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Commit ebe59d59 authored by ac 20's avatar ac 20
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smooth.patch updated to be track agnostic

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matlab/+Batch/processMovie.m
+ 1
− 2
View file @ ebe59d59
......@@ -11,8 +11,7 @@ tProcess.tTrack1=toc(tx);
[conn,CONSTANTS]=openDB(strDB);
tx=tic();
Smooth.Patch.patch11(conn);
Smooth.Patch.patch12(conn);
Smooth.Patch.patch(conn);
tProcess.tPatch=toc(tx);
tx=tic();
......
matlab/+Smooth/+Patch/getPatchCandidates.m deleted 100644 → 0
+ 0
− 20
View file @ ee088cb0
function [qSrc,qDst]=getPatchCandidates(conn)
cmd=[' select min(cost),cellID_src,cellID_dst,trackID_src,C2.trackID as '...
' trackID_dst,tmax as tmax_src from tblDistCC inner join '...
' (select cellID as cellID1,trackID as trackID_src,max(time) as '...
' tmax from tblCells where trackID not in '...
' (select trackID from tblFamilies inner join tblCells as C1 '...
' on cellID_parent=C1.cellID) '...
' group by trackID) on tblDistCC.cellID_src=cellID1 inner join '...
' tblCells as C2 on cellID_dst=C2.cellID ' ...
' group by trackID,cellID_src'];
qSrc=fetch(conn,cmd);
cmd=[' select min(cost),cellID_src,cellID_dst,trackID as trackIDdst,tmin from tblDistCC '...
' inner join (select cellID,trackID,min(time) as tmin from tblCells ' ...
' where cellID not in (select cellID_child1 from tblFamilies) '...
' and cellID not in (select cellID_child2 from tblFamilies) group by trackID) on tblDistCC.cellID_dst=cellID '...
' group by trackID,cellID_dst'];
qDst=fetch(conn,cmd);
matlab/+Smooth/+Patch/getPatchTarget.m deleted 100644 → 0
+ 0
− 28
View file @ ee088cb0
function qTarget=getPatchTarget(conn,qSrc)
cmd=['select min(time) as t0 from tblCells where trackID=(select trackID from '...
' tblCells where cellID=' num2str(qSrc.cellID_dst) ')'];
q=fetch(conn,cmd);
if 1==q.t0 || q.t0<qSrc.tmax_src-3
qTarget=[];
return;
end
cmd=['select dst.trackID as trackID_dst,dst.time as time_dst,src.trackID '...
' as trackID_src,src.time as time_src,min(cost),cellID_src,cellID_dst '...
' from (select tblDistCC.*,time,trackID from tblCells inner join '...
' tblDistCC on cellID=cellID_dst where trackID=(select trackID '...
' from tblCells where cellID=' num2str(qSrc.cellID_dst) ') and time>='...
num2str(qSrc.tmax_src-4) ' and time<=' num2str(qSrc.tmax_src+1) ...
' ) inner join tblCells as dst on cellID_dst=dst.cellID '...
'inner join tblCells as src on cellID_src=src.cellID '...
'group by cellID_dst '];
qTarget=fetch(conn,cmd);
if ~isempty(setdiff(qTarget.trackID_src,[qSrc.trackID_dst,qSrc.trackID_src])) ||...
isempty(intersect(qTarget.trackID_src,[qSrc.trackID_src]))
qTarget=[];
end
matlab/+Smooth/+Patch/patch.m
+ 9
− 58
View file @ ebe59d59
function patch(conn,CONSTANTS)
trackList=fetch(conn,'select trackID from tblCells group by trackID');
qt={};
for i=1:length(trackList.trackID)
qt{i}=fetch(conn,['select time,iNest,cellID from tblCells where trackID=' ...
num2str(trackList.trackID(i)) ' order by time asc' ]);
end
qmax=fetch(conn,'select max(iNest) as maxNest from tblCells');
patchList=[];
patchMap=cell(CONSTANTS.imageData.NumberOfFrames,qmax.maxNest);
for i=1:length(qt)
for j=i+1:length(qt)
if i==j
continue
end
tOverlap=intersect(qt{i}.time,qt{j}.time);
if isempty(tOverlap)
continue
end
iNest=qt{i}.iNest(ismember(qt{i}.time,tOverlap));
jNest=qt{j}.iNest(ismember(qt{j}.time,tOverlap));
% since qt is sorted by time comparison is valid
% todo - check that both times are continuous
if (iNest(1)==jNest(1) && iNest(end)==jNest(end))
patchTime=qt{i}.time(ismember(qt{i}.time,tOverlap));
for k=1:length(patchTime)
idxi=find(ismember(qt{i}.time,tOverlap));
cidi=qt{i}.cellID(idxi(k));
idxj=find(ismember(qt{j}.time,tOverlap));
cidj=qt{j}.cellID(idxj(k));
patchMap{patchTime(k),iNest(k)}=union(patchMap{patchTime(k),iNest(k)},[cidi,cidj]);
end
% np=table(
% patchList=[
np=table(min(qt{i}.time),max(qt{i}.time),trackList.trackID(i),...
min(qt{j}.time),max(qt{j}.time),trackList.trackID(j),...
'VariableNames',{'t0i','t1i','tidi','t0j','t1j','tidj'});
if isempty(patchList)
patchList=np;
else
patchList=[patchList;np];
end
end
end
end
[time,nestList]=find(~cellfun(@isempty,patchMap));
for i=1:length(time)
t=time(i);
iNest=nestList(i);
cids=patchMap{t,iNest};
[newCell,pe]=Ensemble.ensembleCheckMerge(conn,cids,CONSTANTS);
if ~isempty(newCell) && pe>0.75
Ensemble.writeMergedCell(conn,cids,newCell,CONSTANTS);
end
end
function patch(conn)
cmd='select cellID_child1 as cellID from tblFamilies union select cellID_child2 as cellID from tblFamilies';
qChildren=fetch(conn,cmd);
cidChildren=qChildren.cellID;
cmd='select cellID_parent from tblFamilies';
qParents=fetch(conn,cmd);
cidParents=qParents.cellID_parent;
Smooth.Patch.patch11(conn,cidChildren);
Smooth.Patch.patch12(conn,cidParents,cidChildren);
matlab/+Smooth/+Patch/patch11.m
+ 15
− 9
View file @ ebe59d59
% true love patcher!
function patch11(conn)
% sometimes the tracker makes decisions based on longer time projections
% if those fail, we fall back on the original single frame true love
% (1st choice ccDistance <-> 1st choice ccDistance)
function patch11(conn,cidChildren)
cmd=['select cellID,trackID,max(time) as tmax from tblCells '...
' where trackID not in (select trackID from tblCells inner join tblFamilies'...
' on cellID_parent=cellID) group by trackID'];
qSrc=fetch(conn,cmd);
cidList=Helpers.sqlEncodeVector(qSrc.cellID);
if isempty(qSrc)
return
end
cidList=Helpers.sqlEncodeVector(qSrc.cellID);
cmd=['select cellID_src,cellID_dst,min(cost) from tblDistCC where cellID_src in ' ...
cidList ' group by cellID_src'];
qSrcCosts=fetch(conn,cmd);
cmd=['select cellID_src,cellID_dst,min(cost),trackID as trackID_dst,time as time_dst '...
cmd=['select cellID_src,cellID_dst,trackID as trackID_dst,min(cost),time as time_dst '...
' from tblCells inner join tblDistCC on cellID=cellID_dst where cellID_src in '...
cidList ' and cellID_dst not in '...
' (select cellID_child1 from tblFamilies) ' ...
' and cellID_dst not in (select cellID_child2 from tblFamilies) ' ...
' group by cellID_dst '];
cidList];
qPatch=fetch(conn,cmd);
qPatch(qPatch.cellID_dst~=qPatch.trackID_dst,:)=[];
for i=1:length(qPatch.cellID_src)
if ~isempty(intersect(cidChildren,qPatch.cellID_dst(i)))
% can't patch to a mitotic child
continue;
end
% check src costs. true love?
idxSrcCosts=find(qSrcCosts.cellID_src==qPatch.cellID_src(i));
if qSrcCosts.cellID_dst(idxSrcCosts)~=qPatch.cellID_dst(i)
......
matlab/+Smooth/+Patch/patch12.m
+ 56
− 12
View file @ ebe59d59
function patch12(conn)
% the second chance patcher
% here, eligible tracks can get assigned their 1st choice, even if they
% are the corresponding 2nd choice
function patch12(conn,cidParents,cidChildren)
% patch src's are leaf nodes on the tree
% patch dst's are parent nodes on the tree
[qSrc,qDst]=Smooth.Patch.getPatchCandidates(conn);
cmd=' select cellID_child1 as cellID from tblFamilies union select cellID_child2 as cellID from tblFamilies';
qChildren=fetch(conn,cmd);
qSrc=getPatchCandidates(conn);
for i=1:length(qSrc.cellID_dst)
if ~isempty(intersect(qChildren.cellID,qSrc.cellID_dst(i)))
if ~isempty(intersect(cidChildren,qSrc.cellID_dst(i)))
continue
end
if ~isempty(intersect(cidParents,qSrc.cellID_src(i)))
continue
end
qTarget=Smooth.Patch.getPatchTarget(conn,qSrc(i,:));
qTarget=getPatchTarget(conn,qSrc(i,:));
if isempty(qTarget)
continue;
end
cmd=['update tblCells set trackID=' num2str(qSrc.trackID_src(i)) ...
' where trackID=' num2str(qSrc.trackID_dst(i)) ' and time>'...
num2str(qSrc.tmax_src(i))];
cmd=['update tblCells set trackID=(select trackID from tblCells where '...
' cellID=' num2str(qSrc.cellID_src(i)) ') where trackID= '...
' (select trackID from tblCells where cellID=' ...
num2str(qSrc.cellID_dst(i)) ') and time>(select max(time) from '...
' tblCells where trackID=(select trackID from tblCells where cellID='...
num2str(qSrc.cellID_src(i)) '))'];
exec(conn,cmd);
qSrc.trackID_src(qSrc.trackID_src==qSrc.trackID_dst(i))=qSrc.trackID_src(i);
end
function qTarget=getPatchTarget(conn,qSrc)
cmd=['select min(time) as tminDst,trackID as trackID_dst from tblCells where trackID=(select trackID from '...
' tblCells where cellID=' num2str(qSrc.cellID_dst) ')'];
q=fetch(conn,cmd);
cmd=['select max(time) as tmaxSrc, trackID as trackID_src from tblCells where trackID=(select trackID from '...
' tblCells where cellID=' num2str(qSrc.cellID_src) ')'];
qt=fetch(conn,cmd);
if 1==q.tminDst || q.tminDst<qt.tmaxSrc-3
qTarget=[];
return;
end
cmd=['select dst.trackID as trackID_dst,dst.time as time_dst,src.trackID '...
' as trackID_src,src.time as time_src,min(cost),cellID_src,cellID_dst '...
' from (select tblDistCC.*,time,trackID from tblCells inner join '...
' tblDistCC on cellID=cellID_dst where trackID=(select trackID '...
' from tblCells where cellID=' num2str(qSrc.cellID_dst) ') and time>='...
num2str(qt.tmaxSrc-4) ' and time<=' num2str(qt.tmaxSrc+1) ...
' ) inner join tblCells as dst on cellID_dst=dst.cellID '...
'inner join tblCells as src on cellID_src=src.cellID '...
'group by cellID_dst '];
qTarget=fetch(conn,cmd);
if ~isempty(setdiff(qTarget.trackID_src,[q.trackID_dst,qt.trackID_src])) ||...
isempty(intersect(qTarget.trackID_src,[qt.trackID_src]))
qTarget=[];
end
function qSrc=getPatchCandidates(conn)
cmd=[' select min(cost),cellID_src,cellID_dst from tblDistCC inner join '...
' tblCells on cellID_dst=cellID ' ...
' group by trackID,cellID_src'];
qSrc=fetch(conn,cmd);
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