From f9f8ff2065a013b479c63ef5e96fe8a93dbcbbbb Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Fri, 8 Apr 2011 22:25:59 -0500
Subject: [PATCH] LEVer 3.6
---
src/MATLAB/ChangeLabel.m | 12 ++
src/MATLAB/ChangeTrackAndChildrensFamily.m | 2 +-
src/MATLAB/ChangeTrackParent.m | 21 +--
src/MATLAB/ContextChangeLabel.m | 73 ++++++++--
src/MATLAB/ContextChangeParent.m | 12 +-
src/MATLAB/ContextRemoveFromTree.m | 12 +-
src/MATLAB/CreateContextMenuCells.m | 151 ++++++++++++++-------
src/MATLAB/CreateContextMenuTree.m | 83 ++++++++---
src/MATLAB/CreateMenuBar.m | 24 ++++
src/MATLAB/DrawCells.m | 9 +-
src/MATLAB/ErrorHandeling.m | 40 ++++++
src/MATLAB/GetTrackID.m | 15 +-
src/MATLAB/InitializeFigures.m | 3 +
src/MATLAB/LEVer.m | 4 +-
src/MATLAB/OpenData.m | 12 +-
src/MATLAB/ProcessNewborns.m | 10 ++
src/MATLAB/RemoveHull.m | 2 +
src/MATLAB/StraightenTrack.m | 17 +++
src/MATLAB/SwapTrackLabels.m | 12 ++
19 files changed, 415 insertions(+), 99 deletions(-)
create mode 100644 src/MATLAB/ErrorHandeling.m
create mode 100644 src/MATLAB/StraightenTrack.m
diff --git a/src/MATLAB/ChangeLabel.m b/src/MATLAB/ChangeLabel.m
index c5b4a332..3fa5c434 100644
--- a/src/MATLAB/ChangeLabel.m
+++ b/src/MATLAB/ChangeLabel.m
@@ -130,6 +130,18 @@ else %the old track still exists in some fasion
RemoveChildren(newTrackID);
end
end
+
+%check to see if either of the tracks are dead
+familyIDs = [];
+if(~isempty(CellTracks(oldTrackID).timeOfDeath))
+ familyIDs = StraightenTrack(oldTrackID);
+end
+if(~isempty(CellTracks(newTrackID).timeOfDeath))
+ familyIDs = [familyIDs StraightenTrack(newTrackID)];
+end
+if(~isempty(familyIDs))
+ ProcessNewborns(familyIDs);
+end
end
function moveChildren(oldTrackID,newTrackID)
diff --git a/src/MATLAB/ChangeTrackAndChildrensFamily.m b/src/MATLAB/ChangeTrackAndChildrensFamily.m
index c988e5f4..f1a7436d 100644
--- a/src/MATLAB/ChangeTrackAndChildrensFamily.m
+++ b/src/MATLAB/ChangeTrackAndChildrensFamily.m
@@ -21,7 +21,7 @@ if(isempty(CellFamilies(oldFamilyID).tracks))
CellFamilies(oldFamilyID).rootTrackID = [];
CellFamilies(oldFamilyID).startTime = [];
CellFamilies(oldFamilyID).endTime = [];
-else
+else
%update times
CellFamilies(oldFamilyID).startTime = min([CellTracks(CellFamilies(oldFamilyID).tracks).startTime]);
CellFamilies(oldFamilyID).endTime = max([CellTracks(CellFamilies(oldFamilyID).tracks).endTime]);
diff --git a/src/MATLAB/ChangeTrackParent.m b/src/MATLAB/ChangeTrackParent.m
index 11623dda..0685e1a3 100644
--- a/src/MATLAB/ChangeTrackParent.m
+++ b/src/MATLAB/ChangeTrackParent.m
@@ -28,26 +28,27 @@ else
return
end
+oldFamilyID = CellTracks(childTrackID).familyID;
+newFamilyID = CellTracks(siblingTrackID).familyID;
+
childIndex = length(CellTracks(parentTrackID).childrenTracks) + 1;
CellTracks(parentTrackID).childrenTracks(childIndex) = childTrackID;
%clean up old parent
if(~isempty(CellTracks(childTrackID).siblingTrack))
CellTracks(CellTracks(childTrackID).siblingTrack).siblingTrack = [];
- ChangeLabel(CellTracks(CellTracks(childTrackID).siblingTrack).startTime,...
- CellTracks(childTrackID).siblingTrack,CellTracks(childTrackID).parentTrack);
- index = CellTracks(CellTracks(childTrackID).parentTrack).childrenTracks == childTrackID;
- CellTracks(CellTracks(childTrackID).parentTrack).childrenTracks(index) = [];
+ CombineTrackWithParent(CellTracks(childTrackID).siblingTrack);
+% ChangeLabel(CellTracks(CellTracks(childTrackID).siblingTrack).startTime,...
+% CellTracks(childTrackID).siblingTrack,CellTracks(childTrackID).parentTrack);
+% index = CellTracks(CellTracks(childTrackID).parentTrack).childrenTracks == childTrackID;
+% CellTracks(CellTracks(childTrackID).parentTrack).childrenTracks(index) = [];
end
CellTracks(childTrackID).parentTrack = parentTrackID;
%Detatch childTrack and clean up child's family
-oldFamilyID = CellTracks(childTrackID).familyID;
-newFamilyID = CellTracks(siblingTrackID).familyID;
-
-% CellTracks(childTrackID).familyID = newFamilyID;
-
-ChangeTrackAndChildrensFamily(oldFamilyID,newFamilyID,childTrackID);
+if(oldFamilyID~=newFamilyID)
+ ChangeTrackAndChildrensFamily(oldFamilyID,newFamilyID,childTrackID);
+end
CellTracks(childTrackID).siblingTrack = siblingTrackID;
CellTracks(siblingTrackID).siblingTrack = childTrackID;
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index dcec450f..42380afd 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -31,19 +31,38 @@ elseif(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
switch choice
case 'Yes'
oldFamily = CellTracks(trackID).familyID;
- RemoveFromTree(time,trackID,'yes');
History('Push');
+ try
+ RemoveFromTree(time,trackID,'yes');
+ catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(time) ' ' num2str(trackID) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
+
LogAction(['Removed ' num2str(trackID) ' From Tree'], oldFamily,CellTracks(trackID).familyID);
case 'Cancel'
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');
+ 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'
- SwapTrackLabels(time,trackID,newTrackID);
History('Push');
+ try
+ SwapTrackLabels(time,trackID,newTrackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['SwapTrackLabels(' num2str(time) ' ' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
LogAction('Swapped Labels',trackID,newTrackID);
case 'This Frame'
SwapHulls(time,trackID,newTrackID);
@@ -52,20 +71,56 @@ elseif(~isempty(find([HashedCells{time}.trackID]==newTrackID,1)))
end
elseif(isempty(CellTracks(trackID).parentTrack) && isempty(CellTracks(trackID).childrenTracks) && 1==length(CellTracks(trackID).hulls))
hullID = CellTracks(trackID).hulls(1);
- AddSingleHullToTrack(trackID,newTrackID);
History('Push');
+ try
+ AddSingleHullToTrack(trackID,newTrackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['AddSingleHullToTrack(' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
LogAction('Added hull to track',hullID,newTrackID);
elseif(~isempty(CellTracks(trackID).parentTrack) && CellTracks(trackID).parentTrack==newTrackID)
- MoveMitosisUp(time,trackID)
History('Push');
+ try
+ MoveMitosisUp(time,trackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['MoveMitosisUp(' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
LogAction('Moved Mitosis Up',trackID,newTrackID);
-elseif(~isempty(CellTracks(newTrackID).parentTrack) &&CellTracks(newTrackID).parentTrack==trackID)
- MoveMitosisUp(time,newTrackID)
+elseif(~isempty(CellTracks(newTrackID).parentTrack) && CellTracks(newTrackID).parentTrack==trackID)
History('Push');
+ try
+ MoveMitosisUp(time,newTrackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['MoveMitosisUp(' num2str(time) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
LogAction('Moved Mitosis Up',newTrackID,trackID);
else
- ChangeLabel(time,trackID,newTrackID);
History('Push');
+ try
+ ChangeLabel(time,trackID,newTrackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeLabel(' num2str(time) ' ' num2str(trackID) ' ' num2str(newTrackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
LogAction('ChangeLabel',trackID,newTrackID);
end
diff --git a/src/MATLAB/ContextChangeParent.m b/src/MATLAB/ContextChangeParent.m
index 6eaf77b9..3648ed93 100644
--- a/src/MATLAB/ContextChangeParent.m
+++ b/src/MATLAB/ContextChangeParent.m
@@ -23,9 +23,17 @@ elseif(CellTracks(trackID).endTime < CellTracks(newParentID).startTime)
end
oldParent = CellTracks(trackID).parentTrack;
-ChangeTrackParent(newParentID,time,trackID);
-
History('Push');
+try
+ ChangeTrackParent(newParentID,time,trackID);
+catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(newParentID) ' ' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+end
LogAction(['Changed parent of ' num2str(trackID)],oldParent,newParentID);
DrawTree(CellTracks(newParentID).familyID);
diff --git a/src/MATLAB/ContextRemoveFromTree.m b/src/MATLAB/ContextRemoveFromTree.m
index fc187c9f..ce6726ce 100644
--- a/src/MATLAB/ContextRemoveFromTree.m
+++ b/src/MATLAB/ContextRemoveFromTree.m
@@ -7,8 +7,16 @@ global CellTracks
oldFamilyID = CellTracks(trackID).familyID;
-newFamilyID = RemoveFromTree(time, trackID,'yes');
-History('Push');
+try
+ newFamilyID = RemoveFromTree(time, trackID,'yes');
+catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(time) ' ' num2str(trackID) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+end
LogAction(['Removed part or all of ' num2str(trackID) ' from tree'],oldFamilyID,newFamilyID);
DrawTree(oldFamilyID);
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 43d7e464..1faefc48 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -27,9 +27,9 @@ uimenu(Figures.cells.contextMenuHandle,...
'CallBack', @changeLabel,...
'Separator', 'on');
-uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Change Parent',...
- 'CallBack', @changeParent);
+% uimenu(Figures.cells.contextMenuHandle,...
+% 'Label', 'Change Parent',...
+% 'CallBack', @changeParent);
addHull = uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Add Hull',...
@@ -69,9 +69,9 @@ uimenu(Figures.cells.contextMenuHandle,...
'CallBack', @markDeath,...
'Separator', 'on');
-uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Remove From Tree',...
- 'CallBack', @removeFromTree);
+% uimenu(Figures.cells.contextMenuHandle,...
+% 'Label', 'Remove From Tree',...
+% 'CallBack', @removeFromTree);
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Properties',...
@@ -80,17 +80,6 @@ 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
@@ -106,15 +95,35 @@ choice = questdlg('Which Side to Keep?','Merge With Parent',object.UserData,...
switch choice
case num2str(object.UserData)
remove = CellTracks(object.UserData).siblingTrack;
- newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).siblingTrack).startTime,...
- CellTracks(object.UserData).siblingTrack,'yes');
+ History('Push');
+ try
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).siblingTrack).startTime,...
+ CellTracks(object.UserData).siblingTrack,'yes');
+ catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).siblingTrack).startTime)...
+ num2str(CellTracks(object.UserData).siblingTrack) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
case num2str(CellTracks(object.UserData).siblingTrack)
remove = object.UserData;
- newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
+ History('Push');
+ try
+ 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]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
otherwise
return
end
-History('Push');
LogAction(['Removed ' num2str(remove) ' from tree'],Figures.tree.familyID,newTree);
DrawTree(Figures.tree.familyID);
DrawCells();
@@ -126,13 +135,16 @@ 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),''});
+% answer = inputdlg({['Enter new sibling of ' num2str(trackID)],'Enter Time of Mitosis'},...
+% 'Add Mitosis',1,{'',num2str(Figures.time)});
+
+answer = inputdlg({['Enter new sibling of ' num2str(trackID)]},...
+ 'Add Mitosis',1,{''});
if(isempty(answer)),return,end
-time = str2double(answer(1));
-siblingTrack = str2double(answer(2));
+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');
@@ -146,12 +158,31 @@ end
oldParent = CellTracks(siblingTrack).parentTrack;
if(CellTracks(trackID).startTime==time)
- ChangeTrackParent(siblingTrack,time,trackID);
+ History('Push');
+ try
+ ChangeTrackParent(siblingTrack,time,trackID);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(siblingTrack) ' ' num2str(time) ' ' num2str(trackID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
else
- ChangeTrackParent(trackID,time,siblingTrack);
+ History('Push');
+ try
+ ChangeTrackParent(trackID,time,siblingTrack);
+ catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
end
-History('Push');
LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
DrawTree(CellTracks(trackID).familyID);
@@ -204,8 +235,18 @@ global Figures CellFamilies
[hullID trackID] = getClosestCell();
if(isempty(trackID)),return,end
-RemoveHull(hullID);
History('Push');
+try
+ RemoveHull(hullID);
+catch errorMessage
+ try
+ ErrorHandeling(['RemoveHull(' num2str(hullID) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+end
+
LogAction(['Removed hull from track ' num2str(trackID)],hullID,[]);
%if the whole family disapears with this change, pick a diffrent family to
@@ -237,17 +278,19 @@ CellTracks(trackID).timeOfDeath = Figures.time;
%drop children from tree and run ProcessNewborns
if(~isempty(CellTracks(trackID).childrenTracks))
- familyIDs = [];
- for i=1:length(CellTracks(trackID).childrenTracks)
- familyIDs = [familyIDs ...
- RemoveFromTree(CellTracks(CellTracks(trackID).childrenTracks(i)).startTime,...
- CellTracks(trackID).childrenTracks(i),'yes')];
+ History('Push');
+ try
+ ProcessNewborns(StraightenTrack(trackID));
+ catch errorMessage
+ try
+ ErrorHandeling(['ProcessNewborns(StraightenTrack(' num2str(trackID) ')-- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
end
- CellTracks(trackID).childrenTracks = [];
- ProcessNewborns(familyIDs);
-end
+end
-History('Push');
LogAction(['Marked time of death for ' num2str(trackID)],[],[]);
DrawTree(Figures.tree.familyID);
@@ -282,17 +325,33 @@ if ( ~CHullContainsPoint(clickPt(1,1:2), CellHulls(hullID)) )
end
if(~isempty(trackID))
- % Try to split the existing hull
- newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
-
+ % 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
- newTrack = AddNewSegmentHull(clickPt(1,1:2));
-
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;
@@ -302,17 +361,17 @@ DrawTree(Figures.tree.familyID);
DrawCells();
end
-function [hullID trackID] = getClosestCell(bAllowEmpty)
+function [hullID trackID] = getClosestCell(allowEmpty)
hullID = FindHull(get(gca,'CurrentPoint'));
if(0>=hullID)
- if ( bAllowEmpty )
+ 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 07986161..63019c70 100644
--- a/src/MATLAB/CreateContextMenuTree.m
+++ b/src/MATLAB/CreateContextMenuTree.m
@@ -22,13 +22,13 @@ uimenu(Figures.tree.contextMenuHandle,...
'CallBack', @changeLabel,...
'Separator', 'on');
-uimenu(Figures.tree.contextMenuHandle,...
- 'Label', 'Change Parent',...
- 'CallBack', @changeParent);
+% uimenu(Figures.tree.contextMenuHandle,...
+% 'Label', 'Change Parent',...
+% 'CallBack', @changeParent);
-uimenu(Figures.tree.contextMenuHandle,...
- 'Label', 'Remove From Tree',...
- 'CallBack', @removeFromTree);
+% uimenu(Figures.tree.contextMenuHandle,...
+% 'Label', 'Remove From Tree',...
+% 'CallBack', @removeFromTree);
uimenu(Figures.tree.contextMenuHandle,...
'Label', 'Properties',...
@@ -61,23 +61,66 @@ 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');
+ History('Push');
+ try
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).siblingTrack).startTime,...
+ CellTracks(object.UserData).siblingTrack,'yes');
+ catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).siblingTrack).startTime) ' '...
+ num2str(CellTracks(object.UserData).siblingTrack) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
case num2str(CellTracks(object.UserData).siblingTrack)
remove = object.UserData;
- newTree = RemoveFromTree(CellTracks(object.UserData).startTime,object.UserData,'yes');
+ History('Push');
+ try
+ 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]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
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');
+ History('Push');
+ try
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).childrenTracks(2)).startTime,...
+ CellTracks(object.UserData).childrenTracks(2),'yes');
+ catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).childrenTracks(2)).startTime) ' '...
+ num2str(CellTracks(object.UserData).childrenTracks(2)) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
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');
+ History('Push');
+ try
+ newTree = RemoveFromTree(CellTracks(CellTracks(object.UserData).childrenTracks(1)).startTime,...
+ CellTracks(object.UserData).childrenTracks(1),'yes');
+ catch errorMessage
+ try
+ ErrorHandeling(['RemoveFromTree(' num2str(CellTracks(CellTracks(object.UserData).childrenTracks(1)).startTime) ' '...
+ num2str(CellTracks(object.UserData).childrenTracks(1)) ' yes) -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+ end
otherwise
return
end
-History('Push');
+
LogAction(['Removed ' num2str(remove) ' from tree'],Figures.tree.familyID,newTree);
DrawTree(Figures.tree.familyID);
DrawCells();
@@ -108,9 +151,17 @@ end
oldParent = CellTracks(siblingTrack).parentTrack;
-ChangeTrackParent(trackID,time,siblingTrack);
-
History('Push');
+try
+ ChangeTrackParent(trackID,time,siblingTrack);
+catch errorMessage
+ try
+ ErrorHandeling(['ChangeTrackParent(' num2str(trackID) ' ' num2str(time) ' ' num2str(siblingTrack) ') -- ' errorMessage.message]);
+ catch errorMessage2
+ fprintf(errorMessage2.message);
+ return
+ end
+end
LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
DrawTree(CellTracks(trackID).familyID);
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index 3e5af67f..167fe30b 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -93,6 +93,14 @@ siblingsMenu = uimenu(...
'Checked', 'off',...
'Accelerator', 'b');
+imageMenu = uimenu(...
+ 'Parent', viewMenu,...
+ 'Label', 'Show Image',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @toggleImage,...
+ 'Checked', 'on',...
+ 'Accelerator', 'i');
+
playMenu = uimenu(...
'Parent', viewMenu,...
'Label', 'Play',...
@@ -128,6 +136,7 @@ if(strcmp(get(handle,'Tag'),'cells'))
Figures.cells.menuHandles.labelsMenu = labelsMenu;
Figures.cells.menuHandles.playMenu = playMenu;
Figures.cells.menuHandles.siblingsMenu = siblingsMenu;
+ Figures.cells.menuHandles.imageMenu = imageMenu;
else
Figures.tree.menuHandles.saveMenu = saveMenu;
Figures.tree.menuHandles.undoMenu = undoMenu;
@@ -135,6 +144,7 @@ else
Figures.tree.menuHandles.labelsMenu = labelsMenu;
Figures.tree.menuHandles.playMenu = playMenu;
Figures.tree.menuHandles.siblingsMenu = siblingsMenu;
+ Figures.tree.menuHandles.imageMenu = imageMenu;
end
end
@@ -161,6 +171,7 @@ printdlg;
end
function undo(src,evnt)
+History('Push');%put the current state on the stack then go to the previous
History('Pop');
end
@@ -194,6 +205,19 @@ else
end
end
+function toggleImage(src,evnt)
+global Figures
+if(strcmp(get(Figures.cells.menuHandles.imageMenu, 'Checked'), 'on'))
+ set(Figures.cells.menuHandles.imageMenu, 'Checked', 'off');
+ set(Figures.tree.menuHandles.imageMenu, 'Checked', 'off');
+ DrawCells();
+else
+ set(Figures.cells.menuHandles.imageMenu, 'Checked', 'on');
+ set(Figures.tree.menuHandles.imageMenu, 'Checked', 'on');
+ DrawCells();
+end
+end
+
function timeJump(src,evnt)
global Figures HashedCells
answer = inputdlg('Enter Frame Number:','Jump to Time...',1,{num2str(Figures.time)});
diff --git a/src/MATLAB/DrawCells.m b/src/MATLAB/DrawCells.m
index cf6d1500..ed1401c1 100644
--- a/src/MATLAB/DrawCells.m
+++ b/src/MATLAB/DrawCells.m
@@ -14,7 +14,7 @@ if(isempty(CellFamilies(Figures.tree.familyID).tracks)),return,end
figure(Figures.cells.handle);
set(Figures.cells.timeLabel,'String',['Time: ' num2str(Figures.time)]);
%read in image
-fileName = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' num2str(Figures.time,'%03d') '.TIF'];
+fileName = [CONSTANTS.rootImageFolder CONSTANTS.imageDatasetName '_t' num2str(Figures.time,'%03d') '.TIF'];
[img colrMap] = imread(fileName);
xl=xlim;
yl=ylim;
@@ -35,6 +35,11 @@ hold all;
siblingsAlreadyDrawn = [];
+%draw Image or not
+if(strcmp(get(Figures.cells.menuHandles.imageMenu, 'Checked'),'off'))
+ set(im,'Visible','off');
+end
+
%draw labels if turned on
if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
for i=1:length(HashedCells{Figures.time})
@@ -150,5 +155,5 @@ plot([CellHulls(hullID).centerOfMass(2) CellHulls(siblingHullID).centerOfMass(2)
'uicontextmenu', Figures.cells.contextMenuHandle,...
'Tag', 'SiblingRelationship');
-set(Figures.cells.removeMenu,'Visible','on');
+% set(Figures.cells.removeMenu,'Visible','on');
end
diff --git a/src/MATLAB/ErrorHandeling.m b/src/MATLAB/ErrorHandeling.m
new file mode 100644
index 00000000..8b665bca
--- /dev/null
+++ b/src/MATLAB/ErrorHandeling.m
@@ -0,0 +1,40 @@
+function ErrorHandeling(errorMessage)
+%***Possibly Throws Error***
+% ErrorHandeling(errorMessage) will attempt to fix the issue and log the
+% error. If unsuccessful, another log entery will be made and will throw
+% the new error.
+
+%--Eric Wait
+
+global Figures
+
+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');
+LogAction(errorMessage,[],[]);
+
+%let the user know that this might take a while
+set(Figures.tree.handle,'Pointer','watch');
+set(Figures.cells.handle,'Pointer','watch');
+
+try
+ TestDataIntegrity(1);
+ msgbox('Database corrected. Your last action was undone, please try again. If change errors again, save the data file and then send it and the log to the code distributor.',...
+ 'Database Correct','help','modal');
+catch errorMessage2
+ %let the user know that the drawing is done
+ set(Figures.tree.handle,'Pointer','arrow');
+ set(Figures.cells.handle,'Pointer','arrow');
+ LogAction(['Unable to fix database -- ' errorMessage2.message],[],[]);
+ msgbox('Unable to fix database! Please save the data file and then send it and the log to the code distributor. Your last change did not take place!',...
+ 'Database ERROR','error');
+ rethrow(errorMessage2)
+end
+close(msgboxHandle);
+
+%let the user know that the drawing is done
+set(Figures.tree.handle,'Pointer','arrow');
+set(Figures.cells.handle,'Pointer','arrow');
+end
\ No newline at end of file
diff --git a/src/MATLAB/GetTrackID.m b/src/MATLAB/GetTrackID.m
index 856b576c..8da8ff2a 100644
--- a/src/MATLAB/GetTrackID.m
+++ b/src/MATLAB/GetTrackID.m
@@ -1,11 +1,18 @@
function trackID = GetTrackID(hullID)
-%Given a hull ID a track ID will be returned
+%Given a hull ID a track ID will be returned or [] if none found
%--Eric Wait
global CellHulls HashedCells
-hullTime = CellHulls(hullID).time;
-hashedCellIndex = [HashedCells{hullTime}.hullID] == hullID;
-trackID = HashedCells{hullTime}(hashedCellIndex).trackID;
+trackID = [];
+
+if(hullID>length(CellHulls))
+ return
+else
+ hullTime = CellHulls(hullID).time;
+ hashedCellIndex = [HashedCells{hullTime}.hullID] == hullID;
+ if(isempty(hashedCellIndex)),return,end
+ trackID = HashedCells{hullTime}(hashedCellIndex).trackID;
+end
end
diff --git a/src/MATLAB/InitializeFigures.m b/src/MATLAB/InitializeFigures.m
index 99b7f554..64d28f9e 100644
--- a/src/MATLAB/InitializeFigures.m
+++ b/src/MATLAB/InitializeFigures.m
@@ -13,6 +13,9 @@ Figures.time = 1;
Figures.cells.handle = figure();
Figures.tree.handle = figure();
+whitebg(Figures.cells.handle,'k');
+whitebg(Figures.tree.handle,'w');
+
Figures.advanceTimerHandle = timer(...
'TimerFcn', @play,...
'Period', .1,...
diff --git a/src/MATLAB/LEVer.m b/src/MATLAB/LEVer.m
index 4752b1f6..64cc06cf 100644
--- a/src/MATLAB/LEVer.m
+++ b/src/MATLAB/LEVer.m
@@ -14,7 +14,9 @@ end
if(OpenData())
InitializeFigures();
History('Init');
-elseif(~isempty(Figures))
+else %if(~isempty(Figures))
History('Pop');
+ DrawTree(Figures.tree.familyID);
+ DrawCells();
end
end
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index f266c322..7b4f4082 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 3.4\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 3.6\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
@@ -92,29 +92,29 @@ 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),return,end
end
-opened = 1;
-
index = strfind(imageFile,'t');
if (~isempty(index) && filterIndexImage~=0)
CONSTANTS.rootImageFolder = imagePath;
imageDataset = imageFile(1:(index(length(index))-2));
+ CONSTANTS.imageDatasetName = imageDataset;
fileName=[CONSTANTS.rootImageFolder imageDataset '_t001.TIF'];
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
index = strfind(imageFile,'t');
CONSTANTS.rootImageFolder = [imgPath '\'];
imageDataset = imageFile(1:(index(length(index))-2));
fileName=[CONSTANTS.rootImageFolder imageDataSet '_t' num2str(t,'%03d') '.TIF'];
end
+opened = 1;
+
%save out settings
settings.matFilePath = matPath;
settings.imageFile = imageFile;
diff --git a/src/MATLAB/ProcessNewborns.m b/src/MATLAB/ProcessNewborns.m
index e1eee9cf..74c253f7 100644
--- a/src/MATLAB/ProcessNewborns.m
+++ b/src/MATLAB/ProcessNewborns.m
@@ -15,6 +15,7 @@ for i=1:size
%Get all the possible hulls that could have been connected
childHullID = CellTracks(childTrackID).hulls(1);
+ if(childHullID>length(Costs)),continue,end
parentHullCandidates = find(Costs(:,childHullID));
if(isempty(parentHullCandidates)),continue,end
@@ -25,6 +26,7 @@ for i=1:size
for j=1:length(parentHullCandidates)
%Get the length of time that the parentCandidate exists
parentTrackID = GetTrackID(parentHullCandidates(j));
+ if(isempty(parentTrackID)),continue,end
parentTrackTimeFrame = CellTracks(parentTrackID).endTime - CellTracks(parentTrackID).startTime;
%Change the cost of the candidates
@@ -49,6 +51,14 @@ for i=1:size
%Make the connections
parentTrackID = GetTrackID(parentHullID);
+ if(isempty(parentTrackID))
+ try
+ ErrorHandeling(['GetTrackID(' num2str(parentHullID) ') -- while in ProcessNewborns']);
+ catch errorMessage2
+ fprintf(errorMessage2);
+ return
+ end
+ end
connectTime = CellHulls(parentHullID).time;
if(CONSTANTS.minParentHistoryTimeFrame < abs(CellTracks(childTrackID).startTime - CellTracks(parentTrackID).startTime))
ChangeTrackParent(parentTrackID,connectTime,childTrackID);
diff --git a/src/MATLAB/RemoveHull.m b/src/MATLAB/RemoveHull.m
index 78550a63..b43d109d 100644
--- a/src/MATLAB/RemoveHull.m
+++ b/src/MATLAB/RemoveHull.m
@@ -9,6 +9,8 @@ global CellTracks HashedCells CellHulls
trackID = GetTrackID(hullID);
+if(isempty(trackID)),return,end
+
%remove hull from its track
index = find(CellTracks(trackID).hulls==hullID);
CellTracks(trackID).hulls(index) = 0;
diff --git a/src/MATLAB/StraightenTrack.m b/src/MATLAB/StraightenTrack.m
new file mode 100644
index 00000000..83f95ce6
--- /dev/null
+++ b/src/MATLAB/StraightenTrack.m
@@ -0,0 +1,17 @@
+function familyIDs = StraightenTrack(trackID)
+% StraightenTrack(trackID) will drop all right children while traversing
+% left. Usefull for cells that should not have mitosis events such as dead
+% cells.
+
+%--Eric Wait
+
+global CellTracks
+familyIDs = [];
+if(~isempty(CellTracks(trackID).childrenTracks))
+ familyIDs = StraightenTrack(CellTracks(trackID).childrenTracks(1));
+ for i=2:length(CellTracks(trackID).childrenTracks)
+ familyIDs = [familyIDs RemoveFromTree(CellTracks(CellTracks(trackID).childrenTracks(i)).startTime,...
+ CellTracks(trackID).childrenTracks(i),'yes')];
+ end
+end
+end
\ No newline at end of file
diff --git a/src/MATLAB/SwapTrackLabels.m b/src/MATLAB/SwapTrackLabels.m
index a626f3fd..aca5c799 100644
--- a/src/MATLAB/SwapTrackLabels.m
+++ b/src/MATLAB/SwapTrackLabels.m
@@ -66,4 +66,16 @@ if(CellTracks(trackID1).familyID ~= CellTracks(trackID2).familyID)
ChangeTrackAndChildrensFamily(CellTracks(trackID1).familyID,CellTracks(trackID2).familyID,CellTracks(trackID2).childrenTracks(i));
end
end
+
+%check to see if either of the tracks are dead
+familyIDs = [];
+if(~isempty(CellTracks(trackID1).timeOfDeath))
+ familyIDs = StraightenTrack(trackID1);
+end
+if(~isempty(CellTracks(trackID2).timeOfDeath))
+ familyIDs = [familyIDs StraightenTrack(trackID2)];
+end
+if(~isempty(familyIDs))
+ ProcessNewborns(familyIDs);
+end
end
--
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