Jin_Lee_2021/Matlab_function/abmFiringRateMap.m

function [occMat spkMat rawMat skaggsrateMat] = abmFiringRateMap(tmazeMat, finAlzPosMat, imROW, imCOL, thisSCALE, samplingRate)
%Generate firing rate map using Skaggs' adaptive binning methods
%[occMat spkMat rawMat skaggsrateMat] = abmFiringRateMap(tmazeMat, finAlzPosMat, imROW, imCOL, thisSCALE, samplingRate)
%
%Input format
%  tmazeMat	 [n x 3 matrix]									timestamp x-coord y-coord
%  finAlzPosMat [n x 3 matrix]									timestamp x-coord y-coord
%  imROW [1 x 1]												number of rows of ratemap
%  imCOL [1 x 1]												number of columns of ratemap
%  thisSCALE [1 x 1]											if you want to use original resolution, it should be 1. If you want to scale-down the resolusion by 10, it should be 10.
%  samplingRate [1 x 1]											sampling rate for behavioral traces. The current settings use 30 Hz.
%
%Output format
% occMat [imROW x imCOL matrix]									raw occupancy map
% spkMat [imROW x imCOL matrix]									raw spike position map
% rawMat [imROW x imCOL matrix; spkMat ./ (occMat .* samplingRate)]		raw firing rate map
% skaggsrateMat [imROW x imCOL matrix]								Skaggs' ABM firing rate map
%
%Originally from VB codes which Inah Lee has.
%Translate VB codes to matlab was done by [Jangjin Kim, July-13-2008]
%Verification was done
%reviced by SB 4/29/2013 : add 'to avoid error'
%revised by JSW 4/4/2019 : add empty tmazeMat error

    %to avoid error
    tmazeMatSize = size(tmazeMat);
    if tmazeMatSize(1) == 0 && tmazeMatSize(2) == 0
        tmazeMat = zeros(0,3);
    end

    %pINDEX
    pXCOORD = 2;																						%x coordinates [from Neuralynx]
    pYCOORD = 3;																						%y coordinates [from Neuralynx]
    alphaSET = .0001;

    occMat = nan(imROW, imCOL);
    spkMat = zeros(imROW, imCOL);
    rawMat = zeros(imROW, imCOL);
    skaggsrateMat = zeros(imROW, imCOL);

    for rowRUN = 1:1:imROW
        for colRUN = 1:1:imCOL
            if ~isempty(tmazeMat) %revised by JSW 4/4/2019 : add empty tmazeMat error
            numspk =  size(tmazeMat(tmazeMat(:, pXCOORD) ./ thisSCALE > (colRUN - 1) & tmazeMat(:, pXCOORD) ./ thisSCALE <= colRUN & ... 
                                    tmazeMat(:, pYCOORD) ./ thisSCALE > (rowRUN - 1) & tmazeMat(:, pYCOORD) ./ thisSCALE <= rowRUN, :));
                if numspk(1, 1) == 0
                    spkMat(rowRUN, colRUN) = 0;
                else
                    spkMat(rowRUN, colRUN) = numspk(1, 1);
                end	%numspk(1, 1) == 0
            else
                spkMat(rowRUN, colRUN) = 0;
            end
            if ~isempty(finAlzPosMat)
                numocc = size(finAlzPosMat(finAlzPosMat(:, pXCOORD) ./ thisSCALE > (colRUN - 1) & finAlzPosMat(:, pXCOORD) ./ thisSCALE <= colRUN & ... 
                                    finAlzPosMat(:, pYCOORD) ./ thisSCALE > (rowRUN - 1) & finAlzPosMat(:, pYCOORD) ./ thisSCALE <= rowRUN, :));
                if numocc(1, 1) == 0
                    occMat(rowRUN, colRUN) = nan;
                else
                    occMat(rowRUN, colRUN) = numocc(1, 1);
                end	%numocc(1, 1) == 0
            else
                occMat(rowRUN, colRUN) = nan;
            end
        end	%colRUN = 1:1:imCOL
    end	%rowRUN = 1:1:imROW

    rawMat = spkMat ./ occMat .* samplingRate;

    if sum(sum(spkMat)) > 0
        nanIND = find(isnan(occMat));
        occMat(isnan(occMat)) = 0;
        i = -20:20; j = -20:19;
        Ti = zeros(28, 400);
        Tj = zeros(28, 400);

        for colRUN = 1:1:imCOL
            for rowRUN = 1:1:imROW
                if occMat(rowRUN, colRUN) > 0
                    %Equivalent to BuildRTable
                    Nr = zeros(1, 400);

                    for ii = 1:1:41
                        for jj = 1:1:40
                            %r(1, (ii - 1) * 41 + jj) = i(1, ii)^2 + j(1, jj)^2; 
                            %r(ii, jj) = i(1, ii)^2 + j(1, jj)^2; 
                            r = i(1, ii)^2 + j(1, jj)^2 + 1;
                            if r <= 400
                                N = Nr(r);
                                Ti(N + 1, r) = i(1, ii);
                                Tj(N + 1, r) = j(1, jj);
                                Nr(r) = Nr(r) + 1;
                            end	%r <= 400
                        end	%jj = 1:1:40
                    end	%ii = 1:1:41

                    nSPK = spkMat(rowRUN, colRUN);
                    nOCC = occMat(rowRUN, colRUN);

                    lambda = nSPK / nOCC * samplingRate;

                    for colRUN2 = 1:1:imCOL								%i
                        for rowRUN2 = 1:1:imROW							%j
                            if occMat(rowRUN2, colRUN2) == 0
                                skaggsrateMat(rowRUN2, colRUN2) = nan;
                            else
                                EnoughPoints = false;
                                occCount = 1;						%Assume there's at least 1 spk and 1 occ
                                spkCount = 1;
                                r = 0;
                                while (r <= 200 & EnoughPoints == false) % r <= 200 original
                                    for h = 1:1:Nr(r + 1)
                                        ii = (colRUN2 - 1) + Ti(h, r + 1);
                                        jj = (rowRUN2 - 1) + Tj(h, r + 1);	%-1 to compensate VB code
                                        if (ii >= 0 & ii < 64) & (jj >= 0 & jj < 48)
                                            occCount = occCount + occMat(jj + 1, ii + 1);
                                            spkCount = spkCount + spkMat(jj + 1, ii + 1);
                                        end	%(ii >= 0 & ii < 64) & (jj >= 0 & jj < 48)
                                    end	%h = 1:1:Nr(r + 1)
                                    if alphaSET^2 * occCount^2 * r * spkCount > 1
                                        EnoughPoints = true;
                                    end	%alphaSET^2 * occCount^2 * r * spkCount > 1
                                    r = r + 1;
                                end	%(r <= 200 & EnoughPoints == false)
                                if occCount < samplingRate / 2
                                    skaggsrateMat(rowRUN2, colRUN2) = 0;
                                else
                                    skaggsrateMat(rowRUN2, colRUN2) = spkCount / occCount * samplingRate;
                                end	%occCount < samplingRate / 2
                            end	%occMat(colRUN2, rowRUN2) == 0
                            if occMat(rowRUN2, colRUN2) ~= 0 & isnan(skaggsrateMat(rowRUN2, colRUN2))
                                rowRUN2 = rowRUN2;
                            end	%occMat(rowRUN2, colRUN2) ~= 0 & isnan(skaggsrateMat(rowRUN2, colRUN2))
                            if rowRUN2 == 16 & colRUN2 == 39				%Add 1 to compensate VB indices
                                rowRUN2 = rowRUN2;
                            end	%rowRUN2 == 16 & colRUN2 == 39
                        end	%rowRUN2 = 1:1:imROW
                    end	%colRUN2 = 1:1:imCOL
                end	%occMat(rowRUN, colRUN) > 0
            end	%rowRUN = 1:1:imROW
        end	%colRUN = 1:1:imCOL
        occMat(nanIND) = nan;
    else
        skaggsrateMat = rawMat;
    end	%sum(sum(spkMat)) > 0