TD2TestNew.m~

MTD=readtable('Copy of TrackingData (2).xlsx');

MTD.Properties.VariableNames(1:14)={'FrameInterval' 'FrameIntervalAgg' 'from' 'DateTime' 'nTracks' 'nTracksAgg' 'SpaceUnits' 'TimeUnits' 'ParticlenSpots' 'ParticleId' 'ParticleDetectiont' 'ParticleDetectionx' 'ParticleDetectiony' 'ParticleDetectionz'};

Lremainders=rem(MTD.ParticleDetectionx,1);
Ltrue=(Lremainders==0); 
MTD(Ltrue,:)=[]; %removes columns with L(whole number)

Mremainders=rem(MTD.ParticleDetectiony,1);
Mtrue=(Mremainders==0);
MTD(Mtrue,:)=[]; %removes columns with M(whole number)

x=12;
TimePointTotals=MTD.ParticlenSpots>=x;
MTD(~TimePointTotals,:)=[]; %removes data with less than x time points

CellChange=ischange(MTD.ParticleId); %finds changes in particleid
MTD.Deltax=double(CellChange);
MTD.Deltax(1)=1; 
y=nnz(MTD.ParticleId==(max(MTD.ParticleId)))-1;
%y is leftover cells that don't get included in the loops below
 
isChangexIND=[1;find(diff(MTD.ParticleId))+1]; %index when id changes
for i=1:(length(isChangexIND)-1)
    IND1=isChangexIND(i);
    IND2=isChangexIND(i+1)+y;
    
    
    MTD.Deltax(IND1:IND2)=MTD.ParticleDetectionx(IND1:IND2)-MTD.ParticleDetectionx(IND1);
    %difference between particle x and original x positions
end
 
MTD.Deltay=double(CellChange);
MTD.Deltay(1)=1;
 
isChangeyIND=[1;find(diff(MTD.ParticleId))+1];
for i=1:(length(isChangeyIND)-1)
    IND1=isChangeyIND(i);
    IND2=isChangeyIND(i+1)+y;
    
    
    MTD.Deltay(IND1:IND2)=MTD.ParticleDetectiony(IND1:IND2)-MTD.ParticleDetectiony(IND1);
    %difference between particle y and original y positions
end
 
MTD.Deltax(MTD.Deltax==0)=0;
delta2x=diff(MTD.Deltax);  delta2x(isnan(delta2x))=0;

MTD.Deltay(MTD.Deltay==0)=0;
delta2y=diff(MTD.Deltay); delta2y(isnan(delta2y))=0;

deltaposition=sqrt(delta2x.^2+delta2y.^2);
MTD.DeltaPos=[0;deltaposition];

MTD.Deltax(end-y)=0;

zeroIND=MTD.Deltax==0;
for i=1:(length(zeroIND))
    MTD.DeltaPos(zeroIND)=0; 
    %makes the first timepoint of each cell have deltapos of 0
end