Calculations/+Simulator/@TwoDimensionalMOT/calculateLoadingRate.m

function [LoadingRate, StandardError, ConfidenceInterval] = calculateLoadingRate(this, ovenObj)
    n                    = this.NumberOfAtoms;
    DynamicalQuantities  = this.ParticleDynamicalQuantities;
    CollisionEvents      = zeros(1, n);
    NumberOfLoadedAtoms  = zeros(1, n);
    

    % Include the stochastic process of background collisions
    for AtomIndex = 1:n
       this.TimeSpentInInteractionRegion(AtomIndex) = this.computeTimeSpentInInteractionRegion(squeeze(DynamicalQuantities(AtomIndex,:,1:3)));
       CollisionEvents(AtomIndex)                   = this.computeCollisionProbability(ovenObj, this.TimeSpentInInteractionRegion(AtomIndex));
    end

    % Count the number of loaded atoms subject to conditions
    
    switch this.ErrorEstimationMethod
        case 'bootstrap'
            NumberOfTimeSteps    = int64(this.SimulationTime/this.TimeStep);
            NumberOfLoadedAtoms  = zeros(1, NumberOfTimeSteps);
            LoadedAtomIndices    = [];
            for TimeIndex = 1:NumberOfTimeSteps
                if TimeIndex ~= 1
                    NumberOfLoadedAtoms(TimeIndex) = NumberOfLoadedAtoms(TimeIndex-1);
                end
                for AtomIndex = 1:n
                    Position = squeeze(DynamicalQuantities(AtomIndex, TimeIndex, 1:3))';
                    if this.exitCondition(Position, CollisionEvents(AtomIndex))
                        if ~ismember(AtomIndex, LoadedAtomIndices)
                            NumberOfLoadedAtoms(TimeIndex) = NumberOfLoadedAtoms(TimeIndex) + 1;
                            LoadedAtomIndices(end+1)       = AtomIndex;
                        end
                    else
                        if ismember(AtomIndex, LoadedAtomIndices)
                            NumberOfLoadedAtoms(TimeIndex) = NumberOfLoadedAtoms(TimeIndex) - 1;
                            LoadedAtomIndices(LoadedAtomIndices==AtomIndex)   = [];
                        end
                    end
                end
            end
            [LoadingRate, StandardError, ConfidenceInterval] = this.bootstrapErrorEstimation(ovenObj, NumberOfLoadedAtoms);
        case 'jackknife'
            for AtomIndex = 1:n
                if AtomIndex ~= 1
                    NumberOfLoadedAtoms(AtomIndex) = NumberOfLoadedAtoms(AtomIndex-1);
                end
                Position = squeeze(DynamicalQuantities(AtomIndex, end, 1:3))';
                if this.exitCondition(Position, CollisionEvents(AtomIndex))
                    NumberOfLoadedAtoms(AtomIndex) = NumberOfLoadedAtoms(AtomIndex) + 1;
                end
            end
            [LoadingRate, StandardError, ConfidenceInterval] = jackknifeErrorEstimation(this, ovenObj,  NumberOfLoadedAtoms);
    end
end