = uicontextmenu;
+uimenu(Figures.tree.contextMenuHandle,...
+ 'Label', 'Remove Mitosis',...
+ 'CallBack', @removeMitosis);
+
+uimenu(Figures.tree.contextMenuHandle,...
+ 'Label', 'Add Mitosis',...
+ 'CallBack', @addMitosis);
+
uimenu(Figures.tree.contextMenuHandle,...
'Label', 'Change Label',...
- 'CallBack', @changeLabel);
+ 'CallBack', @changeLabel,...
+ 'Separator', 'on');
uimenu(Figures.tree.contextMenuHandle,...
'Label', 'Change Parent',...
@@ -28,6 +37,86 @@ uimenu(Figures.tree.contextMenuHandle,...
end
%% Callback functions
+function removeMitosis(src,evnt)
+global CellTracks Figures
+object = get(gco);
+if(strcmp(object.Type,'text') || strcmp(object.Marker,'o'))
+ %clicked on a node
+ if(isempty(CellTracks(object.UserData).parentTrack))
+ msgbox('No Mitosis to Remove','Unable to Remove Mitosis','error');
+ return
+ end
+ choice = questdlg('Which Side to Keep?','Merge With Parent',object.UserData,...
+ num2str(CellTracks(object.UserData).siblingTrack),'Cancel','Cancel');
+elseif(object.YData(1)==object.YData(2))
+ %clicked on a horizontal line
+ choice = questdlg('Which Side to Keep?','Merge With Parent',...
+ num2str(CellTracks(object.UserData).childrenTracks(1)),...
+ num2str(CellTracks(object.UserData).childrenTracks(2)),'Cancel','Cancel');
+else
+ %clicked on a vertical line
+ msgbox('Please Click on the Node or the Vertical Edge to Remove Mitosis','Unable to Remove Mitosis','warn');
+ return
+end
+switch choice
+ case num2str(object.UserData)
+ remove = CellTracks(object.UserData).siblingTrack;
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).siblingTrack).startTime,...
+ CellTracks(object.UserData).siblingTrack,'yes');
+ case num2str(CellTracks(object.UserData).siblingTrack)
+ remove = object.UserData;
+ newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
+ case num2str(CellTracks(object.UserData).childrenTracks(1))
+ remove = CellTracks(object.UserData).childrenTracks(2);
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).childrenTracks(2)).startTime,...
+ CellTracks(object.UserData).childrenTracks(2),'yes');
+ case num2str(CellTracks(object.UserData).childrenTracks(2))
+ remove = CellTracks(object.UserData).childrenTracks(1);
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).childrenTracks(1)).startTime,...
+ CellTracks(object.UserData).childrenTracks(1),'yes');
+ otherwise
+ return
+end
+History('Push');
+LogAction(['Removed ' num2str(remove) ' from tree'],Figures.tree.familyID,newTree);
+DrawTree(Figures.tree.familyID);
+DrawCells();
+end
+
+function addMitosis(src,evnt)
+global CellTracks
+trackID = get(gco,'UserData');
+time = get(gca,'CurrentPoint');
+time = round(time(1,2));
+
+answer = inputdlg({'Enter Time of Mitosis',['Enter new sibling of ' num2str(trackID)]},...
+ 'Add Mitosis',1,{num2str(time),''});
+
+if(isempty(answer)),return,end
+
+time = str2double(answer(1));
+siblingTrack = str2double(answer(2));
+
+if(isempty(CellTracks(siblingTrack).hulls))
+ msgbox([answer(2) ' is not a valid cell'],'Not a valid cell','error');
+ return
+end
+if(CellTracks(trackID).startTime>time)
+ msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid child','error');
+ return
+end
+
+oldParent = CellTracks(siblingTrack).parentTrack;
+
+ChangeTrackParent(trackID,time,siblingTrack);
+
+History('Push');
+LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
+
+DrawTree(CellTracks(trackID).familyID);
+DrawCells();
+end
+
function changeLabel(src,evnt)
global CellTracks
trackID = get(gco,'UserData');
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index 2f456f0582f3b6d10150d56aa380561d2810b6ad..4e0e9cd071a28e88baa2de3474a40c70b96295fe 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -85,6 +85,14 @@ labelsMenu = uimenu(...
'Checked', 'on',...
'Accelerator', 'l');
+siblingsMenu = uimenu(...
+ 'Parent', viewMenu,...
+ 'Label', 'Show Sibling Relationships',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @toggleSiblings,...
+ 'Checked', 'off',...
+ 'Accelerator', 'b');
+
playMenu = uimenu(...
'Parent', viewMenu,...
'Label', 'Play',...
@@ -107,6 +115,11 @@ uimenu(...
'Callback', @largestTree,...
'Separator', 'on');
+uimenu(...
+ 'Parent', viewMenu,...
+ 'Label', 'Display Tree...',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @displayTree);
if(strcmp(get(handle,'Tag'),'cells'))
Figures.cells.menuHandles.saveMenu = saveMenu;
@@ -114,12 +127,14 @@ if(strcmp(get(handle,'Tag'),'cells'))
Figures.cells.menuHandles.redoMenu = redoMenu;
Figures.cells.menuHandles.labelsMenu = labelsMenu;
Figures.cells.menuHandles.playMenu = playMenu;
+ Figures.cells.menuHandles.siblingsMenu = siblingsMenu;
else
Figures.tree.menuHandles.saveMenu = saveMenu;
Figures.tree.menuHandles.undoMenu = undoMenu;
Figures.tree.menuHandles.redoMenu = redoMenu;
Figures.tree.menuHandles.labelsMenu = labelsMenu;
Figures.tree.menuHandles.playMenu = playMenu;
+ Figures.tree.menuHandles.siblingsMenu = siblingsMenu;
end
end
@@ -166,6 +181,19 @@ else
end
end
+function toggleSiblings(src,evnt)
+global Figures
+if(strcmp(get(Figures.cells.menuHandles.siblingsMenu, 'Checked'), 'on'))
+ set(Figures.cells.menuHandles.siblingsMenu, 'Checked', 'off');
+ set(Figures.tree.menuHandles.siblingsMenu, 'Checked', 'off');
+ DrawCells();
+else
+ set(Figures.cells.menuHandles.siblingsMenu, 'Checked', 'on');
+ set(Figures.tree.menuHandles.siblingsMenu, 'Checked', 'on');
+ DrawCells();
+end
+end
+
function timeJump(src,evnt)
global Figures HashedCells
answer = inputdlg('Enter Frame Number:','Jump to Time...',1,{num2str(Figures.time)});
@@ -199,3 +227,15 @@ Figures.tree.familyID = maxID;
DrawTree(maxID);
DrawCells();
end
+
+function displayTree(src,evnt)
+global CellTracks
+answer = inputdlg('Enter Tree Containing Cell:','Display Tree',1);
+answer = str2double(answer);
+
+if(0>=answer || isempty(CellTracks(answer).hulls))
+ msgbox([num2str(answer) ' is not a valid cell'],'Not Valid','error');
+ return
+end
+DrawTree(CellTracks(answer).familyID);
+end
diff --git a/src/MATLAB/DrawCells.m b/src/MATLAB/DrawCells.m
index 301da85cb7b20c10398b88bd9ca4ee204d7dc5aa..cf6d15005757822fcb75df6c6ae1368ac1db6d32 100644
--- a/src/MATLAB/DrawCells.m
+++ b/src/MATLAB/DrawCells.m
@@ -33,6 +33,7 @@ end
colormap(gray);
hold all;
+siblingsAlreadyDrawn = [];
%draw labels if turned on
if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
@@ -79,6 +80,14 @@ if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
textColor = 'r';
end
+ %draw connection to sibling
+ if(strcmp(get(Figures.cells.menuHandles.siblingsMenu, 'Checked'),'on'))
+ %if the cell is on the current tree or already drawn
+ if(Figures.tree.familyID == CellTracks(curTrackID).familyID && isempty(find(siblingsAlreadyDrawn==curTrackID, 1)))
+ siblingsAlreadyDrawn = [siblingsAlreadyDrawn drawSiblingsLine(curTrackID,curHullID)];
+ end
+ end
+
%draw outline
plot(CellHulls(curHullID).points(:,1),...
CellHulls(curHullID).points(:,2),...
@@ -104,5 +113,42 @@ if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
'UserData', curTrackID,...
'uicontextmenu', Figures.cells.contextMenuHandle);
end
+elseif(strcmp(get(Figures.cells.menuHandles.siblingsMenu, 'Checked'),'on'))
+ %just draw sibling lines
+ for i=1:length(HashedCells{Figures.time})
+ curHullID = HashedCells{Figures.time}(i).hullID;
+ curTrackID = HashedCells{Figures.time}(i).trackID;
+
+ %if the cell is on the current tree or already drawn
+ if(Figures.tree.familyID == CellTracks(curTrackID).familyID && isempty(find(siblingsAlreadyDrawn==curTrackID, 1)))
+ siblingsAlreadyDrawn = [siblingsAlreadyDrawn drawSiblingsLine(curTrackID,curHullID)];
+ end
+ end
+end
end
+
+function tracksDrawn = drawSiblingsLine(trackID,hullID)
+global Figures CellTracks CellHulls HashedCells
+
+tracksDrawn = [];
+siblingID = CellTracks(trackID).siblingTrack;
+parentID = CellTracks(trackID).parentTrack;
+
+if(isempty(siblingID)),return,end
+
+tracksDrawn = [trackID siblingID];
+
+siblingHullID = [HashedCells{Figures.time}.trackID] == siblingID;
+siblingHullID = [HashedCells{Figures.time}(siblingHullID).hullID];
+
+if(isempty(siblingHullID)),return,end
+
+plot([CellHulls(hullID).centerOfMass(2) CellHulls(siblingHullID).centerOfMass(2)],...
+ [CellHulls(hullID).centerOfMass(1) CellHulls(siblingHullID).centerOfMass(1)],...
+ 'Color', CellTracks(parentID).color.background,...
+ 'UserData', trackID,...
+ 'uicontextmenu', Figures.cells.contextMenuHandle,...
+ 'Tag', 'SiblingRelationship');
+
+set(Figures.cells.removeMenu,'Visible','on');
end
diff --git a/src/MATLAB/DrawTree.m b/src/MATLAB/DrawTree.m
index 9afd693de35fa164300d2bb552b28683d12af661..a05b13cb4d320bf6002025c8152268c9c160f859 100644
--- a/src/MATLAB/DrawTree.m
+++ b/src/MATLAB/DrawTree.m
@@ -5,7 +5,7 @@ function DrawTree(familyID)
global CellFamilies HashedCells Figures
-if(isempty(CellFamilies(familyID).tracks)),return,end
+if(isempty(CellFamilies(familyID).tracks) || (isvarname('Figures.tree.familyID') && familyID==Figures.tree.familyID)),return,end
%let the user know that this might take a while
set(Figures.tree.handle,'Pointer','watch');
diff --git a/src/MATLAB/History.m b/src/MATLAB/History.m
index ed2d84e58f2f1edf1950ad1b25e2fb4890da49a1..1582660cc7daaefc64935c06d91bdb18182e6c18 100644
--- a/src/MATLAB/History.m
+++ b/src/MATLAB/History.m
@@ -163,8 +163,13 @@ end
else
set(Figures.cells.menuHandles.redoMenu,'Enable','off');
set(Figures.tree.menuHandles.redoMenu,'Enable','off');
- set(Figures.cells.menuHandles.undoMenu,'Enable','off');
- set(Figures.tree.menuHandles.undoMenu,'Enable','off');
+ if(~full)
+ set(Figures.cells.menuHandles.undoMenu,'Enable','off');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','off');
+ else
+ set(Figures.cells.menuHandles.undoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','on');
+ end
end
else
diff --git a/src/MATLAB/RehashCellTracks.m b/src/MATLAB/RehashCellTracks.m
index 4e6ef60805c4354dc455ca1529e88de6dbe7f1b1..82c460326094b8bc18cdcb36a77581e9c1e1c4d1 100644
--- a/src/MATLAB/RehashCellTracks.m
+++ b/src/MATLAB/RehashCellTracks.m
@@ -42,4 +42,6 @@ if(indexOfLastHull~=length(CellTracks(trackID).hulls))
end
CellTracks(trackID).startTime = newStartTime;
+
+%check to see if this effects the family
end
diff --git a/src/MATLAB/RemoveHull.m b/src/MATLAB/RemoveHull.m
index 91d039c4fb51b8573194e9aca0ce742846f7b29e..78550a63e77e5934694b5654f1530da6018f6f45 100644
--- a/src/MATLAB/RemoveHull.m
+++ b/src/MATLAB/RemoveHull.m
@@ -14,7 +14,29 @@ index = find(CellTracks(trackID).hulls==hullID);
CellTracks(trackID).hulls(index) = 0;
if(1==index)
index = find(CellTracks(trackID).hulls,1,'first');
- RehashCellTracks(trackID,CellHulls(CellTracks(trackID).hulls(index)).time);
+ if(~isempty(index))
+ RehashCellTracks(trackID,CellHulls(CellTracks(trackID).hulls(index)).time);
+ else
+ if(~isempty(CellTracks(trackID).parentTrack))
+ CombineTrackWithParent(CellTracks(trackID).siblingTrack);
+ end
+ if(~isempty(CellTracks(trackID).childrenTracks))
+ for i=1:length(CellTracks(trackID).childrenTracks)
+ RemoveFromTree(CellTracks(trackID).childrenTracks(i))
+ end
+ end
+ RemoveTrackFromFamily(trackID);
+ CellTracks(trackID).familyID = [];
+ CellTracks(trackID).parentTrack = [];
+ CellTracks(trackID).siblingTrack = [];
+ CellTracks(trackID).childrenTracks = [];
+ CellTracks(trackID).hulls = [];
+ CellTracks(trackID).starTime = [];
+ CellTracks(trackID).endTime = [];
+ CellTracks(trackID).hulls = [];
+ CellTracks(trackID).timeOfDeath = [];
+ CellTracks(trackID).color = [];
+ end
elseif(index==length(CellTracks(trackID).hulls))
RehashCellTracks(trackID,CellTracks(trackID).startTime);
end
diff --git a/src/MATLAB/RemoveTrackFromFamily.m b/src/MATLAB/RemoveTrackFromFamily.m
index cf564045eed8a1ab5fe0e28e18801a2915bfd147..6f2853a9f4de31087c8550412091d956c1e32d51 100644
--- a/src/MATLAB/RemoveTrackFromFamily.m
+++ b/src/MATLAB/RemoveTrackFromFamily.m
@@ -25,4 +25,7 @@ CellFamilies(familyID).endTime = max([CellTracks(CellFamilies(familyID).tracks).
if(CellFamilies(familyID).rootTrackID == trackID)
CellFamilies(familyID).rootTrackID = CellFamilies(familyID).tracks(index);
end
+if(isempty(index))
+ CellFamilies(familyID).tracks = [];
+end
end
diff --git a/src/MATLAB/ResegmentHull.m b/src/MATLAB/ResegmentHull.m
index dc58f94af6c03eecc22ed1f6d719862fea894dcd..9f829ac53bdb372f600856fc3817e96b4a2cf806 100644
--- a/src/MATLAB/ResegmentHull.m
+++ b/src/MATLAB/ResegmentHull.m
@@ -31,7 +31,7 @@ for i=1:k
end
nh.indexPixels = hull.indexPixels(bIdxPix);
- nh.centerOfMass = mean([hx hy]);
+ nh.centerOfMass = mean([hy hx]);
nh.time = hull.time;
try
diff --git a/src/MATLAB/SwapHulls.m b/src/MATLAB/SwapHulls.m
new file mode 100644
index 0000000000000000000000000000000000000000..4ba2d49f727c17464923af61d24adb5362d92e11
--- /dev/null
+++ b/src/MATLAB/SwapHulls.m
@@ -0,0 +1,24 @@
+function SwapHulls(time,track1,track2)
+% SwapHulls(time,track1,track2) will swap the hulls at the given time in
+% the given tracks
+
+global CellTracks HashedCells
+
+track1Hash = time - CellTracks(track1).startTime + 1;
+track2Hash = time - CellTracks(track2).startTime + 1;
+
+if(0>=track1Hash || 0>=track2Hash || ...
+ track1Hash>length(CellTracks(track1).hulls) || track2Hash>length(CellTracks(track2).hulls))
+ return
+end
+
+hull1 = CellTracks(track1).hulls(track1Hash);
+hull2 = CellTracks(track2).hulls(track2Hash);
+CellTracks(track1).hulls(track1Hash) = hull2;
+CellTracks(track2).hulls(track2Hash) = hull1;
+
+index = [HashedCells{time}.hullID]==hull1;
+HashedCells{time}(index).trackID = track2;
+index = [HashedCells{time}.hullID]==hull2;
+HashedCells{time}(index).trackID = track1;
+end
diff --git a/src/MATLAB/SwapTrackLabels.m b/src/MATLAB/SwapTrackLabels.m
index 63fa5fbe3753e9be0bde3704a8390f47bc2b2900..74a1c42682a071f68bba6905928f4a17d7bfc7b3 100644
--- a/src/MATLAB/SwapTrackLabels.m
+++ b/src/MATLAB/SwapTrackLabels.m
@@ -22,6 +22,13 @@ CellTracks(trackID1).hulls = [CellTracks(trackID1).hulls track2Hulls];
CellTracks(trackID2).hulls = [CellTracks(trackID2).hulls track1Hulls];
%update times
+% index = find(CellTracks(trackID1).hulls,1,'first');
+% startTime1 = CellHulls(CellTracks(trackID1).hulls(index)).time;
+% index = find(CellTracks(trackID2).hulls,1,'first');
+% startTime2 = CellHulls(CellTracks(trackID2).hulls(index)).time;
+% RehashCellTracks(trackID1,startTime1);
+% RehashCellTracks(trackID2,startTime2);
+
CellTracks(trackID1).startTime = CellHulls(CellTracks(trackID1).hulls(1)).time;
CellTracks(trackID2).startTime = CellHulls(CellTracks(trackID2).hulls(1)).time;
CellTracks(trackID1).endTime = CellHulls(CellTracks(trackID1).hulls(find([CellTracks(trackID1).hulls]~=0,1,'last'))).time;
@@ -36,10 +43,18 @@ tempChildrenTracks = CellTracks(trackID1).childrenTracks;
CellTracks(trackID1).childrenTracks = CellTracks(trackID2).childrenTracks;
CellTracks(trackID2).childrenTracks = tempChildrenTracks;
+for i=1:length(CellTracks(trackID1).childrenTracks)
+ CellTracks(CellTracks(trackID1).childrenTracks(i)).parentTrack = trackID1;
+end
+for i=1:length(CellTracks(trackID2).childrenTracks)
+ CellTracks(CellTracks(trackID2).childrenTracks(i)).parentTrack = trackID2;
+end
+
+
%check to see if the children have moved to a new family
if(CellTracks(trackID1).familyID ~= CellTracks(trackID2).familyID)
for i=1:length(CellTracks(trackID1).childrenTracks)
- ChangeTrackAndChildrensFamily(CellTracks(trackID2).familyID,CellTracks(trackID1).familyID,CellTracks(trackID1).childrenTracks(i));
+ ChangeTrackAndChildrensFamily(CellTracks(trackID2).familyID,CellTracks(trackID1).familyID,CellTracks(trackID1).childrenTracks(1));
end
for i=1:length(CellTracks(trackID2).childrenTracks)
ChangeTrackAndChildrensFamily(CellTracks(trackID1).familyID,CellTracks(trackID2).familyID,CellTracks(trackID2).childrenTracks(i));