Calculations/MOT Capture Process Simulation/@MOTSimulator/calculateLoadingRate.m

function [LoadingRate, StandardError, ConfidenceInterval] = calculateLoadingRate(this, ParticleDynamicalQuantities)
    switch this.SimulationMode
        case "2D"
            n                    = this.NumberOfAtoms;
            NumberOfTimeSteps    = int64(this.SimulationTime/this.TimeStep);
            NumberOfLoadedAtoms  = zeros(1, NumberOfTimeSteps);
            TimeCounts           = zeros(1, n);
            CollisionEvents      = zeros(1, n);
            
            % Include the stochastic process of background collisions
            for AtomIndex = 1:n
               TimeCounts(AtomIndex)       = this.computeTimeSpentInInteractionRegion(squeeze(ParticleDynamicalQuantities(AtomIndex,:,1:3)));
            end
            this.TimeSpentInInteractionRegion = mean(TimeCounts);
            for AtomIndex = 1:n
                CollisionEvents(AtomIndex) = this.computeCollisionProbability();
            end
            
            % Count the number of loaded atoms subject to conditions
            for TimeIndex = 1:NumberOfTimeSteps
                if TimeIndex ~= 1
                    NumberOfLoadedAtoms(TimeIndex) = NumberOfLoadedAtoms(TimeIndex-1);
                end
                for AtomIndex = 1:n
                    Position = squeeze(ParticleDynamicalQuantities(AtomIndex, TimeIndex, 1:3))';
                    Velocity = squeeze(ParticleDynamicalQuantities(AtomIndex, TimeIndex, 4:6))';
                    if this.exitCondition(Position, Velocity, CollisionEvents(AtomIndex))
                        NumberOfLoadedAtoms(TimeIndex) = NumberOfLoadedAtoms(TimeIndex) + 1;
                    end
                end
            end
            
            [LoadingRate, StandardError, ConfidenceInterval] = this.bootstrapErrorEstimation(NumberOfLoadedAtoms);
            
       case "3D"
            % Development In progress
    end
end