diff --git a/src/MATLAB/AddNewSegmentHull.m b/src/MATLAB/AddNewSegmentHull.m
new file mode 100644
index 0000000000000000000000000000000000000000..c0533b1419c8bd2f138cffd9fd9cd2bde1871333
--- /dev/null
+++ b/src/MATLAB/AddNewSegmentHull.m
@@ -0,0 +1,29 @@
+function newTrackID = AddNewSegmentHull(clickPt)
+ global CONSTANTS CellHulls CellFamilies Figures
+
+ fileName = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' num2str(Figures.time,'%03d') '.TIF'];
+ [img colrMap] = imread(fileName);
+ img = mat2gray(img);
+
+ newObj = PartialImageSegment(img, clickPt, 200, 1.0);
+
+ newHull = struct('time', [], 'points', [], 'centerOfMass', [], 'indexPixels', [], 'deleted', 0);
+
+ if ( isempty(newObj) )
+ % Add a point hull since we couldn't find a segmentation containing the click
+ newHull.time = Figures.time;
+ newHull.points = round(clickPt);
+ newHull.centerOfMass = [clickPt(2) clickPt(1)];
+ newHull.indexPixels = sub2ind(size(img), clickPt(2), clickPt(1));
+ else
+ newHull.time = Figures.time;
+ newHull.points = newObj.points;
+ newHull.centerOfMass = newObj.centerOfMass;
+ newHull.indexPixels = newObj.indexPixels;
+ end
+
+ CellHulls(end+1) = newHull;
+ newFamilyIDs = NewCellFamily(length(CellHulls), newHull.time);
+
+ newTrackID = [CellFamilies(newFamilyIDs).rootTrackID];
+end
\ No newline at end of file
diff --git a/src/MATLAB/AddSingleHullToTrack.m b/src/MATLAB/AddSingleHullToTrack.m
index 161ddcbc1152d172581a6823ef594af74b2c397a..d78790265720bedc83bcb8441a12990c74b624cd 100644
--- a/src/MATLAB/AddSingleHullToTrack.m
+++ b/src/MATLAB/AddSingleHullToTrack.m
@@ -16,17 +16,20 @@ if(~isempty(CellTracks(oldTrackID).parentTrack) && ...
error([num2str(oldTrackID) ' is not a single hull track or has a parent/child']);
end
-if(CellTracks(oldTrackID).startTime<CellTracks(newTrackID).startTime)
+if(~any([CellTracks(CellTracks(newTrackID).childrenTracks).endTime]<CellTracks(oldTrackID).startTime))
+ RemoveChildren(newTrackID);
+ AddHullToTrack(CellTracks(oldTrackID).hulls(1),newTrackID,[]);
+elseif(CellTracks(oldTrackID).startTime<CellTracks(newTrackID).startTime)
%old before new
if(~isempty(CellTracks(newTrackID).parentTrack))
- moveMitosisUp(CellTracks(oldTrackID).startTime,...
+ 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);
+ MoveMitosisDown(CellTracks(oldTrackID).startTime,newTrackID);
end
AddHullToTrack(CellTracks(oldTrackID).hulls(1),newTrackID,[]);
else
@@ -54,49 +57,3 @@ 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/CHullContainsPoint.m b/src/MATLAB/CHullContainsPoint.m
new file mode 100644
index 0000000000000000000000000000000000000000..7292d5cbf87edf195d64f18ee7af20f95b452f2d
--- /dev/null
+++ b/src/MATLAB/CHullContainsPoint.m
@@ -0,0 +1,23 @@
+function bInHull = CHullContainsPoint(pt, hulls)
+ bInHull = boolean(zeros(length(hulls),1));
+
+ for i=1:length(hulls)
+
+ if ( size(hulls(i).points,1) <= 1 )
+ continue;
+ end
+
+ cvpts = hulls(i).points;
+ hullvec = diff(cvpts);
+
+ outnrm = [-hullvec(:,2) hullvec(:,1)];
+ %outnrm = outnrm ./ sqrt(sum(outnrm.^2,2));
+
+ ptvec = cvpts(1:end-1,:) - ones(size(outnrm,1),1)*pt;
+ %ptvec = ptvec ./ sqrt(sum(ptvec.^2,2));
+
+ chkIn = sign(sum(outnrm .* ptvec,2));
+
+ bInHull(i) = all(chkIn >= 0);
+ end
+end
\ No newline at end of file
diff --git a/src/MATLAB/ChangeLabel.m b/src/MATLAB/ChangeLabel.m
index 20f00ee6043df61f363ef905da045958c46fe565..c5b4a3329baf97c5ecb847a387ed5d42abb9670b 100644
--- a/src/MATLAB/ChangeLabel.m
+++ b/src/MATLAB/ChangeLabel.m
@@ -123,9 +123,10 @@ else %the old track still exists in some fasion
end
moveChildren(oldTrackID,newTrackID);
end
- elseif(isempty(find(CellTracks(oldTrackID).hulls==lastOldHull, 1)) &&...
- CellHulls(lastOldHull).time>CellTracks(newTrackID).endTime &&...
- ~isempty(CellTracks(newTrackID).childrenTracks))
+ elseif(~isempty(CellTracks(newTrackID).childrenTracks) && ...
+ (((isempty(find(CellTracks(oldTrackID).hulls==lastOldHull, 1)) &&...
+ CellHulls(lastOldHull).time>CellTracks(newTrackID).endTime)) || ...
+ any([CellTracks(CellTracks(newTrackID).childrenTracks).startTime]<CellTracks(newTrackID).endTime)))
RemoveChildren(newTrackID);
end
end
diff --git a/src/MATLAB/ContextChangeLabel.m b/src/MATLAB/ContextChangeLabel.m
index bf4e3f479133034a4b552520517d5471e37afe81..dcec450f790c8713f527b268d6a47bd7b061b7db 100644
--- a/src/MATLAB/ContextChangeLabel.m
+++ b/src/MATLAB/ContextChangeLabel.m
@@ -55,6 +55,14 @@ elseif(isempty(CellTracks(trackID).parentTrack) && isempty(CellTracks(trackID).c
AddSingleHullToTrack(trackID,newTrackID);
History('Push');
LogAction('Added hull to track',hullID,newTrackID);
+elseif(~isempty(CellTracks(trackID).parentTrack) && CellTracks(trackID).parentTrack==newTrackID)
+ MoveMitosisUp(time,trackID)
+ History('Push');
+ LogAction('Moved Mitosis Up',trackID,newTrackID);
+elseif(~isempty(CellTracks(newTrackID).parentTrack) &&CellTracks(newTrackID).parentTrack==trackID)
+ MoveMitosisUp(time,newTrackID)
+ History('Push');
+ LogAction('Moved Mitosis Up',newTrackID,trackID);
else
ChangeLabel(time,trackID,newTrackID);
History('Push');
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 18f532b42b3e3ded87c4edf820d54a9990580cf8..43d7e4649882b5be58eef90e43aff905c5420ba8 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -272,23 +272,45 @@ end
%% Helper functions
function addHull(num)
-global Figures
+global Figures CellHulls
-[hullID trackID] = getClosestCell();
-if(isempty(trackID)),return,end
+[hullID trackID] = getClosestCell(num<2);
+clickPt = get(gca,'CurrentPoint');
-newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
+if ( ~CHullContainsPoint(clickPt(1,1:2), CellHulls(hullID)) )
+ trackID = [];
+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
+
+ History('Push');
+ 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');
+ LogAction('Added cell',[],newTrack);
+else
+ return;
+end
-History('Push');
-LogAction('Split cell',trackID,[trackID newTracks]);
DrawTree(Figures.tree.familyID);
DrawCells();
end
-function [hullID trackID] = getClosestCell()
+function [hullID trackID] = getClosestCell(bAllowEmpty)
hullID = FindHull(get(gca,'CurrentPoint'));
if(0>=hullID)
- warndlg('Please click closer to the center of the desired cell','Unknown Cell');
+ if ( bAllowEmpty )
+ hullID = [];
+ else
+ warndlg('Please click closer to the center of the desired cell','Unknown Cell');
+ end
+
trackID = [];
return
end
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index 4e0e9cd071a28e88baa2de3474a40c70b96295fe..3e5af67f05ca8713c02a085ef2f45b4f60ace873 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -233,6 +233,8 @@ global CellTracks
answer = inputdlg('Enter Tree Containing Cell:','Display Tree',1);
answer = str2double(answer);
+if(isempty(answer)),return,end
+
if(0>=answer || isempty(CellTracks(answer).hulls))
msgbox([num2str(answer) ' is not a valid cell'],'Not Valid','error');
return
diff --git a/src/MATLAB/MoveMitosisDown.m b/src/MATLAB/MoveMitosisDown.m
new file mode 100644
index 0000000000000000000000000000000000000000..c4a327b0039c412a930a8e7ad12d561648a07074
--- /dev/null
+++ b/src/MATLAB/MoveMitosisDown.m
@@ -0,0 +1,38 @@
+function MoveMitosisDown(time,trackID)
+% MoveMitosisDown(time,trackID) will move the Mitosis even down the track
+% to the given time. The hulls from the children between parent mitosis
+% and the given time are broken off into thier own tracks.
+
+%--Eric Wait
+
+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)
+ if(children(i).hulls(j)~=0)
+ AddHullToTrack(children(i).hulls(j),newTrackID,[]);
+ end
+ end
+ end
+end
+end
\ No newline at end of file
diff --git a/src/MATLAB/MoveMitosisUp.m b/src/MATLAB/MoveMitosisUp.m
new file mode 100644
index 0000000000000000000000000000000000000000..c5531c44c2f39d47c33f2b779661e9d668eba2f8
--- /dev/null
+++ b/src/MATLAB/MoveMitosisUp.m
@@ -0,0 +1,20 @@
+function MoveMitosisUp(time,siblingTrackID)
+% MoveMitosisUp(time,siblingTrackID) will move the Mitosis event up the
+% tree. This function takes the hulls from the parent between the old
+% mitosis time and the given time and attaches them to the given track.
+
+%--Eric Wait
+
+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
\ No newline at end of file
diff --git a/src/MATLAB/PartialImageSegment.m b/src/MATLAB/PartialImageSegment.m
new file mode 100644
index 0000000000000000000000000000000000000000..010ad7970ae4562f38bc6297e11b2b8486ff033f
--- /dev/null
+++ b/src/MATLAB/PartialImageSegment.m
@@ -0,0 +1,180 @@
+function hull = PartialImageSegment(img, centerPt, subSize, alpha)
+
+ if ( length(subSize) < 2 )
+ subSize = [subSize(1) subSize(1)];
+ end
+
+ imSize = size(img);
+
+ coordMin = floor([centerPt(1)-subSize(1)/2 centerPt(2)-subSize(2)/2]);
+ coordMin(coordMin < 1) = 1;
+
+ coordMax = ceil([centerPt(1)+subSize(1)/2 centerPt(2)+subSize(2)/2]);
+ if ( coordMax(1) > imSize(2) )
+ coordMax(1) = imSize(2);
+ end
+ if ( coordMax(2) > imSize(1) )
+ coordMax(2) = imSize(1);
+ end
+
+ % Build the subimage to be segmented
+ subImg = img(coordMin(2):coordMax(2), coordMin(1):coordMax(1));
+
+% hold off;figure;imagesc(subImg);colormap(gray);hold on;
+
+ objs = [];
+
+ se=strel('square',3);
+
+ bwDark=0*subImg;
+ level=alpha*graythresh(subImg);
+ bwHalo=im2bw(subImg,level);
+
+ l2=graythresh(subImg);
+ pix=subImg(subImg<l2);
+ lDark=graythresh(pix);
+ bwDark(subImg<lDark)=1;
+
+ bwNorm=0*bwDark;
+
+ gd=imdilate(subImg,se);
+ ge=imerode(subImg,se);
+ ig=gd-ge;
+ lig=graythresh(ig);
+ bwig=im2bw(ig,lig);
+ seBig=strel('square',19);
+ bwmask=imclose(bwig,seBig);
+
+ bwDarkCenters=(bwDark & bwmask );
+ d=bwdist(~bwDarkCenters);
+ bwDarkCenters(d<2)=0;
+
+ bwHaloMask=imdilate(bwHalo,seBig);
+
+ bwHaloHoles=imfill(bwHalo ,8,'holes') & ~bwHalo;
+ bwDarkHoles=imfill(bwDarkCenters ,8,'holes') & ~bwDarkCenters;
+ bwgHoles=bwmorph(bwig | bwDarkCenters,'close',1) ;
+ bwgHoles=imfill( bwgHoles ,8,'holes') & ~(bwig |bwDarkCenters);
+
+ bwHoles=bwHaloHoles |bwDarkHoles|bwgHoles;
+
+ CC = bwconncomp(bwHoles,8);
+ LHoles = labelmatrix(CC);
+ stats = regionprops(CC, 'Area');
+ idx = find([stats.Area] < 500);
+ bwHoles = ismember(LHoles, idx);
+
+ bwCells=bwDarkCenters| bwHoles|bwNorm;
+ bwCells(~bwHaloMask)=0;
+
+
+ CC = bwconncomp(bwHalo,8);
+ LCells = labelmatrix(CC);
+
+ bwCells(bwig)=0;
+
+ bwTails=bwDarkCenters;
+ bwTails(bwHalo)=0;
+ CC = bwconncomp(bwTails,8);
+ LTails = labelmatrix(CC);
+
+ CC = bwconncomp(bwCells,8);
+ LCenters = labelmatrix(CC);
+ stats=regionprops(CC,'eccentricity');
+ d=bwdist(~bwCells);
+
+% [tr,tc] = find(LCenters>0);
+% plot(tc,tr,'.r');
+
+ num=max(LCenters(:));
+ for n=1:num
+ pix=find(LCenters==n);
+ if length(pix)<50
+ bwCells(pix)=0;
+ continue
+ end
+
+ bwPoly=logical(0*subImg);
+ bwPoly(pix)=1;
+ bwPoly=bwmorph(bwPoly,'dilate',1);
+ p=bwperim(bwPoly);
+
+ igRat=length(find(p & bwig))/length(find(p));
+
+ HaloRat=length(find(p & bwHalo))/length(find(p));
+
+ [r c]=ind2sub(imSize,pix);
+ ch=convhull(r,c);
+
+ bwDarkInterior=bwDarkCenters&bwPoly;
+ DarkRat=length(find(bwDarkInterior))/length(find(bwPoly));
+% if HaloRat>0.5 || igRat<.1 ||(DarkRat<.5 && igRat<.5 && length(pix)<175)
+% bwCells(pix)=0;
+% continue
+% end
+ dmax=max(d(pix));
+ if dmax>4
+ bwCells(pix(d(pix)<2))=0;
+ end
+ end
+
+ bwCellFG=0*bwCells;
+
+ CC = bwconncomp(bwCells,8);
+ LCenters = labelmatrix(CC);
+
+% [tr,tc] = find(LCenters>0);
+% plot(tc,tr,'og');
+
+% hold off;figure;imagesc(subImg);colormap(gray);hold on;
+
+ stats=regionprops(CC,'area','Eccentricity');
+ idx = find([stats.Area] >=25);
+ for i=1:length(idx)
+ pix=find(LCenters==idx(i));
+ if length(pix)<20
+ continue
+ end
+ [r c]=ind2sub(size(subImg),pix);
+ bwPoly=roipoly(subImg,c,r);
+ if bwarea(bwPoly)<1
+ continue
+ end
+
+ ch=convhull(r,c);
+ % one last check for parasites
+ if length(find(subImg(pix)>lDark))/length(pix)> 0.5
+ continue
+ end
+ % it's a keeper!
+ bwCellFG(pix)=1;
+
+% plot(c(ch),r(ch),'-r','linewidth',1.5)
+
+ glc = c + coordMin(1);
+ glr = r + coordMin(2);
+
+ no=[];
+ no.points=[glc(ch),glr(ch)];
+ no.centerOfMass = mean([glr glc]);
+
+ %no.indPixels=pix;
+ no.indexPixels = sub2ind(imSize,[glr glc]);
+ no.imagePixels=img(no.indexPixels);
+ % surround completely by Halo?
+ if all(bwHaloHoles(pix))
+ no.BrightInterior=1;
+ else
+ no.BrightInterior=0;
+ end
+
+ no.ID=-1;
+ no.Eccentricity=stats(idx(i)).Eccentricity;
+ objs = [objs no];
+ end
+
+ bInHull = CHullContainsPoint(centerPt, objs);
+
+ hull = objs(bInHull);
+end
+