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CSTMergeSegmAndTrack.m
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CSTMergeSegmAndTrack.m
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function CSTMergeSegmAndTrack(fileDBEntry, listOfWormsSegm, currentImageFileName, currentFrame, axesImage, nbOfFrames)
% Copyright (c) 2013 Rutgers
% Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
% The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
global listOfWorms traceOn timingOn timings timingsTime plotAllOn flagRobustness fileToLog;
if timingOn; tic; end
if traceOn; fprintf(fileToLog, ['comparing frame ', num2str(currentFrame), ' from ', fileDBEntry.name,' : ', currentImageFileName, '\n']); end
if plotAllOn; hold(axesImage, 'on'); end
% ===========
% LOAD THE IMAGE
% ===========
if plotAllOn
try
currentImage = double(imread( fullfile( fileDBEntry.directory, currentImageFileName) ));
catch em
if flagRobustness
fprintf(fileToLog, ['*** There was an error reading file: ', num2str(currentImageFileName),' , skipping this file. ***','\n']);
fprintf(fileToLog, [getReport(em, 'basic'),'\n']);
return
else
rethrow(em)
end
end
imagesc(currentImage,'parent', axesImage);
end
try
nbOfWormsSegm = length(listOfWormsSegm.skel);
nbOfWormsTrack = length(listOfWorms.skel);
cosDraw = cos(2*pi*(0:48)/48);
sinDraw = sin(2*pi*(0:48)/48);
% ===========
% COMPUTE THE BOUNDING BOXES OF ALL WORMS
% ===========
bboxT = zeros(4, nbOfWormsTrack);
for wormT = 1:nbOfWormsTrack
cbl = listOfWorms.skel{wormT}{currentFrame};
width = listOfWorms.width{wormT}{currentFrame};
if plotAllOn
listOfIndices = 1:length(cbl);
tmp = zeros(2, length(listOfIndices)*length(cosDraw));
for vv = 1:length(listOfIndices)
tmp(:,(vv-1)*length(cosDraw)+(1:length(cosDraw))) = [cbl(1,listOfIndices(vv))+width(listOfIndices(vv))*cosDraw ; ...
cbl(2,listOfIndices(vv))+width(listOfIndices(vv))*sinDraw];
end
plot(tmp(1,:), tmp(2,:), '-r', 'parent', axesImage,'linewidth', 2)
plot(cbl(1,:), cbl(2,:), '-r')
end
bboxT(:,wormT) = [ floor(min(cbl(2,:)-width));... % row min
ceil( max(cbl(2,:)+width));... % row max
floor(min(cbl(1,:)-width));... % col min
ceil( max(cbl(1,:)+width))... % col max
];
end
bboxS = zeros(4, nbOfWormsSegm);
riskOfOverlap = false(nbOfWormsSegm, nbOfWormsTrack);
for wormS = 1:nbOfWormsSegm
cbl = listOfWormsSegm.skel{wormS};
width = listOfWormsSegm.width{wormS};
if plotAllOn
listOfIndices = 1:length(cbl);
tmp = zeros(2, length(listOfIndices)*length(cosDraw));
for vv = 1:length(listOfIndices)
tmp(:,(vv-1)*length(cosDraw)+(1:length(cosDraw))) = [cbl(1,listOfIndices(vv))+width(listOfIndices(vv))*cosDraw ; ...
cbl(2,listOfIndices(vv))+width(listOfIndices(vv))*sinDraw];
end
plot(tmp(1,:), tmp(2,:), '-g', 'parent', axesImage,'linewidth', 1)
plot(cbl(1,:), cbl(2,:), '-g')
end
bboxS(:,wormS) = [ floor(min(cbl(2,:)-width));... % row min
ceil( max(cbl(2,:)+width));... % row max
floor(min(cbl(1,:)-width));... % col min
ceil( max(cbl(1,:)+width))... % col max
];
riskOfOverlap(wormS, :) = ( (bboxS(1,wormS) <= bboxT(2,:)) & (bboxT(1,:) <= bboxS(2,wormS))...
& (bboxS(3,wormS) <= bboxT(4,:)) & (bboxT(3,:) <= bboxS(4,wormS)));
end
% -----------
% Compute the matching between the worms
% -----------
overlapVertices = Inf(nbOfWormsSegm,nbOfWormsTrack);
for wormS = 1:nbOfWormsSegm
cblS = listOfWormsSegm.skel{wormS};
widthS = listOfWormsSegm.width{wormS};
for wormT = 1:nbOfWormsTrack
if riskOfOverlap(wormS, wormT)
cblT = listOfWorms.skel{wormT}{currentFrame};
widthT = listOfWorms.width{wormT}{currentFrame};
distStoT = zeros(1,length(widthS));
for idx = 1:length(widthS)
% ...........
% Take width into account
% ...........
distStoT(idx) = min(hypot(cblT(1,:) - cblS(1,idx), cblT(2,:) - cblS(2,idx)) - widthT - widthS(idx));
end
overlapVertices(wormS, wormT) = mean(distStoT);
end
end
end
% -----------
% Match worms that agree with each other
% -----------
matchesTtoS = zeros(1,nbOfWormsTrack);
unmatchedT = false(1,nbOfWormsTrack);
for wormT = 1:nbOfWormsTrack
% Find the best match
[valTmp, bestMatchS] = min(overlapVertices(:, wormT));
if valTmp < 0
% found a match
matchesTtoS(wormT) = bestMatchS;
else
unmatchedT(wormT) = true;
end
end
finalMatchesStoT = zeros(1,nbOfWormsSegm);
finalMatchesTtoS = zeros(1,nbOfWormsTrack);
unmatchedS = false(1, nbOfWormsSegm);
for wormS = 1:nbOfWormsSegm
[valTmp, bestMatchT] = min(overlapVertices(wormS,:));
if valTmp < 0
if matchesTtoS(bestMatchT) == wormS
% agreed
finalMatchesStoT(wormS) = bestMatchT;
finalMatchesTtoS(bestMatchT) = wormS;
else
end
else
% missed
unmatchedS(wormS) = true;
end
end
% -----------
% Match worms that have been left out
% -----------
for wormT = find(unmatchedT)
cblT = listOfWorms.skel{wormT}{currentFrame};
widthT = listOfWorms.width{wormT}{currentFrame};
for wormS = find(unmatchedS)
% Compare how well they match
cblS = listOfWormsSegm.skel{wormS};
widthS = listOfWormsSegm.width{wormS};
distStoT = zeros(1,length(widthS));
for idx = 1:length(widthS)
distStoT(idx) = min(hypot(cblT(1,:) - cblS(1,idx), cblT(2,:) - cblS(2,idx)) - widthT - widthS(idx));
end
ratioOverlapStoT = sum(distStoT < 0) / length(distStoT);
distTtoS = zeros(1,length(widthT));
for idx = 1:length(widthT)
distTtoS(idx) = min(hypot(cblS(1,:) - cblT(1,idx), cblS(2,:) - cblT(2,idx)) - widthS - widthT(idx));
end
ratioOverlapTtoS = sum(distTtoS < 0) / length(distTtoS);
if ratioOverlapTtoS * ratioOverlapStoT >= 0.25
% ok, try to match them
if finalMatchesStoT(wormS) == 0 && finalMatchesTtoS(wormT) == 0
% no other candidates so far
finalMatchesStoT(wormS) = wormT;
finalMatchesTtoS(wormT) = wormS;
else
% there were other candidates, too ambiguous, leave all worms as such
if finalMatchesStoT(wormS) ~= 0
finalMatchesTtoS(finalMatchesStoT(wormS)) = Inf;
end
if finalMatchesTtoS(wormT) ~= 0
finalMatchesStoT(finalMatchesTtoS(wormT)) = Inf;
end
finalMatchesStoT(wormS) = Inf;
finalMatchesTtoS(wormT) = Inf;
end
end
end
end
% -----------
% Update matching worms
% -----------
for wormT = 1:nbOfWormsTrack
if isfinite(finalMatchesTtoS(wormT)) && finalMatchesTtoS(wormT) ~= 0
% update wormT by wormS
listOfWorms.skel{wormT}{currentFrame} = listOfWormsSegm.skel{finalMatchesTtoS(wormT)};
listOfWorms.width{wormT}{currentFrame} = listOfWormsSegm.width{finalMatchesTtoS(wormT)};
listOfWorms.localthreshold{wormT} = listOfWormsSegm.localthreshold{finalMatchesTtoS(wormT)};
listOfWorms.lengthWorms(wormT,currentFrame) = listOfWormsSegm.lengthWorms(finalMatchesTtoS(wormT));
end
end
% -----------
% Try to match to lost worms, even if no overlap
% -----------
lostWormsT = find(listOfWorms.lost(:, currentFrame))';
if ~isempty(lostWormsT)
for wormS = find(finalMatchesStoT == 0)
centerS = mean(listOfWormsSegm.skel{wormS},2);
% -----------
% Compare with lost worms
% -----------
distances = Inf(1,nbOfWormsTrack);
for lostWorm = lostWormsT
centerT = mean(listOfWorms.skel{lostWorm}{currentFrame},2);
distances(lostWorm) = norm(centerS - centerT);
end
[valTmp, wormT] = min(distances);
if ~isinf(valTmp)
listOfWorms.skel{wormT}{currentFrame} = listOfWormsSegm.skel{wormS};
listOfWorms.width{wormT}{currentFrame} = listOfWormsSegm.width{wormS};
listOfWorms.localthreshold{wormT} = listOfWormsSegm.localthreshold{wormS};
listOfWorms.lengthWorms(wormT,currentFrame) = listOfWormsSegm.lengthWorms(wormS);
finalMatchesStoT(wormS) = wormT;
listOfWorms.missed(wormT,currentFrame) = false;
listOfWorms.lost(wormT,currentFrame) = false;
if traceOn; fprintf(fileToLog, ['found lost worm ', num2str(wormS), ' using ', num2str(wormT), '\n']); end
end
end
end
% -----------
% Create new worms if need be
% -----------
for wormS = find(finalMatchesStoT == 0)
newWorm = 1 + length(listOfWorms.skel);
listOfWorms.skel{newWorm} = cell(nbOfFrames,1);
listOfWorms.width{newWorm} = cell(nbOfFrames,1);
for frame = 1:currentFrame
listOfWorms.skel{newWorm}{frame} = listOfWormsSegm.skel{wormS};
listOfWorms.width{newWorm}{frame} = listOfWormsSegm.width{wormS};
end
listOfWorms.lengthWorms(newWorm,currentFrame) = listOfWormsSegm.lengthWorms(wormS);
listOfWorms.localthreshold{newWorm} = listOfWormsSegm.localthreshold{wormS};
listOfWorms.missed(newWorm,:) = false;
listOfWorms.lost(newWorm,nbOfFrames:end) = false;
listOfWorms.lost(newWorm,1:nbOfFrames-1) = true;
listOfWorms.overlapped(newWorm,:) = false;
end
catch em
if flagRobustness
if traceOn; fprintf(fileToLog, ['*** There was an error matching worms ','\n']); end
if traceOn; fprintf(fileToLog, [getReport(em, 'basic'),'\n']); end
else
rethrow(em)
end
end
if timingOn; timings(11) = timings(11) + toc ;timingsTime(11) = timingsTime(11)+1; tic; end
end