TwoTrackSep.asv

function [HCluster,HSort,Clusterspecies,SepID] = TwoTrackSep(data_ev,data_particle,SepID,...
    appear_part,maximalval)
%TWOTRACKSEP Summary of this function goes here
%   Detailed explanation goes here

%% Input data
% convID =data_ev(:,1); 
% convDiffco = data_particle(1,3);
% conv_diam = data_particle(1,2);
% position = data_particle(:,5:6);
% [sz,~] = size(data_particle);
% numbCdSep = [];
% ol_spec_sep = [];
[sz,~] = size(data_particle);
Clusterspecies = [];
HCluster = [];
HSort = [];
if sz ~= 0 && data_particle(1,2) > maximalval/0.75 %0.75 is omega for Dimer
    obspos = data_particle(sz,5:6);
    obstime = data_particle(sz,4);
    obspart = data_particle(sz,:);
    % Determination of max particle movement
    t =30; % in frames
    r_length_max = sqrt(4*data_particle(1,3)*(t/30)*log(1/(1-0.95))); % MaxMovement of particle in nm to a certain percentage
    r_max = ceil (r_length_max/166);
    % Which appearing particles are in time window of observed particle?
    TimeMatches = appear_part((appear_part(:,4) > obstime & appear_part(:,4) < obstime+t),:);
    % Which particles are smaller than the fading signal
    SizeMatches = TimeMatches(TimeMatches(:,2) < obspart(:,2),:);
    % KDTreeSearch for every particle in r_max:
    MdlKDT_Time = KDTreeSearcher(SizeMatches(:,5:6));
    IdxKDT_r_max = rangesearch(MdlKDT_Time,obspos,r_max);
    lines = sort(IdxKDT_r_max {1,1});
    XYMatches = SizeMatches(sort(lines(1:end)),:);  
    % Cluster out of fading particles, these would be the fading species
    Cluster = [obspart;XYMatches(:,:)];
    [appsz,~] = size (XYMatches);
%     [FCsz,~] = size (Cluster);
%     FdSort = {};
    if appsz >=2
        SID = [];
        AppSort(1:appsz,1) = {'Appearing'};
        FdSort = {'Fading'};
        Sort = [FdSort;AppSort];
        [Clustersz,~] = size(Cluster);
        SID(1:Clustersz,1) = SepID;
        HCluster = [SID,Cluster];
        HSort = [HSort,Sort];
        SepID = SepID+1;
        [Clusterspecies,SpeciesCode,Code] = SpeciesDetermine(data_ev,HCluster,maximalval);
        % Now check if particles belong to different species, for sppraration the
        % species has to be smaller than the later species. If Something is unknown
        % this will be kicked out directly in this window.

        ObsparticleSpecies = cell2mat(SpeciesCode(1,1));
        if ObsparticleSpecies ~= 8
            Check4Cell = iscell(Code);
            if Check4Cell == 0
                NewParticles = SpeciesCode(2:end,1);
                NewMaxSpec = Code(2:end,1);
                NewClusterspecies = Clusterspecies(2:end,1);
                NewPartCheck = NewParticles(1:end,1) < 8;
                NewParticleAmount = sum(NewPartCheck);
                if NewParticleAmount >=1
                    % If there is an unknown particle kick it out
                    NewParticles = NewParticles(NewPartCheck);
                    NewMaxSpec = NewMaxSpec(NewPartCheck);
                    NewSort = AppSort(NewPartCheck,1);
                    NewCluster = XYMatches(NewPartCheck,:);
                    NewClusterspecies = NewClusterspecies(NewPartCheck,1);
                    % If the particles are smaller than the fvanishing one
                    % kick them out
                    SpeciesCheck = NewMaxSpec(:,1) < Code(1,1);
                    NewParticles = NewParticles(SpeciesCheck,1);
                    NewSort = NewSort(SpeciesCheck,1);
                    NewCluster = NewCluster(SpeciesCheck,:);
                    NewClusterspecies = NewClusterspecies(SpeciesCheck,1);
                    % If there are still more than two particles appearing
                    % then use the cluster, otherwise kick it.
                    if length(NewParticles) >=2
                        % Put together the whole results:
                        Clusterspecies = [Clusterspecies(1,1);NewClusterspecies];
                        HCluster = [HCluster(1,:);NewCluster(:,:)];
                        HSort = [HSort(1,1);NewSort];
                    else 
                        Clusterspecies = [];
                        HCluster = [];
                        HSort = [];
                        SepID = SepID-1;
                    end
                else 
                    Clusterspecies = [];
                    HCluster = [];
                    HSort = [];
                    SepID = SepID-1;
                end
            else
                MaxSpec = zeros(length(Code),1);
                OverallSpec = zeros(length(SpeciesCode),1);
                for xx = 1:length(Code)
                    CheckRow = isnumeric(cell2mat(Code(xx,1)));
                    CheckRow2 = isnumeric(cell2mat(SpeciesCode(xx,1)));
                    if CheckRow == 0
                        Convert = cell2mat(Code(xx,1));
                        Convert2 = cell2mat(SpeciesCode(xx,1));
                        LengthConvert = length(Convert);
                        LengthConvert2 = length(Convert2);
                        if LengthConvert == 6
                            MaxSpec(xx,1) = min([str2num(Convert(1,1)),str2num(Convert(1,6))]);
                        else 
                            MaxSpec(xx,1) = min([str2num(Convert(1:3)),str2num(Convert(7:end))]);
                        end
                        OverallSpec (xx,1) = min([str2num(Convert(1,1)),str2num(Convert(1,6))]);
                    else
                        MaxSpec(xx,1) = cell2mat(Code(xx,1));
                        OverallSpec(xx,1) = cell2mat(SpeciesCode(xx,1)); 
                    end
                end
                % Check the appearing particles for known particles:
                NewParticles = OverallSpec(2:end,1);
                NewMaxSpec = MaxSpec(2:end,1);
                NewClusterspecies = Clusterspecies(2:end,1);
                NewCluster = HCluster(2:end,:);
                NewPartCheck = NewParticles(1:end,1) < 8;
                NewParticleAmount = sum(NewPartCheck);
                if NewParticleAmount >=1
                    % If there is an unknown particle kick it out
                    NewParticles = NewParticles(NewPartCheck);
                    NewMaxSpec = NewMaxSpec(NewPartCheck);
                    NewSort = AppSort(NewPartCheck,1);
                    NewCluster = NewCluster(NewPartCheck,:);
                    NewClusterspecies = NewClusterspecies(NewPartCheck,1);
                    % If the particles are smaller than the fvanishing one
                    % kick them out
                    SpeciesCheck = NewMaxSpec(:,1) < MaxSpec(1,1);
                    NewParticles = NewParticles(SpeciesCheck,1);
                    NewSort = NewSort(SpeciesCheck,1);
                    NewCluster = NewCluster(SpeciesCheck,:);
                    NewClusterspecies = NewClusterspecies(SpeciesCheck,1);
                    % If there are still more than two particles appearing
                    % then use the cluster, otherwise kick it.
                    if length(NewParticles) >=2
                        if length(NewParticles)==2
                            SeparationSpecies = zeros(length(NewParticles)-1,1);
                            for xx = 2:length(NewParticles)
                                SeparationSpecies(xx-1,1) = NewParticles(xx-1,1)+NewParticles(xx,1);
                            end
                            SeparationParticles = zeros(length(NewParticles),1);
                            SeparationCount = 0;
                            for yy = 1:length(SeparationSpecies)
                                SeparationTest = OverallSpec(1,1) == SeparationSpecies(yy,1);
                                SeparationCount = SeparationTest+SeparationCount;
                            end
                            if SeparationCount~=0
                                % Put together the whole results:
                                Clusterspecies = [Clusterspecies(1,1);NewClusterspecies];
                                HCluster = [HCluster(1,:);NewCluster(:,:)];
                                HSort = [HSort(1,1);NewSort];
                            else
                                Clusterspecies = [];
                                HCluster = [];
                                HSort = [];
                                SepID = SepID-1;
                            end
                        else
                            % Put together the whole results:
                            Clusterspecies = [Clusterspecies(1,1);NewClusterspecies];
                            HCluster = [HCluster(1,:);NewCluster(:,:)];
                            HSort = [HSort(1,1);NewSort];
                        end
%                          % Put together the whole results:
%                         Clusterspecies = [Clusterspecies(1,1);NewClusterspecies];
%                         HCluster = [HCluster(1,:);NewCluster(:,:)];
%                         HSort = [HSort(1,1);NewSort];
                    else 
                        Clusterspecies = [];
                        HCluster = [];
                        HSort = [];
                        SepID = SepID-1;
                    end
                else 
                    Clusterspecies = [];
                    HCluster = [];
                    HSort = [];
                    SepID = SepID-1;
                end
            end
        else
            Clusterspecies = [];
            HCluster = [];
            HSort = [];
            SepID = SepID-1;
        end
    end
end

end