FLICAfunc.m

function DataOut=FLICAfunc( traWin,timeShiftWin, inputPath,outputPath,LamdaTHS )
%FLICAFUNC Summary of this function goes here
%   Detailed explanation goes here
% LamdaTHS is a percentile of network density time series values
% If LamdaTHS is not set, by default, it is a mean of a network density
load(inputPath); % ===== trajectories input file
%============== process parts
if exist(outputPath, 'file')
    load(outputPath)
    if (exist('DataOut','var'))
        CorrMat=DataOut.CorrMat;
        NetDVec=DataOut.NetDVec;
        RankMat=DataOut.RankMat;
        VelMat=DataOut.VelMat;
        outVelConvexMat=DataOut.outVelConvexMat;
        outPosConvexMat=DataOut.outPosConvexMat;
        OrderMat=DataOut.OrderMat;
    else
        [ VelMat ] = TrajVel( TrajectoryXY );
    end
else
    [CorrMat,NetDVec,RankMat] = CreateMatFromTrajectory(TrajectoryXY,timeShiftWin,traWin);
    [ VelMat ] = TrajVel( TrajectoryXY );
    [ outVelConvexMat ] = scanOutConvexHull( VelMat );
    [ outPosConvexMat ] = Position_Convexhull( TrajectoryXY );
    [ OrderMat ] = ConvertPageRankMat2RankOrderMat( RankMat );
end

if ( ~exist('LamdaTHS','var') || isempty(LamdaTHS)) % we use mean of network density (\lambda) as default
    LamdaTHS=-1;
    LamdaTHS_ = mean(NetDVec);
else
    LamdaTHS_=prctile(NetDVec,LamdaTHS);
end
[ NetPeriods ] = DetectPeriodTypes( NetDVec,LamdaTHS_,traWin); % coordination events inference
if isempty(NetPeriods)
    return;
end

[ InitRankOrderMat ] = GetRankOrder( OrderMat,NetPeriods );
[ GlobalRankOrderMat ] = GetGlobalRankOrder( OrderMat );
 RankPosOutConvexMat=GetConvexHullRank( outPosConvexMat,NetPeriods,'Position' );
 RankVelOutConvexMat=GetConvexHullRank( outVelConvexMat,NetPeriods,'Velocity' );
[localPRRankOrderMat,localVCHRankOrderMat,localPCHRankOrderMat]=GetLocalRankOrder( OrderMat,outVelConvexMat,outPosConvexMat,NetPeriods );
[features] = GetModelSelectionFeatures( OrderMat,outVelConvexMat,outPosConvexMat,InitRankOrderMat,RankVelOutConvexMat,RankPosOutConvexMat,NetPeriods );
% %============== output
DataOut.NetDVec=NetDVec;
DataOut.CorrMat=CorrMat;
DataOut.RankMat=RankMat;
DataOut.OrderMat=OrderMat;
DataOut.NetPeriods=NetPeriods;
DataOut.VelMat=VelMat;
DataOut.InitRankOrderMat=InitRankOrderMat;
DataOut.GlobalRankOrderMat=GlobalRankOrderMat;
DataOut.RankPosOutConvexMat=RankPosOutConvexMat;
DataOut.RankVelOutConvexMat=RankVelOutConvexMat;
DataOut.features=features;
DataOut.outVelConvexMat=outVelConvexMat;
DataOut.outPosConvexMat=outPosConvexMat;
DataOut.traWin=traWin;
DataOut.LamdaTHS=LamdaTHS;
DataOut.localPRRankOrderMat=localPRRankOrderMat;
DataOut.localVCHRankOrderMat=localVCHRankOrderMat;
DataOut.localPCHRankOrderMat=localPCHRankOrderMat;
% methodComparePlot3( RankOrderMat,RankPosOutConvexMat,RankVelOutConvexMat,traWin, timeShiftWin);
save(outputPath,'DataOut');

end