diff --git a/src/MATLAB/AddHullToTrack.m b/src/MATLAB/AddHullToTrack.m
index 1b72f845bc7ae9f898a26880444a18f356e47297..ed6e5a114bc948940bde81871c713272ac7ce8b9 100644
--- a/src/MATLAB/AddHullToTrack.m
+++ b/src/MATLAB/AddHullToTrack.m
@@ -1,11 +1,11 @@
function AddHullToTrack(hullID,trackID,previousHullID)
-% function AddHullToTrack(time,hullID,trackID,previousTime,previousHullID)
-%The hullID will be added to the track and hashed at the given time
+% function AddHullToTrack(hullID,trackID,previousHullID)
+%The hullID will be added to the track
%
-%If trackID is given, previousTime & previousHullID are not used. Safe to
-%send [] or vice versa.
+%If trackID is given, previousHullID is not used. Safe to
+%send [] for either trackID or previousHullID.
%Prereq to leave trackID empty - Track to be added to exists and the
-%previousHullID at previousTime exists in that track. Also, it has been
+%previousHullID exists in that track. Also, it has been
%removed from any previous track assosiation.
%--Eric Wait
diff --git a/src/MATLAB/AddSingleHullToTrack.m b/src/MATLAB/AddSingleHullToTrack.m
new file mode 100644
index 0000000000000000000000000000000000000000..161ddcbc1152d172581a6823ef594af74b2c397a
--- /dev/null
+++ b/src/MATLAB/AddSingleHullToTrack.m
@@ -0,0 +1,102 @@
+function AddSingleHullToTrack(oldTrackID,newTrackID)
+% AddSingleHullToTrack(oldTrackID,newTrackID)
+% This function is indended for the oldTrack to be just a single hull,
+% typicaly when a hull has been split and now that new hull is being added
+% to a track. This function takes the hull and merges it into the
+% newTrack. The parent and child relationships of the newTrack will be
+% maintained.
+
+%--Eric Wait
+
+global CellTracks HashedCells CellFamilies Figures
+
+if(~isempty(CellTracks(oldTrackID).parentTrack) && ...
+ ~isempty(CellTracks(oldTrackID).childrenTracks) && ...
+ 1~=length(CellTracks(oldTrackID).hulls))
+ error([num2str(oldTrackID) ' is not a single hull track or has a parent/child']);
+end
+
+if(CellTracks(oldTrackID).startTime<CellTracks(newTrackID).startTime)
+ %old before new
+ if(~isempty(CellTracks(newTrackID).parentTrack))
+ moveMitosisUp(CellTracks(oldTrackID).startTime,...
+ CellTracks(newTrackID).siblingTrack);
+ end
+ AddHullToTrack(CellTracks(oldTrackID).hulls(1),newTrackID,[]);
+elseif(CellTracks(oldTrackID).startTime>CellTracks(newTrackID).endTime)
+ %new before old
+ if(~isempty(CellTracks(newTrackID).childrenTracks))
+ moveMitosisDown(CellTracks(oldTrackID).startTime,newTrackID);
+ end
+ AddHullToTrack(CellTracks(oldTrackID).hulls(1),newTrackID,[]);
+else
+ %old within new
+ if(~isempty(find([HashedCells{Figures.time}.trackID]==newTrackID,1)))
+ SwapTrackLabels(CellTracks(oldTrackID).startTime,oldTrackID,newTrackID);
+ else
+ AddHullToTrack(CellTracks(oldTrackID).hulls(1),newTrackID,[]);
+ end
+end
+
+%clean out old track/family
+familyID = CellTracks(oldTrackID).familyID;
+CellFamilies(familyID).rootTrackID = [];
+CellFamilies(familyID).tracks = [];
+CellFamilies(familyID).startTime = [];
+CellFamilies(familyID).endTime = [];
+CellTracks(oldTrackID).familyID = [];
+CellTracks(oldTrackID).parentTrack = [];
+CellTracks(oldTrackID).siblingTrack = [];
+CellTracks(oldTrackID).childrenTracks = [];
+CellTracks(oldTrackID).hulls = [];
+CellTracks(oldTrackID).startTime = [];
+CellTracks(oldTrackID).endTime = [];
+CellTracks(oldTrackID).timeOfDeath = [];
+CellTracks(oldTrackID).color = [];
+end
+
+function moveMitosisUp(time,siblingTrackID)
+global CellTracks
+
+%remove hulls from parent
+hash = time - CellTracks(CellTracks(siblingTrackID).parentTrack).startTime + 1;
+hulls = CellTracks(CellTracks(siblingTrackID).parentTrack).hulls(hash:end);
+CellTracks(CellTracks(siblingTrackID).parentTrack).hulls(hash:end) = 0;
+RehashCellTracks(CellTracks(siblingTrackID).parentTrack,CellTracks(CellTracks(siblingTrackID).parentTrack).startTime);
+
+%add hulls to sibling
+for i=1:length(hulls)
+ AddHullToTrack(hulls(i),siblingTrackID,[]);
+end
+end
+
+function moveMitosisDown(time,trackID)
+global CellTracks CellFamilies
+
+remove = 0;
+children = {};
+
+for i=1:length(CellTracks(trackID).childrenTracks)
+ if(CellTracks(CellTracks(trackID).childrenTracks(i)).endTime <= time)
+ remove = 1;
+ break
+ end
+ hash = time - CellTracks(CellTracks(trackID).childrenTracks(i)).startTime + 1;
+ if(0<hash)
+ children(i).startTime = CellTracks(CellTracks(trackID).childrenTracks(i)).startTime;
+ children(i).hulls = CellTracks(CellTracks(trackID).childrenTracks(i)).hulls(1:hash);
+ end
+end
+
+if(remove)
+ RemoveChildren(trackID);
+else
+ for i=1:length(children)
+ familyID = NewCellFamily(children(i).hulls(1),children(i).startTime);
+ newTrackID = CellFamilies(familyID).rootTrackID;
+ for j=2:length(children(i).hulls)
+ AddHullToTrack(children(i).hulls(j),newTrackID,[]);
+ end
+ end
+end
+end
diff --git a/src/MATLAB/ChangeLabel.m b/src/MATLAB/ChangeLabel.m
index 4d8109b0142dd6dfb93fa368edccd6bcab58ba56..20f00ee6043df61f363ef905da045958c46fe565 100644
--- a/src/MATLAB/ChangeLabel.m
+++ b/src/MATLAB/ChangeLabel.m
@@ -17,7 +17,7 @@ function ChangeLabel(time,oldTrackID,newTrackID)
%--Eric Wait
-global CellTracks CellFamilies CellHulls
+global CellTracks CellHulls
bothHaveChildren = 0;%flag to deal with conflicting children
%flags to deal with position of tracks relitive to one another
@@ -58,7 +58,7 @@ if(oldEmptied)
if(oldBeforeNew)
%deal with any children
if(~isempty(CellTracks(oldTrackID).childrenTracks))
- dropChildren(oldTrackID);
+ RemoveChildren(oldTrackID);
end
if(~isempty(CellTracks(newTrackID).siblingTrack) && ...
isempty(find(CellTracks(oldTrackID).childrenTracks==CellTracks(newTrackID).siblingTrack, 1)))
@@ -79,7 +79,7 @@ if(oldEmptied)
CellTracks(newTrackID).childrenTracks = [];
CellTracks(oldTrackID).siblingTrack = [];
else
- dropChildren(newTrackID);
+ RemoveChildren(newTrackID);
end
moveChildren(oldTrackID,newTrackID);
elseif(~isempty(CellTracks(newTrackID).childrenTracks))
@@ -90,7 +90,7 @@ if(oldEmptied)
CellTracks(newTrackID).childrenTracks = [];
CellTracks(oldTrackID).siblingTrack = [];
else
- dropChildren(newTrackID);
+ RemoveChildren(newTrackID);
end
elseif(~isempty(CellTracks(oldTrackID).childrenTracks))
moveChildren(oldTrackID,newTrackID);
@@ -103,8 +103,10 @@ if(oldEmptied)
%clean up other fields
RemoveTrackFromFamily(oldTrackID);
+ CellTracks(oldTrackID).familyID = [];
CellTracks(oldTrackID).parentTrack = [];
CellTracks(oldTrackID).siblingTrack = [];
+ CellTracks(oldTrackID).hulls = [];
CellTracks(oldTrackID).startTime = [];
CellTracks(oldTrackID).endTime = [];
CellTracks(oldTrackID).color = [];
@@ -114,41 +116,31 @@ else %the old track still exists in some fasion
%the last hull from the old track has been moved over and had
%children
if(CellHulls(lastOldHull).time<CellTracks(newTrackID).endTime)
- dropChildren(oldTrackID);
+ RemoveChildren(oldTrackID);
elseif(CellHulls(lastOldHull).time>=CellTracks(newTrackID).endTime)
if(~isempty(CellTracks(newTrackID).childrenTracks))
- dropChildren(newTrackID);
+ RemoveChildren(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(newTrackID);
+ RemoveChildren(newTrackID);
end
end
end
-function dropChildren(trackID)
-%remove children from tree
-global CellTracks
-
-familyIDs = [];
-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
-
function moveChildren(oldTrackID,newTrackID)
global CellTracks
if(isempty(CellTracks(oldTrackID).childrenTracks))
%no children
elseif(isempty(CellTracks(newTrackID).childrenTracks))
CellTracks(newTrackID).childrenTracks = CellTracks(oldTrackID).childrenTracks;
+ for i=1:length(CellTracks(newTrackID).childrenTracks)
+ CellTracks(CellTracks(newTrackID).childrenTracks(i)).parentTrack = newTrackID;
+ end
+
if(CellTracks(oldTrackID).familyID ~= CellTracks(newTrackID).familyID)
for i=1:length(CellTracks(oldTrackID).childrenTracks)
ChangeTrackAndChildrensFamily(CellTracks(oldTrackID).familyID,CellTracks(newTrackID).familyID,CellTracks(oldTrackID).childrenTracks(i));
diff --git a/src/MATLAB/ChangeTrackAndChildrensFamily.m b/src/MATLAB/ChangeTrackAndChildrensFamily.m
index 043a07ee89ab7983ee599b696ace05101dacd50d..c988e5f4aaa569e5be6cd6cf4195e551dc8f1747 100644
--- a/src/MATLAB/ChangeTrackAndChildrensFamily.m
+++ b/src/MATLAB/ChangeTrackAndChildrensFamily.m
@@ -33,6 +33,7 @@ function trackList = traverseTree(newFamilyID,trackID)
%will add the tracks to the new family along the way
global CellFamilies CellTracks
+RemoveTrackFromFamily(trackID);
%add track
CellFamilies(newFamilyID).tracks(end+1) = trackID;
@@ -50,6 +51,4 @@ 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 fcc5aef54a441e864fc33d52e692112c7a8caf72..11623dda9b857252f40b8812bace48e5abdf946d 100644
--- a/src/MATLAB/ChangeTrackParent.m
+++ b/src/MATLAB/ChangeTrackParent.m
@@ -45,7 +45,7 @@ CellTracks(childTrackID).parentTrack = parentTrackID;
oldFamilyID = CellTracks(childTrackID).familyID;
newFamilyID = CellTracks(siblingTrackID).familyID;
-CellTracks(childTrackID).familyID = newFamilyID;
+% CellTracks(childTrackID).familyID = newFamilyID;
ChangeTrackAndChildrensFamily(oldFamilyID,newFamilyID,childTrackID);
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index 8af1d7d45dcb0531292e6039aaa22297a2906951..bf4e3f479133034a4b552520517d5471e37afe81 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -50,6 +50,11 @@ elseif(~isempty(find([HashedCells{time}.trackID]==newTrackID,1)))
case 'Cancel'
return
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');
+ LogAction('Added hull to track',hullID,newTrackID);
else
ChangeLabel(time,trackID,newTrackID);
History('Push');
diff --git a/src/MATLAB/ConvertTrackingData.m b/src/MATLAB/ConvertTrackingData.m
index 6ec6b58e3f8161ce8c4b46853be7257f4603511d..f4890427f47646fb2b711282172640216b125d2b 100644
--- a/src/MATLAB/ConvertTrackingData.m
+++ b/src/MATLAB/ConvertTrackingData.m
@@ -36,48 +36,48 @@ end
%loop through the data
for i=2:length(objHulls)
- 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);
+% 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));
+end
- 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
+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
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 2be7ab2dabf4bfeb38c3cd94d937a1dc39c236b5..18f532b42b3e3ded87c4edf820d54a9990580cf8 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -145,7 +145,11 @@ end
oldParent = CellTracks(siblingTrack).parentTrack;
-ChangeTrackParent(trackID,time,siblingTrack);
+if(CellTracks(trackID).startTime==time)
+ ChangeTrackParent(siblingTrack,time,trackID);
+else
+ ChangeTrackParent(trackID,time,siblingTrack);
+end
History('Push');
LogAction(['Changed parent of ' num2str(siblingTrack)],oldParent,trackID);
diff --git a/src/MATLAB/DrawTree.m b/src/MATLAB/DrawTree.m
index a05b13cb4d320bf6002025c8152268c9c160f859..9afd693de35fa164300d2bb552b28683d12af661 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) || (isvarname('Figures.tree.familyID') && familyID==Figures.tree.familyID)),return,end
+if(isempty(CellFamilies(familyID).tracks)),return,end
%let the user know that this might take a while
set(Figures.tree.handle,'Pointer','watch');
diff --git a/src/MATLAB/InitializeFigures.m b/src/MATLAB/InitializeFigures.m
index 6fbebddfc2e04edcd0e785743023f1f058fa7f56..99b7f554bd08ef55a65b99928187f20e1405352b 100644
--- a/src/MATLAB/InitializeFigures.m
+++ b/src/MATLAB/InitializeFigures.m
@@ -137,8 +137,10 @@ if(Figures.cells.currentHullID == -1)
end
trackID = [HashedCells{Figures.time}(:).hullID]==Figures.cells.currentHullID;
trackID = HashedCells{Figures.time}(trackID).trackID;
-DrawTree(CellTracks(trackID).familyID);
-DrawCells();
+if(CellTracks(trackID).familyID~=Figures.tree.familyID)
+ DrawTree(CellTracks(trackID).familyID);
+ DrawCells();
+end
set(Figures.cells.handle,'WindowButtonUpFcn','');
end
diff --git a/src/MATLAB/LogAction.m b/src/MATLAB/LogAction.m
index fda88eddadf2dbeb4630af5e994d855664f1adc5..6f87193d3a9e665e97f99657cb227d43f64d146a 100644
--- a/src/MATLAB/LogAction.m
+++ b/src/MATLAB/LogAction.m
@@ -40,4 +40,5 @@ file = fopen([settings.matFilePath CONSTANTS.datasetName '_log.csv'],'a');
fprintf(file,row);
fclose(file);
+% TestDataIntegrity(0)
end
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index 6506455d56a214e8a82266b0295dc3fd8c8fec14..f266c322f6528e0ef761db78c7b580d94626425f 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 3.1\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 3.4\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
diff --git a/src/MATLAB/RemoveChildren.m b/src/MATLAB/RemoveChildren.m
new file mode 100644
index 0000000000000000000000000000000000000000..43e6be64c13fe2bbdf710a2e18aed48cbad74ab2
--- /dev/null
+++ b/src/MATLAB/RemoveChildren.m
@@ -0,0 +1,18 @@
+function RemoveChildren(trackID)
+% RemoveChildren(trackID) removes the children of the given track and moves
+% them to thier own trees. Those new trees are attempted to be added to
+% other trees. eg ProcessNewborns
+
+%--Eric Wait
+
+global CellTracks
+
+familyIDs = [];
+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/SplitHull.m b/src/MATLAB/SplitHull.m
index 7e8bebccf1edadbe6e8d0946fe410804928445e4..b2586ef4a2bb8ddc00fe54a243fe0679ab232ca5 100644
--- a/src/MATLAB/SplitHull.m
+++ b/src/MATLAB/SplitHull.m
@@ -4,7 +4,7 @@ function newTrackIDs = SplitHull(hullID, k)
%--Mark Winter
-global CellHulls
+global CellHulls CellFamilies
newHulls = ResegmentHull(CellHulls(hullID), k);
@@ -15,11 +15,11 @@ 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
+newFamilyIDs = [];
for i=2:length(newHulls)
- CellHulls(end+i-1) = newHulls(i);
- NewCellFamily(length(CellHulls), newHulls(i).time);
+ CellHulls(end+1) = newHulls(i);
+ newFamilyIDs = [newFamilyIDs NewCellFamily(length(CellHulls), newHulls(i).time)];
end
-
+newTrackIDs = [CellFamilies(newFamilyIDs).rootTrackID];
end
diff --git a/src/MATLAB/SplitTrack.m b/src/MATLAB/SplitTrack.m
index 944b5691da57134760b1ae5e8492b6a36a4e25bc..095d2ea4b083465220c3a4b52932aea060ef6cee 100644
--- a/src/MATLAB/SplitTrack.m
+++ b/src/MATLAB/SplitTrack.m
@@ -38,7 +38,7 @@ CellTracks(newTrackID).color = CellTracks(trackID).color;
%attach the parents children to the newTrack
CellTracks(newTrackID).childrenTracks = CellTracks(trackID).childrenTracks;
for i=1:length(CellTracks(newTrackID).childrenTracks)
- CellTracks(CellTracks(newTrackID).childrenTracks(i)).parent = newTrackID;
+ CellTracks(CellTracks(newTrackID).childrenTracks(i)).parentTrack = newTrackID;
end
CellTracks(trackID).childrenTracks = newTrackID;
diff --git a/src/MATLAB/SwapTrackLabels.m b/src/MATLAB/SwapTrackLabels.m
index 74a1c42682a071f68bba6905928f4a17d7bfc7b3..a626f3fdbfb5972b966990b2d16e567bb568eb1c 100644
--- a/src/MATLAB/SwapTrackLabels.m
+++ b/src/MATLAB/SwapTrackLabels.m
@@ -15,9 +15,15 @@ track2Hulls = CellTracks(trackID2).hulls(track2Hash:end);
%clear out the hulls copied
CellTracks(trackID1).hulls(track1Hash:end) = [];
-CellTracks(trackID2).hulls(track1Hash:end) = [];
+CellTracks(trackID2).hulls(track2Hash:end) = [];
%copy the hulls to the other track
+if(CellTracks(trackID1).startTime + length(CellTracks(trackID1).hulls) - 1 ~= time)
+ error('');
+end
+if(CellTracks(trackID2).startTime + length(CellTracks(trackID2).hulls) - 1 ~= time)
+ error('');
+end
CellTracks(trackID1).hulls = [CellTracks(trackID1).hulls track2Hulls];
CellTracks(trackID2).hulls = [CellTracks(trackID2).hulls track1Hulls];
@@ -54,7 +60,7 @@ 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(1));
+ ChangeTrackAndChildrensFamily(CellTracks(trackID2).familyID,CellTracks(trackID1).familyID,CellTracks(trackID1).childrenTracks(i));
end
for i=1:length(CellTracks(trackID2).childrenTracks)
ChangeTrackAndChildrensFamily(CellTracks(trackID1).familyID,CellTracks(trackID2).familyID,CellTracks(trackID2).childrenTracks(i));
diff --git a/src/MATLAB/TestDataIntegrity.m b/src/MATLAB/TestDataIntegrity.m
new file mode 100644
index 0000000000000000000000000000000000000000..4d5d189d87737d0ab1f1cd8f2b5be4f3156a096c
--- /dev/null
+++ b/src/MATLAB/TestDataIntegrity.m
@@ -0,0 +1,126 @@
+function TestDataIntegrity(correct)
+%TestDataIntegrity(correct) tests to make sure that the database is consistant.
+%Takes the CellTracks as the most accurate. If correct=='yes', this
+%function will attempt to correct the error using the data from CellTracks
+%***USE SPARINGLY, TAKES A LOT OF TIME***
+
+%--Eric Wait
+
+global CellTracks CellHulls CellFamilies HashedCells
+
+hullsList = [];
+fprintf('Checking CellTracks');
+for i=1:length(CellTracks)
+ fprintf(', %d',i);
+ %% Check child/parent/sibling relationships
+ if(~isempty(CellTracks(i).parentTrack))
+ if(isempty(find(CellTracks(CellTracks(i).parentTrack).childrenTracks==i, 1)))
+ error(['Parent ' num2str(CellTracks(i).parentTrack) ' does not recognize track ' num2str(i) ' as a child']);
+ end
+ if(CellTracks(CellTracks(i).siblingTrack).siblingTrack~=i)
+ error(['Track ' num2str(CellTracks(i).siblingTrack) ' does not recognize track ' num2str(i) ' as a sibling']);
+ end
+ end
+ currentFamily = CellTracks(i).familyID;
+ if(~isempty(CellTracks(i).childrenTracks))
+ for j=1:length(CellTracks(i).childrenTracks)
+ if(CellTracks(CellTracks(i).childrenTracks(j)).parentTrack~=i)
+ error(['Child ' num2str(CellTracks(i).childrenTracks(j)) ' does not recognize track ' num2str(i) ' as a parent']);
+ end
+ if(CellTracks(CellTracks(i).childrenTracks(j)).familyID~=currentFamily)
+ error(['Track ' num2str(i) ' and child ' num2str(CellTracks(i).childrenTracks(j)) ' do not agree on family ' num2str(currentFamily)]);
+ end
+ end
+ end
+
+ %% check if the current track is in the correct family and not in any
+ %other
+ if(~isempty(currentFamily))
+ index = find(CellFamilies(currentFamily).tracks==i);
+ if(isempty(index))
+ if(correct)
+ CellFamilies(currentFamily).tracks(end+1) = i;
+ fprintf('Track %d added to family %d\n',i,currentFamily);
+ else
+ error(['Track ' num2str(i) ' not in family ' num2str(currentFamily)])
+ end
+ elseif(1<length(index))
+ if(correct)
+ for j=2:length(index)
+ CellFamilies(currentFamily).tracks(index(j)) = 0;
+ end
+ CellFamilies(currentFamily).tracks = find(CellFamilies(currentFamily).tracks);
+ fprintf('Removed additional(s) track %d from family %d\n',i,currentFamily);
+ else
+ error(['Too many of track ' num2str(i) ' in family ' num2str(currentFamily)]);
+ end
+ end
+
+ %check for parent familyIDs
+ if(~isempty(CellTracks(i).parentTrack))
+ if(CellTracks(CellTracks(i).parentTrack).familyID~=currentFamily)
+ error(['Track ' num2str(i) ' and its parent ' num2str(CellTracks(i).parentTrack) ' do not agree on a family ' num2str(currentFamily)]);
+ end
+ end
+
+ for j=1:length(CellFamilies)
+% fprintf('CellFamilies %d ',j);
+ if(currentFamily==j),continue,end
+ index = find(CellFamilies(j).tracks==i);
+ if(~isempty(index))
+ if(correct)
+ CellFamilies(j).tracks(index) = [];
+ fprintf('Removed track %d from family %d\n',i,j);
+ else
+ error(['Track ' num2str(i) ' is in family ' num2str(j) ' as well']);
+ end
+ end
+ end
+ end
+
+ %% check hulls for a given track
+ for j=1:length(CellTracks(i).hulls)
+% fprintf('Hulls %d ',j);
+ if(~CellTracks(i).hulls(j)),continue,end
+ if(any(ismember(hullsList,CellTracks(i).hulls(j))))
+ tracks = [];
+ for q=1:i
+ if(~isempty(CellTracks(q).hulls) && ~isempty(find(CellTracks(q).hulls==CellTracks(i).hulls(j), 1)))
+ tracks = [tracks q];
+ end
+ end
+ error(['Hull ' num2str(CellTracks(i).hulls(j)) ' is in track ' num2str(i) ' as well as other tracks']);
+ end
+ hullsList = [hullsList CellTracks(i).hulls(j)];
+ time = j + CellTracks(i).startTime - 1;
+ if(time ~= CellHulls(CellTracks(i).hulls(j)).time)
+ error(['Hull ' num2str(CellTracks(i).hulls(j)) ' is not hashed correctly in track ' num2str(i)]);
+ end
+ index = find([HashedCells{time}.hullID]==CellTracks(i).hulls(j));
+ if(isempty(index))
+ error(['Hull ' num2str(CellTracks(i).hulls(j)) ' is not found in HashedCells at ' num2str(time)]);
+ elseif(1<length(index))
+ error(['Hull ' num2str(CellTracks(i).hulls(j)) ' is in HashedCells more than once at ' num2str(time)]);
+ end
+ if(HashedCells{time}(index).trackID~=i)
+ error(['Hull ' num2str(CellTracks(i).hulls(j)) ' does not have the correct track ' num2str(i)]);
+ end
+ end
+
+end
+fprintf('\n');
+
+%% check CellHulls
+% if(length(hullsList)~=length(find([CellHulls.deleted]==0)))
+missingHulls = find(ismember(find([CellHulls.deleted]==0),hullsList')==0);
+if(~isempty(missingHulls))
+ if(correct)
+ for i=1:length(missingHulls)
+ if(isempty(CellHulls(missingHulls(i)).points))
+ CellHulls(missingHulls(i)).deleted = 1;
+ end
+ end
+ end
+ error('HullsList ~= CellHulls');
+end
+end