From 9dba44f6d5be4841fb8ae8fb76e46bd63e2ffd41 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Fri, 8 Apr 2011 22:16:19 -0500
Subject: [PATCH] LEVer 3.2
---
src/MATLAB/AddHashedCell.m | 2 +
src/MATLAB/AddHullToTrack.m | 2 +-
src/MATLAB/ChangeLabel.m | 82 +++++---
src/MATLAB/ChangeTrackAndChildrensFamily.m | 19 +-
src/MATLAB/ChangeTrackParent.m | 10 +-
src/MATLAB/CloseFigure.m | 4 +
src/MATLAB/CombineTrackWithParent.m | 3 +
src/MATLAB/ContextChangeLabel.m | 5 +-
src/MATLAB/ContextChangeParent.m | 11 +-
src/MATLAB/ContextProperties.m | 2 +
src/MATLAB/ContextRemoveFromTree.m | 5 +-
src/MATLAB/ConvertTrackingData.m | 8 +-
src/MATLAB/CreateColors.m | 2 +
src/MATLAB/CreateContextMenuCells.m | 128 +++++++++---
src/MATLAB/CreateContextMenuTree.m | 6 +-
src/MATLAB/CreateMenuBar.m | 25 +++
src/MATLAB/DeleteHullFromTrack.m | 2 +
src/MATLAB/DrawCells.m | 5 +-
src/MATLAB/DrawTree.m | 12 +-
src/MATLAB/ExportImage.m | 2 +
src/MATLAB/FindHull.m | 2 +
src/MATLAB/GetNextColor.m | 2 +
src/MATLAB/GetTrackID.m | 2 +
src/MATLAB/GrayOutColor.m | 4 +-
src/MATLAB/History.m | 231 ++++++++++++---------
src/MATLAB/InSubTree.m | 42 ++++
src/MATLAB/InitializeFigures.m | 2 +
src/MATLAB/LEVer.m | 4 +
src/MATLAB/LogAction.m | 2 +
src/MATLAB/NewCellFamily.m | 5 +
src/MATLAB/NewCellTrack.m | 5 +
src/MATLAB/OpenData.m | 4 +-
src/MATLAB/ProcessNewborns.m | 2 +
src/MATLAB/RehashCellTracks.m | 15 +-
src/MATLAB/RemoveFromTree.m | 37 +++-
src/MATLAB/RemoveHull.m | 28 +++
src/MATLAB/RemoveTrackFromFamily.m | 28 +++
src/MATLAB/ResegmentHull.m | 48 +++++
src/MATLAB/SaveData.m | 17 +-
src/MATLAB/SaveDataAs.m | 4 +
src/MATLAB/SiblingDistance.m | 7 +-
src/MATLAB/SplitHull.m | 25 +++
src/MATLAB/SplitTrack.m | 2 +
src/MATLAB/SwapTrackLabels.m | 2 +
src/MATLAB/TimeChange.m | 2 +
src/MATLAB/TogglePlay.m | 5 +
src/MATLAB/UpdateHashedCellsTrackID.m | 8 +-
src/MATLAB/UpdateTimeIndicatorLine.m | 2 +
src/MATLAB/driver.m | 65 ------
49 files changed, 666 insertions(+), 271 deletions(-)
create mode 100644 src/MATLAB/RemoveHull.m
create mode 100644 src/MATLAB/RemoveTrackFromFamily.m
create mode 100644 src/MATLAB/ResegmentHull.m
create mode 100644 src/MATLAB/SplitHull.m
delete mode 100644 src/MATLAB/driver.m
diff --git a/src/MATLAB/AddHashedCell.m b/src/MATLAB/AddHashedCell.m
index a6c71dd9..a0260fd9 100644
--- a/src/MATLAB/AddHashedCell.m
+++ b/src/MATLAB/AddHashedCell.m
@@ -2,6 +2,8 @@ function AddHashedCell(t,cellHullID,cellTrackID)
%This will either add an entry to HashedHulls or update an entry based on
%cellHullID
+%--Eric Wait
+
global HashedCells
if(isempty(HashedCells))
diff --git a/src/MATLAB/AddHullToTrack.m b/src/MATLAB/AddHullToTrack.m
index ae8d4b5d..1b72f845 100644
--- a/src/MATLAB/AddHullToTrack.m
+++ b/src/MATLAB/AddHullToTrack.m
@@ -8,6 +8,7 @@ function AddHullToTrack(hullID,trackID,previousHullID)
%previousHullID at previousTime exists in that track. Also, it has been
%removed from any previous track assosiation.
+%--Eric Wait
global HashedCells CellTracks CellFamilies CellHulls
@@ -37,7 +38,6 @@ if(0 >= hash)
end
end
CellTracks(curTrackID).hulls(hash) = hullID;
-% CellTracks(curTrackID).hulls(hash).time = time;
if(CellTracks(curTrackID).endTime < time)
CellTracks(curTrackID).endTime = time;
diff --git a/src/MATLAB/ChangeLabel.m b/src/MATLAB/ChangeLabel.m
index 3fe1b834..4d8109b0 100644
--- a/src/MATLAB/ChangeLabel.m
+++ b/src/MATLAB/ChangeLabel.m
@@ -1,4 +1,5 @@
function ChangeLabel(time,oldTrackID,newTrackID)
+%ChangLabel(time,oldTrackID,newTrackID)
%This will attempt to change the trackID from a given time until the end of
%the track. However, the trackID will only be changed up to the point that
%the newTrackID does not exist. If when moving hulls from the oldTrack to
@@ -14,6 +15,8 @@ function ChangeLabel(time,oldTrackID,newTrackID)
%The only time that the subtree would not move with the change would be as
%stated above.
+%--Eric Wait
+
global CellTracks CellFamilies CellHulls
bothHaveChildren = 0;%flag to deal with conflicting children
@@ -51,70 +54,91 @@ else
RehashCellTracks(oldTrackID,CellHulls(firstHull).time);
end
-%Handle children
if(oldEmptied)
- %update parent and sibling
- if(~isempty(CellTracks(oldTrackID).siblingTrack))
- CombineTrackWithParent(CellTracks(oldTrackID).siblingTrack);
- index = CellTracks(CellTracks(oldTrackID).parentTrack).childrenTracks == oldTrackID;
- CellTracks(CellTracks(oldTrackID).parentTrack).childrenTracks(index) = [];
- end
-
- %update family
- index = [CellFamilies(CellTracks(oldTrackID).familyID).tracks]==oldTrackID;
- CellFamilies(CellTracks(oldTrackID).familyID).tracks(index) = [];
-
- %clean up other fields
- CellTracks(oldTrackID).parentTrack = [];
- CellTracks(oldTrackID).siblingTrack = [];
- CellTracks(oldTrackID).startTime = [];
- CellTracks(oldTrackID).endTime = [];
- CellTracks(oldTrackID).color = [];
-
- %deal with any children
if(oldBeforeNew)
+ %deal with any children
if(~isempty(CellTracks(oldTrackID).childrenTracks))
- dropChildren(CellTracks(oldTrackID).childrenTracks);
+ dropChildren(oldTrackID);
+ end
+ if(~isempty(CellTracks(newTrackID).siblingTrack) && ...
+ isempty(find(CellTracks(oldTrackID).childrenTracks==CellTracks(newTrackID).siblingTrack, 1)))
+ CombineTrackWithParent(CellTracks(newTrackID).siblingTrack);
end
+ CellTracks(newTrackID).parentTrack = CellTracks(oldTrackID).parentTrack;
+ index = CellTracks(CellTracks(newTrackID).parentTrack).childrenTracks==oldTrackID;
+ CellTracks(CellTracks(newTrackID).parentTrack).childrenTracks(index) = newTrackID;
+ CellTracks(newTrackID).siblingTrack = CellTracks(oldTrackID).siblingTrack;
+ CellTracks(newTrackID).familyID = CellTracks(oldTrackID).familyID;
elseif(newBeforeOld)
+ %deal with any children
if(bothHaveChildren)
- dropChildren(CellTracks(newTrackID).childrenTracks);
+ index = CellTracks(newTrackID).childrenTracks==oldTrackID;
+ if(~isempty(find(index, 1)))
+ RemoveFromTree(CellTracks(CellTracks(newTrackID).childrenTracks(~index)).startTime,...
+ CellTracks(newTrackID).childrenTracks(~index),'no');
+ CellTracks(newTrackID).childrenTracks = [];
+ CellTracks(oldTrackID).siblingTrack = [];
+ else
+ dropChildren(newTrackID);
+ end
moveChildren(oldTrackID,newTrackID);
elseif(~isempty(CellTracks(newTrackID).childrenTracks))
- dropChildren(CellTracks(newTrackID).childrenTracks);
+ index = CellTracks(newTrackID).childrenTracks==oldTrackID;
+ if(~isempty(find(index, 1)))
+ RemoveFromTree(CellTracks(CellTracks(newTrackID).childrenTracks(~index)).startTime,...
+ CellTracks(newTrackID).childrenTracks(~index),'no');
+ CellTracks(newTrackID).childrenTracks = [];
+ CellTracks(oldTrackID).siblingTrack = [];
+ else
+ dropChildren(newTrackID);
+ end
elseif(~isempty(CellTracks(oldTrackID).childrenTracks))
moveChildren(oldTrackID,newTrackID);
end
+ if(~isempty(CellTracks(oldTrackID).siblingTrack) && ...
+ isempty(find(CellTracks(newTrackID).childrenTracks==CellTracks(oldTrackID).siblingTrack, 1)))
+ CombineTrackWithParent(CellTracks(oldTrackID).siblingTrack);
+ end
end
+
+ %clean up other fields
+ RemoveTrackFromFamily(oldTrackID);
+ CellTracks(oldTrackID).parentTrack = [];
+ CellTracks(oldTrackID).siblingTrack = [];
+ CellTracks(oldTrackID).startTime = [];
+ CellTracks(oldTrackID).endTime = [];
+ CellTracks(oldTrackID).color = [];
else %the old track still exists in some fasion
if(isempty(find(CellTracks(oldTrackID).hulls==lastOldHull, 1)) &&...
~isempty(CellTracks(oldTrackID).childrenTracks))
%the last hull from the old track has been moved over and had
%children
if(CellHulls(lastOldHull).time<CellTracks(newTrackID).endTime)
- dropChildren(CellTracks(oldTrackID).childrenTracks);
+ dropChildren(oldTrackID);
elseif(CellHulls(lastOldHull).time>=CellTracks(newTrackID).endTime)
if(~isempty(CellTracks(newTrackID).childrenTracks))
- dropChildren(CellTracks(newTrackID).childrenTracks);
+ dropChildren(newTrackID);
end
moveChildren(oldTrackID,newTrackID);
end
elseif(isempty(find(CellTracks(oldTrackID).hulls==lastOldHull, 1)) &&...
CellHulls(lastOldHull).time>CellTracks(newTrackID).endTime &&...
~isempty(CellTracks(newTrackID).childrenTracks))
- dropChildren(CellTracks(newTrackID).childrenTracks);
+ dropChildren(newTrackID);
end
end
end
-function dropChildren(children)
+function dropChildren(trackID)
%remove children from tree
global CellTracks
familyIDs = [];
-for i=1:length(children)
- familyIDs = [familyIDs RemoveFromTree(CellTracks(children(i)).startTime,children(i))];
+while ~isempty(CellTracks(trackID).childrenTracks)
+ familyIDs = [familyIDs RemoveFromTree(CellTracks(CellTracks(trackID).childrenTracks(1)).startTime,CellTracks(trackID).childrenTracks(1),'no')];
end
+
+CellTracks(trackID).childrenTracks = [];
%run processNewborns on them
ProcessNewborns(familyIDs);
end
diff --git a/src/MATLAB/ChangeTrackAndChildrensFamily.m b/src/MATLAB/ChangeTrackAndChildrensFamily.m
index 227c1b91..043a07ee 100644
--- a/src/MATLAB/ChangeTrackAndChildrensFamily.m
+++ b/src/MATLAB/ChangeTrackAndChildrensFamily.m
@@ -4,6 +4,8 @@ function ChangeTrackAndChildrensFamily(oldFamilyID,newFamilyID,trackID)
%This DOES NOT make the parent child relationship, it is just updates the
%CellFamilies data structure.
+%--Eric Wait
+
global CellFamilies CellTracks
%get the full list of tracks to be updateded
@@ -12,8 +14,7 @@ trackList = traverseTree(newFamilyID,trackID);
%remove tracks from family
for i=1:length(trackList)
CellTracks(trackList(i)).familyID = newFamilyID;
- index = CellFamilies(oldFamilyID).tracks == trackList(i);
- CellFamilies(oldFamilyID).tracks(index) = [];
+% RemoveTrackFromFamily(trackList(i));
end
if(isempty(CellFamilies(oldFamilyID).tracks))
@@ -22,16 +23,8 @@ if(isempty(CellFamilies(oldFamilyID).tracks))
CellFamilies(oldFamilyID).endTime = [];
else
%update times
- CellFamilies(oldFamilyID).startTime = CellTracks(CellFamilies(oldFamilyID).tracks(1)).startTime;
- CellFamilies(oldFamilyID).endTime = CellTracks(CellFamilies(oldFamilyID).tracks(1)).endTime;
- for i=2:length(CellFamilies(oldFamilyID).tracks)
- if(CellTracks(CellFamilies(oldFamilyID).tracks(i)).startTime < CellFamilies(oldFamilyID).startTime)
- CellFamilies(oldFamilyID).startTime = CellTracks(CellFamilies(oldFamilyID).tracks(i)).startTime;
- end
- if(CellTracks(CellFamilies(oldFamilyID).tracks(i)).endTime > CellFamilies(oldFamilyID).endTime)
- CellFamilies(oldFamilyID).endTime = CellTracks(CellFamilies(oldFamilyID).tracks(i)).endTime;
- end
- end
+ CellFamilies(oldFamilyID).startTime = min([CellTracks(CellFamilies(oldFamilyID).tracks).startTime]);
+ CellFamilies(oldFamilyID).endTime = max([CellTracks(CellFamilies(oldFamilyID).tracks).endTime]);
end
end
@@ -57,4 +50,6 @@ if(~isempty(CellTracks(trackID).childrenTracks))
trackList = [trackList traverseTree(newFamilyID, CellTracks(trackID).childrenTracks(i))];
end
end
+
+RemoveTrackFromFamily(trackID);
end
diff --git a/src/MATLAB/ChangeTrackParent.m b/src/MATLAB/ChangeTrackParent.m
index c4e4216d..fcc5aef5 100644
--- a/src/MATLAB/ChangeTrackParent.m
+++ b/src/MATLAB/ChangeTrackParent.m
@@ -5,7 +5,15 @@ function ChangeTrackParent(parentTrackID,time,childTrackID)
%there should be a new track and the child track that are siblings with the
%parent track being the parent.
-global CellTracks
+%--Eric Wait
+
+global CellTracks CellFamilies
+
+%see if the child exists before time
+if(time > CellTracks(childTrackID).startTime)
+ newFamilyID = RemoveFromTree(time,childTrackID,'yes');
+ childTrackID = CellFamilies(newFamilyID).rootTrackID;
+end
%find where the child should attach to the parent
hash = time - CellTracks(parentTrackID).startTime + 1;
diff --git a/src/MATLAB/CloseFigure.m b/src/MATLAB/CloseFigure.m
index edb65e73..d6cc4533 100644
--- a/src/MATLAB/CloseFigure.m
+++ b/src/MATLAB/CloseFigure.m
@@ -1,4 +1,8 @@
function CloseFigure(varargin)
+%Closes both figures and cleans up the Figures global var
+
+%--Eric Wait
+
global Figures
if(strcmp(get(Figures.cells.menuHandles.saveMenu,'Enable'),'on'))
choice = questdlg('Save current edits before closing?','Closing','Yes','No','Cancel','Cancel');
diff --git a/src/MATLAB/CombineTrackWithParent.m b/src/MATLAB/CombineTrackWithParent.m
index 9a0556bd..b55598df 100644
--- a/src/MATLAB/CombineTrackWithParent.m
+++ b/src/MATLAB/CombineTrackWithParent.m
@@ -1,4 +1,5 @@
function CombineTrackWithParent(trackID)
+% CombineTrackWithParent(trackID)
%Combine childTrack with its parent track - in otherwords the childtrack
%will be merged into the parent track making it all one edge.
%Afterward all of the hulls previously associated with the given track will
@@ -7,6 +8,8 @@ function CombineTrackWithParent(trackID)
%***Make sure that the sibling of the given track has been delt with prior
%to calling this function. IT WILL BE LOST
+%--Eric Wait
+
global CellFamilies CellTracks CellHulls
parentID = CellTracks(trackID).parentTrack;
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index 05111ec7..5ce3f145 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -1,5 +1,8 @@
function ContextChangeLabel(time,trackID)
%context menu callback function
+
+%--Eric Wait
+
global CellTracks HashedCells
newTrackID = inputdlg('Enter New Label','New Label',1,{num2str(trackID)});
@@ -11,7 +14,7 @@ if(newTrackID>length(CellTracks) || isempty(CellTracks(newTrackID).hulls))
switch choice
case 'Yes'
oldFamily = CellTracks(trackID).familyID;
- RemoveFromTree(time,trackID);
+ RemoveFromTree(time,trackID,'yes');
History('Push');
LogAction(['Removed ' num2str(trackID) ' From Tree'], oldFamily,CellTracks(trackID).familyID);
case 'Cancel'
diff --git a/src/MATLAB/ContextChangeParent.m b/src/MATLAB/ContextChangeParent.m
index 82714593..2172cf5f 100644
--- a/src/MATLAB/ContextChangeParent.m
+++ b/src/MATLAB/ContextChangeParent.m
@@ -1,12 +1,15 @@
-function ContextChangeParent(trackID)
+function ContextChangeParent(trackID,time)
%Function for context menu call back
+
+%--Eric Wait
+
global CellTracks
newParentID = inputdlg('Enter New Parent','New Parent',1,{num2str(CellTracks(trackID).parentTrack)});
if(isempty(newParentID)),return,end;
newParentID = str2double(newParentID(1));
-if(CellTracks(newParentID).startTime > CellTracks(trackID).startTime)
+if(CellTracks(newParentID).startTime > time)
msgbox(['Parent ' num2str(newParentID) ' comes after ' num2str(trackID) ' consider a different edit.'],'Parent Change','warn');
return
elseif(CellTracks(trackID).endTime < CellTracks(newParentID).startTime)
@@ -15,11 +18,11 @@ elseif(CellTracks(trackID).endTime < CellTracks(newParentID).startTime)
end
oldParent = CellTracks(trackID).parentTrack;
-ChangeTrackParent(newParentID,CellTracks(trackID).startTime,trackID);
+ChangeTrackParent(newParentID,time,trackID);
History('Push');
LogAction(['Changed parent of ' num2str(trackID)],oldParent,newParentID);
-DrawTree(CellTracks(trackID).familyID);
+DrawTree(CellTracks(newParentID).familyID);
DrawCells();
end
diff --git a/src/MATLAB/ContextProperties.m b/src/MATLAB/ContextProperties.m
index a528f090..7e007c8f 100644
--- a/src/MATLAB/ContextProperties.m
+++ b/src/MATLAB/ContextProperties.m
@@ -1,6 +1,8 @@
function ContextProperties(hullID,trackID)
%context menu callback function
+%--Eric Wait
+
global CellTracks Figures
%collect all the data that will be passed to the properties UI
diff --git a/src/MATLAB/ContextRemoveFromTree.m b/src/MATLAB/ContextRemoveFromTree.m
index c32bad1c..fc187c9f 100644
--- a/src/MATLAB/ContextRemoveFromTree.m
+++ b/src/MATLAB/ContextRemoveFromTree.m
@@ -1,10 +1,13 @@
function ContextRemoveFromTree(time,trackID)
%context menu callback function
+
+%--Eric Wait
+
global CellTracks
oldFamilyID = CellTracks(trackID).familyID;
-newFamilyID = RemoveFromTree(time, trackID);
+newFamilyID = RemoveFromTree(time, trackID,'yes');
History('Push');
LogAction(['Removed part or all of ' num2str(trackID) ' from tree'],oldFamilyID,newFamilyID);
diff --git a/src/MATLAB/ConvertTrackingData.m b/src/MATLAB/ConvertTrackingData.m
index 8141d4eb..bad774e2 100644
--- a/src/MATLAB/ConvertTrackingData.m
+++ b/src/MATLAB/ConvertTrackingData.m
@@ -2,10 +2,12 @@ function ConvertTrackingData(objHulls,gConnect)
%Takes the data structure from the tracking data and creates LEVer's data
%scheme
+%--Eric Wait
+
global CONSTANTS Costs HashedCells CellHulls CellFamilies
%Initialize CONSTANTS
-CONSTANTS.ImageSize = unique([objHulls(:).imSize]);
+CONSTANTS.imageSize = unique([objHulls(:).imSize]);
CONSTANTS.maxPixelDistance = 40;
CONSTANTS.maxCenterOfMassDistance = 80;
CONSTANTS.minParentCandidateTimeFrame = 5;
@@ -23,7 +25,8 @@ CellHulls = struct(...
'time', {objHulls(1).t},...
'points', {objHulls(1).pts},...
'centerOfMass', {objHulls(1).COM},...
- 'indexPixels', {objHulls(1).indPixels});
+ 'indexPixels', {objHulls(1).indPixels},...
+ 'deleted', {0});
if objHulls(1).inID == 0
NewCellFamily(1,objHulls(1).t);
@@ -37,6 +40,7 @@ for i=2:length(objHulls)
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);
diff --git a/src/MATLAB/CreateColors.m b/src/MATLAB/CreateColors.m
index 7a41b7fe..04f7f8a0 100644
--- a/src/MATLAB/CreateColors.m
+++ b/src/MATLAB/CreateColors.m
@@ -4,6 +4,8 @@ function colors = CreateColors()
%the text is typicaly white or black depending on the darkness of the
%background
+%--Eric Wait
+
colors = [1,0,0,0,0,0,0.4,0.15,0.15;...
1,0.5,0,0,0,0,0.4,0.2,0.15;...
1,1,0,0,0,0,0.4,0.4,0.15;...
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 7fc174a8..544d213a 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -2,6 +2,8 @@ function CreateContextMenuCells()
%creates the context menu for the figure that displays the image data and
%the subsequent function calls
+%--Eric Wait
+
global Figures
figure(Figures.cells.handle);
@@ -15,16 +17,38 @@ uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Change Parent',...
'CallBack', @changeParent);
-uimenu(Figures.cells.contextMenuHandle,...
+addHull = uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Add Hull',...
- 'CallBack', @addHull,...
+ 'Separator', 'on');
+
+uimenu(addHull,...
+ 'Label', 'Number of Hulls to add');
+
+uimenu(addHull,...
+ 'Label', '1',...
'Separator', 'on',...
- 'Enable', 'off');
+ 'CallBack', @addHull1);
+
+uimenu(addHull,...
+ 'Label', '2',...
+ 'CallBack', @addHull2);
+
+uimenu(addHull,...
+ 'Label', '3',...
+ 'CallBack', @addHull3);
+
+uimenu(addHull,...
+ 'Label', '4',...
+ 'CallBack', @addHull4);
+
+uimenu(addHull,...
+ 'Label', 'Other',...
+ 'Separator', 'on',...
+ 'CallBack', @addHullOther);
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Remove Hull',...
- 'CallBack', @removeHull,...
- 'Enable', 'off');
+ 'CallBack', @removeHull);
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Mark Death',...
@@ -43,37 +67,63 @@ end
%% Callback functions
function changeLabel(src,evnt)
-global Figures HashedCells
+global Figures
-hullID = FindHull(get(gca,'CurrentPoint'));
-tempIndex = [HashedCells{Figures.time}.hullID]==hullID;
-trackID = HashedCells{Figures.time}(tempIndex).trackID;
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
ContextChangeLabel(Figures.time,trackID);
end
function changeParent(src,evnt)
-global Figures HashedCells
+global Figures
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
-hullID = FindHull(get(gca,'CurrentPoint'));
-tempIndex = [HashedCells{Figures.time}.hullID]==hullID;
-trackID = HashedCells{Figures.time}(tempIndex).trackID;
+ContextChangeParent(trackID,Figures.time);
+end
+
+function addHull1(src,evnt)
+addHull(1);
+end
-ContextChangeParent(trackID);
+function addHull2(src,evnt)
+addHull(2);
end
-function addHull(src,evnt)
+function addHull3(src,evnt)
+addHull(3);
+end
+
+function addHull4(src,evnt)
+addHull(4);
+end
+
+function addHullOther(src,evnt)
+num = inputdlg('Enter Number of Hulls to Add','Add Hulls',1,{1});
+if(isempty(num)),return,end;
+num = str2double(num(1));
+addHull(num);
end
function removeHull(src,evnt)
+global Figures
+
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
+
+RemoveHull(hullID);
+History('Push');
+LogAction(['Removed hull from track ' num2str(trackID)],hullID,[]);
+DrawTree(Figures.tree.familyID);
+DrawCells();
end
function markDeath(src,evnt)
-global Figures HashedCells CellTracks
+global Figures CellTracks
-hullID = FindHull(get(gca,'CurrentPoint'));
-tempIndex = [HashedCells{Figures.time}.hullID]==hullID;
-trackID = HashedCells{Figures.time}(tempIndex).trackID;
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
CellTracks(trackID).timeOfDeath = Figures.time;
@@ -83,7 +133,7 @@ if(~isempty(CellTracks(trackID).childrenTracks))
for i=1:length(CellTracks(trackID).childrenTracks)
familyIDs = [familyIDs ...
RemoveFromTree(CellTracks(CellTracks(trackID).childrenTracks(i)).startTime,...
- CellTracks(trackID).childrenTracks(i))];
+ CellTracks(trackID).childrenTracks(i),'yes')];
end
CellTracks(trackID).childrenTracks = [];
ProcessNewborns(familyIDs);
@@ -97,20 +147,42 @@ DrawCells();
end
function removeFromTree(src,evnt)
-global Figures HashedCells
+global Figures
-hullID = FindHull(get(gca,'CurrentPoint'));
-tempIndex = [HashedCells{Figures.time}.hullID]==hullID;
-trackID = HashedCells{Figures.time}(tempIndex).trackID;
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
ContextRemoveFromTree(Figures.time,trackID);
end
function properties(src,evnt)
-global Figures HashedCells
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
-hullID = FindHull(get(gca,'CurrentPoint'));
-tempIndex = [HashedCells{Figures.time}.hullID]==hullID;
-trackID = HashedCells{Figures.time}(tempIndex).trackID;
ContextProperties(hullID,trackID);
end
+
+%% Helper functions
+function addHull(num)
+global Figures
+
+[hullID trackID] = getClosestCell();
+if(isempty(trackID)),return,end
+
+newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
+
+History('Push');
+LogAction('Split cell',trackID,[trackID newTracks]);
+DrawTree(Figures.tree.familyID);
+DrawCells();
+end
+
+function [hullID trackID] = getClosestCell()
+hullID = FindHull(get(gca,'CurrentPoint'));
+if(0>=hullID)
+ warndlg('Please click closer to the center of the desired cell','Unknown Cell');
+ trackID = [];
+ return
+end
+trackID = GetTrackID(hullID);
+end
diff --git a/src/MATLAB/CreateContextMenuTree.m b/src/MATLAB/CreateContextMenuTree.m
index 70472b08..ac1a048c 100644
--- a/src/MATLAB/CreateContextMenuTree.m
+++ b/src/MATLAB/CreateContextMenuTree.m
@@ -2,6 +2,8 @@ function CreateContextMenuTree()
%creates the context menu for the figure that displays the tree data and
%the subsequent function calls
+%--Eric Wait
+
global Figures
figure(Figures.tree.handle);
@@ -33,8 +35,9 @@ ContextChangeLabel(CellTracks(trackID).startTime,trackID);
end
function changeParent(src,evnt)
+global CellTracks
trackID = get(gco,'UserData');
-ContextChangeParent(trackID);
+ContextChangeParent(trackID,CellTracks(trackID).startTime);
end
function removeFromTree(src,evnt)
@@ -45,7 +48,6 @@ end
function properties(src,evnt)
global CellTracks
-
trackID = get(gco,'UserData');
ContextProperties(CellTracks(trackID).hulls(1),trackID);
end
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index 4a4f530a..2f456f05 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -1,6 +1,8 @@
function CreateMenuBar(handle)
%This sets up the custom menu bar for the given figure handle
+%--Eric Wait
+
global Figures
fileMenu = uimenu(...
@@ -98,6 +100,13 @@ uimenu(...
'Callback', @timeJump,...
'Accelerator', 't');
+uimenu(...
+ 'Parent', viewMenu,...
+ 'Label', 'Display Largest Tree',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @largestTree,...
+ 'Separator', 'on');
+
if(strcmp(get(handle,'Tag'),'cells'))
Figures.cells.menuHandles.saveMenu = saveMenu;
@@ -174,3 +183,19 @@ end
UpdateTimeIndicatorLine();
DrawCells();
end
+
+function largestTree(src,evnt)
+global CellFamilies Figures
+
+maxID = 1;
+for i=2:length(CellFamilies)
+ if(length(CellFamilies(maxID).tracks) < length(CellFamilies(i).tracks))
+ maxID = i;
+ end
+end
+if(Figures.tree.familyID == maxID),return,end
+
+Figures.tree.familyID = maxID;
+DrawTree(maxID);
+DrawCells();
+end
diff --git a/src/MATLAB/DeleteHullFromTrack.m b/src/MATLAB/DeleteHullFromTrack.m
index 67f2a5ca..e48f2f18 100644
--- a/src/MATLAB/DeleteHullFromTrack.m
+++ b/src/MATLAB/DeleteHullFromTrack.m
@@ -6,4 +6,6 @@ function DeleteHullFromTrack(hullID,trackID)
%It is intended that AddHullToTrack will be run after this function,
%otherwise this hull will cease to exist in any family or track
+%--Eric Wait
+
end
diff --git a/src/MATLAB/DrawCells.m b/src/MATLAB/DrawCells.m
index ec170ab9..301da85c 100644
--- a/src/MATLAB/DrawCells.m
+++ b/src/MATLAB/DrawCells.m
@@ -5,6 +5,8 @@ function DrawCells()
%will be more boldly colored, others will be with square labels and be
%slightly grayed out
+%--Eric Wait
+
global CellFamilies CellTracks CellHulls HashedCells Figures CONSTANTS
if(isempty(CellFamilies(Figures.tree.familyID).tracks)),return,end
@@ -20,7 +22,8 @@ yl=ylim;
%adjust the image display
hold off;
-imagesc(img);
+im = imagesc(img);
+set(im,'uicontextmenu',Figures.cells.contextMenuHandle);
set(gca,'Position',[.01 .01 .98 .98],'uicontextmenu',Figures.cells.contextMenuHandle);
axis off;
if xl(1)~=0 && xl(2)~=1
diff --git a/src/MATLAB/DrawTree.m b/src/MATLAB/DrawTree.m
index bf464e40..9afd693d 100644
--- a/src/MATLAB/DrawTree.m
+++ b/src/MATLAB/DrawTree.m
@@ -1,10 +1,16 @@
function DrawTree(familyID)
-%This will draw the family tree of the given family. Assumes binary tree
+%This will draw the family tree of the given family.
+
+%--Eric Wait
global CellFamilies HashedCells Figures
if(isempty(CellFamilies(familyID).tracks)),return,end
+%let the user know that this might take a while
+set(Figures.tree.handle,'Pointer','watch');
+set(Figures.cells.handle,'Pointer','watch');
+
Figures.tree.familyID = familyID;
trackID = CellFamilies(familyID).tracks(1);
@@ -27,6 +33,10 @@ set(gca,...
Figures.tree.axesHandle = gca;
hold off
UpdateTimeIndicatorLine();
+
+%let the user know that the drawing is done
+set(Figures.tree.handle,'Pointer','arrow');
+set(Figures.cells.handle,'Pointer','arrow');
end
function [xMin xCenter xMax] = traverseTree(trackID,initXmin)
diff --git a/src/MATLAB/ExportImage.m b/src/MATLAB/ExportImage.m
index fc07b4d7..247a888f 100644
--- a/src/MATLAB/ExportImage.m
+++ b/src/MATLAB/ExportImage.m
@@ -2,6 +2,8 @@ function ExportImage(figureHandle)
%this function is intended to create a high resolution file of the given
%figure for printing or sharing
+%--Eric Wait
+
global Figures
if(figureHandle == Figures.cells.handle)
diff --git a/src/MATLAB/FindHull.m b/src/MATLAB/FindHull.m
index cb4556ed..aab17521 100644
--- a/src/MATLAB/FindHull.m
+++ b/src/MATLAB/FindHull.m
@@ -2,6 +2,8 @@ function hullID = FindHull(curPoint)
%This function will find the closest hull to the given point and return the
%hullID if it is within CONSTANTS.clickMargin
+%--Eric Wait
+
global CONSTANTS CellHulls HashedCells Figures
centerOfMasses = reshape([CellHulls([HashedCells{Figures.time}(:).hullID]).centerOfMass]',2,[])';
diff --git a/src/MATLAB/GetNextColor.m b/src/MATLAB/GetNextColor.m
index ddc3f5a5..63d7ab1d 100644
--- a/src/MATLAB/GetNextColor.m
+++ b/src/MATLAB/GetNextColor.m
@@ -2,6 +2,8 @@ function color = GetNextColor()
%Takes the global Colors list and selects the next in the list and returns
%it
+%--Eric Wait
+
global Colors
persistent index
diff --git a/src/MATLAB/GetTrackID.m b/src/MATLAB/GetTrackID.m
index aeac1249..856b576c 100644
--- a/src/MATLAB/GetTrackID.m
+++ b/src/MATLAB/GetTrackID.m
@@ -1,6 +1,8 @@
function trackID = GetTrackID(hullID)
%Given a hull ID a track ID will be returned
+%--Eric Wait
+
global CellHulls HashedCells
hullTime = CellHulls(hullID).time;
diff --git a/src/MATLAB/GrayOutColor.m b/src/MATLAB/GrayOutColor.m
index 8529fe2a..1972f7b2 100644
--- a/src/MATLAB/GrayOutColor.m
+++ b/src/MATLAB/GrayOutColor.m
@@ -1,7 +1,9 @@
function grayedColor = GrayOutColor(color)
-%this will take the given color and give back a grayed out color of similar
+%This will take the given color and give back a grayed out color of similar
%hue
+%--Eric Wait
+
grayedColor = [0 0 0];
parfor i=1:3
if(0==color(i))
diff --git a/src/MATLAB/History.m b/src/MATLAB/History.m
index cc2aad32..ed2d84e5 100644
--- a/src/MATLAB/History.m
+++ b/src/MATLAB/History.m
@@ -1,5 +1,6 @@
function History(action)
-%This will keep track of any state changes.
+%This will keep track of any state changes. Call this function once the
+%new state is established. After the changes take place.
%Possible actions are:
%History('Push') = save current state to the stack
%History('Pop') = retrive the last state
@@ -10,158 +11,194 @@ function History(action)
%All of the data structures are saved on the stack, so do not set this
%value too high or you might run out of working memory
+%--Eric Wait
+
global CellFamilies CellTracks HashedCells CONSTANTS Figures CellHulls
-persistent hist;
-persistent top;
-persistent bottom;
-persistent redo;
-persistent empty;
-persistent full;
+persistent hist; %stack
+persistent current; %points to the last state saved on the stack
+persistent bottom; %points to the oldest or bottom most valid history
+persistent top; %points to the youngest or top most valid history
+persistent empty; %flag will be "empty" if only the original opened state is on the stack
+persistent full; %flag
+persistent exceededLimit; %flag to denote if CONSTANTS.historySize has ever been reached
if (isempty(hist))
- top = 1;%points to next place to push or is one greater than the current history
- bottom = 0;%points to the oldest or bottom most valid history
- redo = 0;%points to the youngest or top most valid history
- empty = 1;%flag will be "empty" if only the original opened state is on the stack
- full = 0;%flag
+ current = 1;
+ bottom = 0;
+ top = 0;
+ empty = 1;
+ full = 0;
+ exceededLimit = 0;
end
switch action
case 'Push'
- set(Figures.cells.menuHandles.undoMenu,'Enable','on');
- set(Figures.cells.menuHandles.saveMenu,'Enable','on');
- set(Figures.tree.menuHandles.undoMenu,'Enable','on');
- set(Figures.tree.menuHandles.saveMenu,'Enable','on');
if (empty)
empty = 0;
bottom = 1;
elseif (full)
%drop oldest history
+ exceededLimit = 1;
if (bottom < CONSTANTS.historySize)
bottom = bottom + 1;
else
bottom = 1;
end
end
-
- hist(top).CellFamilies = CellFamilies;
- hist(top).CellTracks = CellTracks;
- hist(top).HashedCells = HashedCells;
- hist(top).CellHulls = CellHulls;
- hist(top).Figures.tree.familyID = Figures.tree.familyID;
-
- redo = top;
- top = top + 1;
- if (top > CONSTANTS.historySize)
- top = 1;
+ current = current + 1;
+ if (current > CONSTANTS.historySize)
+ current = 1;
end
- if (top==bottom)
+ top = current;
+
+ hist(current).CellFamilies = CellFamilies;
+ hist(current).CellTracks = CellTracks;
+ hist(current).HashedCells = HashedCells;
+ hist(current).CellHulls = CellHulls;
+ hist(current).Figures.tree.familyID = Figures.tree.familyID;
+
+ if (current==bottom)
full = 1;
empty = 0;
end
-
- %"Disable" redo
- set(Figures.cells.menuHandles.redoMenu,'Enable','off');
- set(Figures.tree.menuHandles.redoMenu,'Enable','off');
-
+ setMenus();
case 'Pop'
if (~empty)
- if(redo < top)
- top = top - 2;
- else
- top = top - 1;
- end
- if (top == 0)
- top = CONSTANTS.historySize;
+ current = current - 1;
+ if (current == 0)
+ current = CONSTANTS.historySize;
end
full = 0;
- if (top==bottom)
+ if (current==bottom)
empty = 1;
- set(Figures.cells.menuHandles.undoMenu,'Enable','off');
- set(Figures.cells.menuHandles.saveMenu,'Enable','off');
- set(Figures.tree.menuHandles.undoMenu,'Enable','off');
- set(Figures.tree.menuHandles.saveMenu,'Enable','off');
- else
- set(Figures.cells.menuHandles.saveMenu,'Enable','on');
- set(Figures.tree.menuHandles.saveMenu,'Enable','on');
- end
-
- CellFamilies = hist(top).CellFamilies;
- CellTracks = hist(top).CellTracks;
- HashedCells = hist(top).HashedCells;
- CellHulls = hist(top).CellHulls;
- Figures.tree.familyID = hist(top).Figures.tree.familyID;
-
- %increment again so that top is always the next available place
- top = top + 1;
- if (top > CONSTANTS.historySize)
- top = 1;
end
- set(Figures.cells.menuHandles.redoMenu,'Enable','on');
- set(Figures.tree.menuHandles.redoMenu,'Enable','on');
+ CellFamilies = hist(current).CellFamilies;
+ CellTracks = hist(current).CellTracks;
+ HashedCells = hist(current).HashedCells;
+ CellHulls = hist(current).CellHulls;
+ Figures.tree.familyID = hist(current).Figures.tree.familyID;
%Update displays
DrawTree(Figures.tree.familyID);
DrawCells();
-
+ setMenus();
LogAction('Undo',[],[]);
- else
- set(Figures.cells.menuHandles.redoMenu,'Enable','off');
- set(Figures.tree.menuHandles.redoMenu,'Enable','off');
end
-
case 'Redo'
- if (redo>=top || (top<bottom && redo<top))
+ if (top>current || (bottom>top && top~=current))
%redo possible
-
- CellFamilies = hist(top).CellFamilies;
- CellTracks = hist(top).CellTracks;
- HashedCells = hist(top).HashedCells;
- CellHulls = hist(top).CellHulls;
- Figures.tree.familyID = hist(top).Figures.tree.familyID;
-
- %increment again so that top is always the next available place
- top = top + 1;
- if (top > CONSTANTS.historySize)
- top = 1;
+ current = current + 1;
+ if (current > CONSTANTS.historySize)
+ current = 1;
end
+ CellFamilies = hist(current).CellFamilies;
+ CellTracks = hist(current).CellTracks;
+ HashedCells = hist(current).HashedCells;
+ CellHulls = hist(current).CellHulls;
+ Figures.tree.familyID = hist(current).Figures.tree.familyID;
+
empty = 0;
- if(top==bottom)
+ if(current==bottom)
full = 1;
end
%Update displays
DrawTree(Figures.tree.familyID);
DrawCells();
-
- if (top>redo)
+ setMenus();
+ LogAction('Redo',[],[]);
+ end
+ case 'Init'
+ current = 1;
+ bottom = 1;
+ top = 1;
+ empty = 0;
+ full = 0;
+ exceededLimit = 0;
+ hist(current).CellFamilies = CellFamilies;
+ hist(current).CellTracks = CellTracks;
+ hist(current).HashedCells = HashedCells;
+ hist(current).CellHulls = CellHulls;
+ hist(current).Figures.tree.familyID = Figures.tree.familyID;
+ 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');
+ set(Figures.cells.menuHandles.saveMenu,'Enable','off');
+ set(Figures.tree.menuHandles.saveMenu,'Enable','off');
+end
+
+ function setMenus()
+ if(top>bottom)
+ %not "rolled over"
+ if(current<top)
+ %redo possible
+ set(Figures.cells.menuHandles.redoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.redoMenu,'Enable','on');
+ else
set(Figures.cells.menuHandles.redoMenu,'Enable','off');
- set(Figures.cells.menuHandles.undoMenu,'Enable','on');
set(Figures.tree.menuHandles.redoMenu,'Enable','off');
+ end
+ if(current>bottom)
+ %undo possible
+ set(Figures.cells.menuHandles.undoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','on');
+ else
+ set(Figures.cells.menuHandles.undoMenu,'Enable','off');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','off');
+ end
+ elseif(top==bottom && ~empty)
+ if(current~=top)
+ %redo and undo possible
+ set(Figures.cells.menuHandles.redoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.redoMenu,'Enable','on');
+ set(Figures.cells.menuHandles.undoMenu,'Enable','on');
set(Figures.tree.menuHandles.undoMenu,'Enable','on');
+ 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');
end
+ else
+ %"rolled over"
+ if(current>=bottom || current<top)
+ %redo possible
+ set(Figures.cells.menuHandles.redoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.redoMenu,'Enable','on');
+ else
+ set(Figures.cells.menuHandles.redoMenu,'Enable','off');
+ set(Figures.tree.menuHandles.redoMenu,'Enable','off');
+ end
+ if(current>bottom || current<=top)
+ %undo possible
+ set(Figures.cells.menuHandles.undoMenu,'Enable','on');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','on');
+ else
+ set(Figures.cells.menuHandles.undoMenu,'Enable','off');
+ set(Figures.tree.menuHandles.undoMenu,'Enable','off');
+ end
+ end
+
+ %check to see if we are at the original state from the .mat file
+ if(exceededLimit)
set(Figures.cells.menuHandles.saveMenu,'Enable','on');
set(Figures.tree.menuHandles.saveMenu,'Enable','on');
- LogAction('Redo',[],[]);
+ else
+ if(empty)
+ set(Figures.cells.menuHandles.saveMenu,'Enable','off');
+ set(Figures.tree.menuHandles.saveMenu,'Enable','off');
+ else
+ set(Figures.cells.menuHandles.saveMenu,'Enable','on');
+ set(Figures.tree.menuHandles.saveMenu,'Enable','on');
+ end
end
- case 'Init'
- top = 1;
- bottom = 1;
- redo = 1;
- empty = 0;
- full = 0;
- hist(top).CellFamilies = CellFamilies;
- hist(top).CellTracks = CellTracks;
- hist(top).HashedCells = HashedCells;
- hist(top).CellHulls = CellHulls;
- hist(top).Figures.tree.familyID = Figures.tree.familyID;
- top = 2;
-end
+ end %setMenu
end
diff --git a/src/MATLAB/InSubTree.m b/src/MATLAB/InSubTree.m
index e69de29b..10d43adb 100644
--- a/src/MATLAB/InSubTree.m
+++ b/src/MATLAB/InSubTree.m
@@ -0,0 +1,42 @@
+function bool = InSubTree(rootTrack,questionTrack)
+% InSubTree(rootTrack,questionTrack) will return a flag which represents
+% whether or not the questionTrack falls within the subtree rooted at
+% rootTrack
+
+%--Eric Wait
+
+global CellTracks
+bool = 0;
+
+%check if they are in the same family
+if(CellTracks(rootTrack).familyID ~= CellTracks(questionTrack).familyID),return,end
+
+%check if the track in question exists after the root
+if(CellTracks(rootTrack).endTime > CellTracks(questionTrack).startTime),return,end
+
+bool = traverse(rootTrack,questionTrack);
+end
+
+function bool = traverse(rootTrack,questionTrack)
+%modified depth first search wich does not go passed the time of the
+%questionTrack
+
+global CellTracks
+
+bool = 0;
+
+if (rootTrack == questionTrack)
+ bool = 1;
+ return
+elseif (CellTracks(rootTrack).endTime > CellTracks(questionTrack).startTime)
+ return
+end
+
+for i=1:length(CellTracks(rootTrack).childrenTracks)
+ bool = traverse(CellTracks(rootTrack).childrenTracks(i),questionTrack);
+ %once found, return
+ if(bool)
+ return
+ end
+end
+end
diff --git a/src/MATLAB/InitializeFigures.m b/src/MATLAB/InitializeFigures.m
index 16e63ce6..6fbebddf 100644
--- a/src/MATLAB/InitializeFigures.m
+++ b/src/MATLAB/InitializeFigures.m
@@ -4,6 +4,8 @@ function InitializeFigures()
%Figures will have all the menus, button actions, and context menus set up
%here
+%--Eric Wait
+
global Figures CONSTANTS
Figures.time = 1;
diff --git a/src/MATLAB/LEVer.m b/src/MATLAB/LEVer.m
index 8c121922..4752b1f6 100644
--- a/src/MATLAB/LEVer.m
+++ b/src/MATLAB/LEVer.m
@@ -1,4 +1,8 @@
function LEVer()
+%Main program
+
+%--Eric Wait
+
global Figures
%if LEVer is already opened, save state just in case the User cancels the
diff --git a/src/MATLAB/LogAction.m b/src/MATLAB/LogAction.m
index e6537f2c..fda88edd 100644
--- a/src/MATLAB/LogAction.m
+++ b/src/MATLAB/LogAction.m
@@ -5,6 +5,8 @@ function LogAction(action,oldValue,newValue)
%oldValue and newValue are used to show what numbers are changed. Please
%use the action string to denote what the values represent
+%--Eric Wait
+
global Figures CONSTANTS
time = clock;%[year month day hour minute seconds]
diff --git a/src/MATLAB/NewCellFamily.m b/src/MATLAB/NewCellFamily.m
index 9bae9820..a7d130f6 100644
--- a/src/MATLAB/NewCellFamily.m
+++ b/src/MATLAB/NewCellFamily.m
@@ -1,4 +1,9 @@
function curFamilyID = NewCellFamily(cellHullID,t)
+%Create a empty Family that will contain one track that contains only one
+%hull
+
+%--Eric Wait
+
global CellFamilies
if(isempty(CellFamilies))
diff --git a/src/MATLAB/NewCellTrack.m b/src/MATLAB/NewCellTrack.m
index 87c4a14c..6f5b3116 100644
--- a/src/MATLAB/NewCellTrack.m
+++ b/src/MATLAB/NewCellTrack.m
@@ -1,4 +1,9 @@
function curCellTrackID = NewCellTrack(familyID,cellHullID,t)
+%Creates a new track in the Family that contains just the given hull.
+%***Use this with empty Families only***
+
+%--Eric Wait
+
global CellTracks
curCellTrackID = 1;
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index e2b4f237..6506455d 100644
--- a/src/MATLAB/OpenData.m
+++ b/src/MATLAB/OpenData.m
@@ -3,9 +3,11 @@ function opened = OpenData()
%results. If the latter, the data will be converted to LEVer's data scheme
%and save out to a new file.
+%--Eric Wait
+
global Figures Colors CONSTANTS CellFamilies CellHulls HashedCells Costs CellTracks
if(isempty(Figures))
- fprintf('LEVer ver 3.0\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 3.1\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
diff --git a/src/MATLAB/ProcessNewborns.m b/src/MATLAB/ProcessNewborns.m
index ee67775e..e1eee9cf 100644
--- a/src/MATLAB/ProcessNewborns.m
+++ b/src/MATLAB/ProcessNewborns.m
@@ -2,6 +2,8 @@ function ProcessNewborns(families)
%This takes all the families with start times > 1 and attempts to attach
%that families' tracks to other families that start before said family
+%--Eric Wait
+
global CellFamilies CellTracks CellHulls Costs CONSTANTS
size = length(families);
for i=1:size
diff --git a/src/MATLAB/RehashCellTracks.m b/src/MATLAB/RehashCellTracks.m
index da278792..4e6ef608 100644
--- a/src/MATLAB/RehashCellTracks.m
+++ b/src/MATLAB/RehashCellTracks.m
@@ -1,25 +1,30 @@
function RehashCellTracks(trackID, newStartTime)
-%This function will rearange the hulls in the given track so that the
-%newTime will hash correctly
+%RehashedCellTracks(trackID,newStartTime) will rearange the hulls in the
+%given track so that the newTime will hash correctly.
%The hulls are hashed so that the index into the cell array is time of hull
%subtract start time of track. eg hash = time of hull -
%CellTracks(i).startTime
%
+%If newStartTime == oldStartTime, only the endTime will change. Good for
+%removing all of the 0's at the end of the hulls list for a given track.
+%
%***WARNING*** if oldStartTime < newStartTime and there are hulls within
%[oldStartTime newStartTime) THEY WILL BE REMOVED FROM THE TRACK!!!
+%--Eric Wait
+
global CellTracks CellHulls
dif = CellTracks(trackID).startTime - newStartTime;
-if(sign(dif))
+if(0<dif)
for i=length(CellTracks(trackID).hulls):-1:1
CellTracks(trackID).hulls(i+dif) = CellTracks(trackID).hulls(i);
end
for i=1:dif
CellTracks(trackID).hulls(i) = 0;
end
-else
+elseif(0>dif)
oldLength = length(CellTracks(trackID).hulls);
for i=1-dif:length(CellTracks(trackID).hulls)
CellTracks(trackID).hulls(i+dif) = CellTracks(trackID).hulls(i);
@@ -35,4 +40,6 @@ if(indexOfLastHull~=length(CellTracks(trackID).hulls))
CellTracks(trackID).hulls = CellTracks(trackID).hulls(1:indexOfLastHull);
CellTracks(trackID).endTime = CellHulls(CellTracks(trackID).hulls(end)).time;
end
+
+CellTracks(trackID).startTime = newStartTime;
end
diff --git a/src/MATLAB/RemoveFromTree.m b/src/MATLAB/RemoveFromTree.m
index 98b16353..7064453d 100644
--- a/src/MATLAB/RemoveFromTree.m
+++ b/src/MATLAB/RemoveFromTree.m
@@ -1,6 +1,14 @@
-function newFamilyID = RemoveFromTree(time,trackID)
+function newFamilyID = RemoveFromTree(time,trackID,combineSiblingWithParent)
+%newFamily = RemoveFromTree(time,trackID,dealWithSibling)
%This will remove the track and any of its children from its current family
%and create a new family rooted at the given track
+%If you want the current track's sibling to be combined with its parent,
+%pass combineSiblingWithParent='yes' otherwise 'no'
+%
+%***IF YOU PASS 'NO', YOU MUST DEAL WITH ANY SIBLING YOURSELF!!! OTHERWISE
+%THERE WILL BE ISSUES WITH THE DATA****
+
+%--Eric Wait
global CellFamilies CellTracks CellHulls
@@ -8,8 +16,9 @@ hash = time - CellTracks(trackID).startTime + 1;
oldFamilyID = CellTracks(trackID).familyID;
newFamilyID = NewCellFamily(CellTracks(trackID).hulls(hash),time);
newTrackID = CellFamilies(newFamilyID).rootTrackID;
+CellTracks(trackID).hulls(hash) = 0;
-for i=0:length(CellTracks(trackID).hulls(hash+1:end))
+for i=1:length(CellTracks(trackID).hulls(hash:end))-1
if(CellTracks(trackID).hulls(hash+i)~=0)
AddHullToTrack(CellTracks(trackID).hulls(hash+i),newTrackID,[]);
end
@@ -20,29 +29,37 @@ for i=1:length(CellTracks(trackID).childrenTracks)
ChangeTrackAndChildrensFamily(oldFamilyID,newFamilyID,CellTracks(trackID).childrenTracks(i));
CellTracks(CellTracks(trackID).childrenTracks(i)).parentTrack = newTrackID;
end
-index = CellFamilies(oldFamilyID).tracks == trackID;
-CellFamilies(oldFamilyID).tracks(index) = [];
-CellFamilies(newFamilyID).tracks(end+1) = newTrackID;
+
+if(~isempty(find(CellFamilies(oldFamilyID).tracks==newTrackID, 1)))
+ CellFamilies(newFamilyID).tracks(end+1) = newTrackID;
+end
CellTracks(newTrackID).familyID = newFamilyID;
CellTracks(newTrackID).childrenTracks = CellTracks(trackID).childrenTracks;
+for i=1:length(CellTracks(newTrackID).childrenTracks)
+ CellTracks(CellTracks(newTrackID).childrenTracks(i)).parentTrack = newTrackID;
+end
+CellTracks(trackID).childrenTracks = [];
%clean up old track
if(isempty(find([CellTracks(trackID).hulls]~=0, 1)))
- if(~isempty(CellTracks(trackID).siblingTrack))
- if(~isempty(CellTracks(CellTracks(trackID).parentTrack).startTime))
+ if(~isempty(CellTracks(trackID).siblingTrack)&& strcmp(combineSiblingWithParent,'yes'))
+% if(~isempty(CellTracks(CellTracks(trackID).parentTrack).startTime))
CombineTrackWithParent(CellTracks(trackID).siblingTrack);
- end
+% end
+ end
+ RemoveTrackFromFamily(trackID);
+ if(~isempty(CellTracks(trackID).parentTrack))
+ index = CellTracks(CellTracks(trackID).parentTrack).childrenTracks==trackID;
+ CellTracks(CellTracks(trackID).parentTrack).childrenTracks(index) = [];
end
CellTracks(trackID).familyID = [];
CellTracks(trackID).parentTrack = [];
CellTracks(trackID).siblingTrack = [];
- CellTracks(trackID).childrenTracks = [];
CellTracks(trackID).hulls = [];
CellTracks(trackID).startTime = [];
CellTracks(trackID).endTime = [];
CellTracks(trackID).color = [];
else
- CellTracks(trackID).childrenTracks = [];
index = find([CellTracks(trackID).hulls]~=0, 1,'last');
CellTracks(trackID).endTime = CellHulls(CellTracks(trackID).hulls(index)).time;
end
diff --git a/src/MATLAB/RemoveHull.m b/src/MATLAB/RemoveHull.m
new file mode 100644
index 00000000..91d039c4
--- /dev/null
+++ b/src/MATLAB/RemoveHull.m
@@ -0,0 +1,28 @@
+function RemoveHull(hullID)
+% RemoveHull(hullID) will LOGICALLY remove the hull. Which means that the
+% hull will have a flag set that means that it does not exist anywhere and
+% should not be drawn on the cells figure
+
+%--Eric Wait
+
+global CellTracks HashedCells CellHulls
+
+trackID = GetTrackID(hullID);
+
+%remove hull from its track
+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);
+elseif(index==length(CellTracks(trackID).hulls))
+ RehashCellTracks(trackID,CellTracks(trackID).startTime);
+end
+
+%remove hull from HashedCells
+time = CellHulls(hullID).time;
+index = [HashedCells{time}.hullID]==hullID;
+HashedCells{time}(index) = [];
+
+CellHulls(hullID).deleted = 1;
+end
diff --git a/src/MATLAB/RemoveTrackFromFamily.m b/src/MATLAB/RemoveTrackFromFamily.m
new file mode 100644
index 00000000..cf564045
--- /dev/null
+++ b/src/MATLAB/RemoveTrackFromFamily.m
@@ -0,0 +1,28 @@
+function RemoveTrackFromFamily(trackID)
+% RemoveTrackFromFamily(trackID) only removes the track from the tracks
+% list currently assosiated in the CellFamily entery and updated the other
+% CellFamily fields.
+% This is not intended to change the structure, just to keep the data
+% correct
+
+%--Eric Wait
+
+global CellFamilies CellTracks
+familyID = CellTracks(trackID).familyID;
+if(isempty(familyID)),return,end
+
+index = CellFamilies(familyID).tracks==trackID;
+
+%remove track
+CellFamilies(familyID).tracks(index) = [];
+
+%update times
+[minimum index] = min([CellTracks(CellFamilies(familyID).tracks).startTime]);
+CellFamilies(familyID).startTime = minimum;
+CellFamilies(familyID).endTime = max([CellTracks(CellFamilies(familyID).tracks).endTime]);
+
+%set new root
+if(CellFamilies(familyID).rootTrackID == trackID)
+ CellFamilies(familyID).rootTrackID = CellFamilies(familyID).tracks(index);
+end
+end
diff --git a/src/MATLAB/ResegmentHull.m b/src/MATLAB/ResegmentHull.m
new file mode 100644
index 00000000..dc58f94a
--- /dev/null
+++ b/src/MATLAB/ResegmentHull.m
@@ -0,0 +1,48 @@
+function newHulls = ResegmentHull(hull, k)
+% Splits hull int k pieces using kmeans, returns the k split hulls or [] if
+% there are errors.
+
+%--Mark Winter
+
+global CONSTANTS
+
+newHulls = [];
+
+% k-means clustering of (x,y) coordinates of cell interior
+[r c] = ind2sub(CONSTANTS.imageSize, hull.indexPixels);
+kIdx = kmeans([c,r], k, 'Replicates',5, 'EmptyAction','drop');
+
+if ( any(isnan(kIdx)) )
+ return;
+end
+
+nh = struct('time', [], 'points', [], 'centerOfMass', [], 'indexPixels', [], 'deleted', 0);
+for i=1:k
+ bIdxPix = (kIdx == i);
+
+ hx = c(bIdxPix);
+ hy = r(bIdxPix);
+
+ % If any sub-object is less than 15 pixels then cannot split this
+ % hull
+ if ( nnz(bIdxPix) < 15 )
+ newHulls = [];
+ return;
+ end
+
+ nh.indexPixels = hull.indexPixels(bIdxPix);
+ nh.centerOfMass = mean([hx hy]);
+ nh.time = hull.time;
+
+ try
+ chIdx = convhull(hx, hy);
+ catch excp
+ newHulls = [];
+ return;
+ end
+
+ nh.points = [hx(chIdx) hy(chIdx)];
+
+ newHulls = [newHulls nh];
+end
+end
diff --git a/src/MATLAB/SaveData.m b/src/MATLAB/SaveData.m
index e4f57dfe..03269839 100644
--- a/src/MATLAB/SaveData.m
+++ b/src/MATLAB/SaveData.m
@@ -1,14 +1,21 @@
function SaveData()
%This will save the current state back to the opened dataset
-global CellFamilies CellTracks HashedCells CONSTANTS Costs CellHulls
+
+%--Eric Wait
+
+global CellFamilies CellTracks HashedCells CONSTANTS Costs CellHulls Figures
if (exist('LEVerSettings.mat','file')~=0)
load('LEVerSettings.mat');
else
- settings.matPath = ['.\' CONSTANTS.datasetName '_v3.mat'];
+ settings.matPath = ['.\' CONSTANTS.datasetName '_LEVer_edits.mat'];
end
-save(settings.matPath,...
+%let the user know that this might take a while
+set(Figures.tree.handle,'Pointer','watch');
+set(Figures.cells.handle,'Pointer','watch');
+
+save([settings.matFilePath CONSTANTS.datasetName '_LEVer_edits.mat'],...
'CellFamilies','CellHulls','CellTracks','HashedCells','Costs','CONSTANTS');
%no longer "dirty"
@@ -16,4 +23,8 @@ set(Figures.tree.menuHandles.saveMenu,'Enable','off');
set(Figures.cells.menuHandles.saveMenu,'Enable','off');
LogAction('Saved',[],[]);
+
+%let the user know that the drawing is done
+set(Figures.tree.handle,'Pointer','arrow');
+set(Figures.cells.handle,'Pointer','arrow');
end
diff --git a/src/MATLAB/SaveDataAs.m b/src/MATLAB/SaveDataAs.m
index 327c01ba..b0af3b07 100644
--- a/src/MATLAB/SaveDataAs.m
+++ b/src/MATLAB/SaveDataAs.m
@@ -1,4 +1,8 @@
function SaveDataAs()
+%Save the current state to a user defined dir
+
+%--Eric Wait
+
global CellFamilies CellTracks HashedCells CONSTANTS Costs CellHulls Figures
if (exist('LEVerSettings.mat','file')~=0)
diff --git a/src/MATLAB/SiblingDistance.m b/src/MATLAB/SiblingDistance.m
index 129cb9be..bc3fd117 100644
--- a/src/MATLAB/SiblingDistance.m
+++ b/src/MATLAB/SiblingDistance.m
@@ -4,8 +4,9 @@ function distance = SiblingDistance(cell1HullID,cell2HullID)
%and maxPixelDistance. Make sure they are set in the global CONSTANTS
%variable.
+%--Eric Wait
+
global CellHulls CONSTANTS
-distance = Inf;
pixelsCell1 = CellHulls(cell1HullID).indexPixels;
pixelsCell2 = CellHulls(cell2HullID).indexPixels;
@@ -16,8 +17,8 @@ if (length(pixelsCell2) < length(pixelsCell1))
pixelsCell2 = temp;
end
-[yCell1 xCell1] = ind2sub(CONSTANTS.ImageSize,pixelsCell1);
-[yCell2 xCell2] = ind2sub(CONSTANTS.ImageSize,pixelsCell2);
+[yCell1 xCell1] = ind2sub(CONSTANTS.imageSize,pixelsCell1);
+[yCell2 xCell2] = ind2sub(CONSTANTS.imageSize,pixelsCell2);
minPixelDistance = Inf;
diff --git a/src/MATLAB/SplitHull.m b/src/MATLAB/SplitHull.m
new file mode 100644
index 00000000..7e8bebcc
--- /dev/null
+++ b/src/MATLAB/SplitHull.m
@@ -0,0 +1,25 @@
+function newTrackIDs = SplitHull(hullID, k)
+% Attempt to split hull corresponding to hullId into k pieces, and update
+% associated data structures if successful.
+
+%--Mark Winter
+
+global CellHulls
+
+newHulls = ResegmentHull(CellHulls(hullID), k);
+
+if ( isempty(newHulls) )
+ return;
+end
+
+% Just arbitrarily assign clone's hull for now
+CellHulls(hullID) = newHulls(1);
+
+newTrackIDs = [length(CellHulls)+1 length(CellHulls)+length(newHulls)];
+% Other hulls are just added off the clone
+for i=2:length(newHulls)
+ CellHulls(end+i-1) = newHulls(i);
+ NewCellFamily(length(CellHulls), newHulls(i).time);
+end
+
+end
diff --git a/src/MATLAB/SplitTrack.m b/src/MATLAB/SplitTrack.m
index 22f98153..944b5691 100644
--- a/src/MATLAB/SplitTrack.m
+++ b/src/MATLAB/SplitTrack.m
@@ -4,6 +4,8 @@ function newTrackID = SplitTrack(trackID,hullID)
%given track. Returns the trackID of the new track, which is the first
%child of the given track.
+%--Eric Wait
+
global CellFamilies CellTracks
%get all the hulls that come after hullID (in time that is)
diff --git a/src/MATLAB/SwapTrackLabels.m b/src/MATLAB/SwapTrackLabels.m
index 5d036872..63fa5fbe 100644
--- a/src/MATLAB/SwapTrackLabels.m
+++ b/src/MATLAB/SwapTrackLabels.m
@@ -2,6 +2,8 @@ function SwapTrackLabels(time,trackID1,trackID2)
%This function will swap the hulls of the two tracks from the given time
%forward. Any children will also be swaped
+%--Eric Wait
+
global CellTracks CellHulls
track1Hash = time - CellTracks(trackID1).startTime + 1;
diff --git a/src/MATLAB/TimeChange.m b/src/MATLAB/TimeChange.m
index 0a7bf254..05dea765 100644
--- a/src/MATLAB/TimeChange.m
+++ b/src/MATLAB/TimeChange.m
@@ -2,6 +2,8 @@ function TimeChange(time)
%Takes the given time and changes the figures to that time or the closest
%time within [1 length(HashedCells)]
+%--Eric Wait
+
global Figures HashedCells
if(time > length(HashedCells))
diff --git a/src/MATLAB/TogglePlay.m b/src/MATLAB/TogglePlay.m
index b067bcc0..214b7d2e 100644
--- a/src/MATLAB/TogglePlay.m
+++ b/src/MATLAB/TogglePlay.m
@@ -1,5 +1,10 @@
function TogglePlay(src,evnt)
+% Turn the timer on and off depending on previous state
+
+%--Eric Wait
+
global Figures
+
if(strcmp(Figures.advanceTimerHandle.Running,'off'))
set(Figures.cells.menuHandles.playMenu, 'Checked', 'on');
start(Figures.advanceTimerHandle);
diff --git a/src/MATLAB/UpdateHashedCellsTrackID.m b/src/MATLAB/UpdateHashedCellsTrackID.m
index 9826e2cc..d803e733 100644
--- a/src/MATLAB/UpdateHashedCellsTrackID.m
+++ b/src/MATLAB/UpdateHashedCellsTrackID.m
@@ -2,13 +2,13 @@ function UpdateHashedCellsTrackID(newTrackID,hulls,startTime)
%This will take the list of hulls and update their trackIDs to the given
%trackID
+%--Eric Wait
+
global HashedCells
for i=1:length(hulls)
if(~hulls(i)),continue,end
- index = [HashedCells{startTime+i-1}(:).hullID]==hulls(i);
- %if(~isempty(index))
- HashedCells{startTime+i-1}(index).trackID = newTrackID;
- %end
+ index = [HashedCells{startTime+i-1}.hullID]==hulls(i);
+ HashedCells{startTime+i-1}(index).trackID = newTrackID;
end
end
diff --git a/src/MATLAB/UpdateTimeIndicatorLine.m b/src/MATLAB/UpdateTimeIndicatorLine.m
index 0b732814..19d114e3 100644
--- a/src/MATLAB/UpdateTimeIndicatorLine.m
+++ b/src/MATLAB/UpdateTimeIndicatorLine.m
@@ -2,6 +2,8 @@ function UpdateTimeIndicatorLine()
%Changes the postition of the Red Line that indicates the current time
%displayed
+%--Eric Wait
+
global Figures
if(ishandle(Figures.tree.timeIndicatorLine))
diff --git a/src/MATLAB/driver.m b/src/MATLAB/driver.m
deleted file mode 100644
index 521b0154..00000000
--- a/src/MATLAB/driver.m
+++ /dev/null
@@ -1,65 +0,0 @@
-function convert()
-%preallocate tables for speed
-
-global CellFamilies CellHulls HashedCells Costs CONSTANTS Figures Colors
-%CONSTANTS.datasetName = 'ER81_E12pt5_0527090025_3_3AC05_07';
-CONSTANTS.datasetName = 'ER81_E12_0527090025_3_3AC03_02';
-%CONSTANTS.datasetName = 'ER81_E12pt5_0527090025_3_2AB02_05';
-data = [CONSTANTS.datasetName ' tracked_hulls.mat'];
-CONSTANTS.rootFolder = ['..\..\Templetiffs\Temple Lineages\' CONSTANTS.datasetName '\'];
-load(data);
-load 'colors.mat'
-
-Colors = colors;
-Costs = gConnect;
-
-CONSTANTS.ImageSize = unique([objHulls(:).imSize]);
-CONSTANTS.maxPixelDistance = 40;
-CONSTANTS.maxCenterOfMassDistance = 80;
-CONSTANTS.minParentCandidateTimeFrame = 5;
-CONSTANTS.minParentHistoryTimeFrame = 5;
-CONSTANTS.minFamilyTimeFrame = 5;
-CONSTANTS.maxFrameDifference = 1;
-
-HashedCells = cell(0,length(objHulls));
-i=1;
-
-CellHulls = struct(...
- 'time', {objHulls(i).t},...
- 'points', {objHulls(i).pts},...
- 'centerOfMass', {objHulls(i).COM},...
- 'indexPixels', {objHulls(i).indPixels});
-
-if objHulls(i).inID == 0
- NewCellFamily(i,objHulls(i).t);
-else
- AddHullToTrack(i,[],objHulls(i).inID);
-end
-
-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;
-
- if objHulls(i).inID == 0
- NewCellFamily(i,objHulls(i).t);
- else
- AddHullToTrack(i,[],objHulls(i).inID);
- end
-end
-
-ProcessNewborns();
-Figures.tree = figure;
-Figures.cells = figure;
-
-% for i=1:length(CellFamilies)
-% if(isempty(CellFamilies(i).tracks)),return,end
-% DrawTree(i);
-% DrawCells(450,i);
-% pause(1);
-% i
-% end
-DrawTree(10);
-DrawCells(1,10);
-end
--
GitLab