MAP

function UTIL_showMAP (showMapOptions, paramChanges)

% UTIL_showMAP produces summaries of the output from MAP's mmost recent run

%  All MAP outputs are stored in global variables and UTIL_showMAP

%  simply assumes that they are in place.

%

% showMapOptions

% showMapOptions.printModelParameters=1; % print model parameters

% showMapOptions.showModelOutput=1;      % plot all stages output

% showMapOptions.printFiringRates=1;     % mean activity at all stages

% showMapOptions.showACF=1;              % SACF (probabilities only)

% showMapOptions.showEfferent=1;         % plot of efferent activity

% showMapOptions.surfProbability=0;      % HSR (probability) surf plot

% showMapOptions.fileName=[];            % parameter filename for plot title

% dbstop if warning

global dt ANdt  savedBFlist saveAN_spikesOrProbability saveMAPparamsName...

    savedInputSignal OMEextEarPressure TMoutput OMEoutput ARattenuation ...

    DRNLoutput IHC_cilia_output IHCrestingCiliaCond IHCrestingV...

    IHCoutput ANprobRateOutput ANoutput savePavailable ANtauCas  ...

    CNtauGk CNoutput  ICoutput ICmembraneOutput ICfiberTypeRates ...

    MOCattenuation

global OMEParams DRNLParams IHC_cilia_RPParams IHCpreSynapseParams

global AN_IHCsynapseParams MacGregorParams MacGregorMultiParams

global ICrate

restorePath=path;

addpath ( ['..' filesep 'utilities'], ['..' filesep 'parameterStore'])

if nargin<1

    showMapOptions=[];

end

% defaults (plot staged outputs and print rates only) if options omitted

if ~isfield(showMapOptions,'printModelParameters')

    showMapOptions.printModelParameters=0; end

if ~isfield(showMapOptions,'showModelOutput'),showMapOptions.showModelOutput=1;end

if ~isfield(showMapOptions,'printFiringRates'),showMapOptions.printFiringRates=1;end

if ~isfield(showMapOptions,'showACF'),showMapOptions.showACF=0;end

if ~isfield(showMapOptions,'showEfferent'),showMapOptions.showEfferent=0;end

if ~isfield(showMapOptions,'surfProbability'),showMapOptions.surfProbability=0;end

if ~isfield(showMapOptions,'fileName'),showMapOptions.fileName=[];end

if ~isfield(showMapOptions,'surfSpikes'),showMapOptions.surfSpikes=0;end

if ~isfield(showMapOptions,'ICrates'),showMapOptions.ICrates=0;end

%% send all model parameters to command window

if showMapOptions.printModelParameters

    % Read parameters from MAPparams<***> file in 'parameterStore' folder

    %  and print out all parameters

    if nargin>1

        cmd=['MAPparams' saveMAPparamsName '(-1, 1/dt, 1, paramChanges);'];

        eval(cmd);

    else

        cmd=['MAPparams' saveMAPparamsName '(-1, 1/dt, 1);'];

        eval(cmd);

        disp(' no parameter changes found')

    end

end

%% summarise firing rates in command window

if showMapOptions.printFiringRates

    %% print summary firing rates

    fprintf('\n')

    disp('summary')

    disp(['AR: ' num2str(min(ARattenuation))])

    disp(['MOC: ' num2str(min(min(MOCattenuation)))])

    nANfiberTypes=length(ANtauCas);

    if strcmp(saveAN_spikesOrProbability, 'spikes')

        nANfibers=size(ANoutput,1);

        nHSRfibers=nANfibers/nANfiberTypes;

        duration=size(TMoutput,2)*dt;

        disp(['AN(HSR): ' num2str(sum(sum(ANoutput(end-nHSRfibers+1:end,:)))/...

            (nHSRfibers*duration))])

        nCNneurons=size(CNoutput,1);

        nHSRCNneuronss=nCNneurons/nANfiberTypes;

        disp(['CN(HSR): ' num2str(sum(sum(CNoutput(end-nHSRCNneuronss+1:end,:)))...

            /(nHSRCNneuronss*duration))])

        nICneurons=size(ICoutput,1);

        nHSRICneurons= round(nICneurons/nANfiberTypes);

        ICrate=sum(sum(ICoutput(end-nHSRICneurons+1:end,:)))/duration/nHSRICneurons;

        disp(['IC(HSR): ' num2str(ICrate)])

        %         disp(['IC by type: ' num2str(mean(ICfiberTypeRates,2)')])

    else

        HSRprobOutput= ANprobRateOutput(end-length(savedBFlist)+1:end,:);

        disp(['AN(HSR): ' num2str(mean(mean(HSRprobOutput)))])

        PSTH= UTIL_PSTHmakerb(HSRprobOutput, dt, 0.001);

        disp(['max max AN: ' num2str(max(max(PSTH)))])

    end

end

%% figure (99): display output from all model stages

if showMapOptions.showModelOutput

    plotInstructions.figureNo=99;

    % ignore zero elements in signal

    signalRMS=mean(savedInputSignal(find(savedInputSignal)).^2)^0.5;

    signalRMSdb=20*log10(signalRMS/20e-6);

    % plot signal (1)

    plotInstructions.displaydt=dt;

    plotInstructions.numPlots=6;

    plotInstructions.subPlotNo=1;

    plotInstructions.title=...

        ['stimulus (Pa).  ' num2str(signalRMSdb, '%4.0f') ' dB SPL'];

    r=size(savedInputSignal,1);

    if r==1, savedInputSignal=savedInputSignal'; end

    UTIL_plotMatrix(savedInputSignal', plotInstructions);

    % stapes (2)

    plotInstructions.subPlotNo=2;

    plotInstructions.title= ['stapes displacement (m)'];

    UTIL_plotMatrix(OMEoutput, plotInstructions);

    % DRNL (3)

    plotInstructions.subPlotNo=3;

    plotInstructions.yValues= savedBFlist;

    [r c]=size(DRNLoutput);

    if r>1

        plotInstructions.title= ['BM displacement'];

    UTIL_plotMatrix(abs(DRNLoutput), plotInstructions);

    else

        plotInstructions.title= ['BM displacement. BF=' ...

            num2str(savedBFlist) ' Hz'];

    UTIL_plotMatrix(DRNLoutput, plotInstructions);

    end

    switch saveAN_spikesOrProbability

        case 'spikes'

            % AN (4)

            plotInstructions.displaydt=ANdt;

            plotInstructions.title='AN';

            plotInstructions.subPlotNo=4;

            plotInstructions.yLabel='BF';

            plotInstructions.yValues= savedBFlist;

            plotInstructions.rasterDotSize=1;

            if length(ANtauCas)==2

                plotInstructions.plotDivider=1;

            else

                plotInstructions.plotDivider=0;

            end

            if sum(sum(ANoutput))<100

                plotInstructions.rasterDotSize=3;

            end

            UTIL_plotMatrix(ANoutput, plotInstructions);

            % CN (5)

            plotInstructions.displaydt=ANdt;

            plotInstructions.subPlotNo=5;

            plotInstructions.title='CN spikes';

            if sum(sum(CNoutput))<100

                plotInstructions.rasterDotSize=3;

            end

            UTIL_plotMatrix(CNoutput, plotInstructions);

            % IC (6)

            plotInstructions.displaydt=ANdt;

            plotInstructions.subPlotNo=6;

            plotInstructions.title='Brainstem 2nd level';

            if size(ICoutput,1)>1

                if sum(sum(ICoutput))<100

                    plotInstructions.rasterDotSize=3;

                end

                UTIL_plotMatrix(ICoutput, plotInstructions);

            else

                plotInstructions.title='IC (HSR) membrane potential';

                plotInstructions.displaydt=dt;

                plotInstructions.yLabel='V';

                plotInstructions.zValuesRange= [-.1 0];

                UTIL_plotMatrix(ICmembraneOutput, plotInstructions);

            end

        otherwise % AN rate based on probability of firing

            PSTHbinWidth=0.001;

            PSTH= UTIL_PSTHmakerb(ANprobRateOutput, dt, PSTHbinWidth);

%             PSTH = makeANsmooth(PSTH, 1/PSTHbinWidth);

            plotInstructions.displaydt=PSTHbinWidth;

            plotInstructions.numPlots=2;

            plotInstructions.subPlotNo=2;

            plotInstructions.yLabel='BF';

            plotInstructions.xLabel='time';

            plotInstructions.zValuesRange= [0 300];

            if nANfiberTypes>1,

                plotInstructions.yLabel='LSR    HSR';

                plotInstructions.plotDivider=1;

            end

            plotInstructions.title='AN - spike rate';

            UTIL_plotMatrix(PSTH, plotInstructions);

            shading interp

            colorbar('southOutside')

    end

    set(gcf,'name','MAP output')

end

if showMapOptions.surfProbability &&...

        strcmp(saveAN_spikesOrProbability,'probability') && ...

        length(savedBFlist)>2

    %% surface plot of probability

        % select only HSR fibers

        figure(97), clf

        HSRprobOutput= ANprobRateOutput(end-length(savedBFlist)+1:end,:);

        PSTHbinWidth=0.001;

        PSTH=UTIL_PSTHmakerb(HSRprobOutput, ANdt, PSTHbinWidth);

        [nY nX]=size(PSTH);

        time=PSTHbinWidth*(1:nX);

        surf(time, savedBFlist, PSTH)

        shading interp

        set(gca, 'yScale','log')

        xlim([0 max(time)])

        ylim([0 max(savedBFlist)])

        zlim([0 1000])

        xlabel('time (s)')

        ylabel('best frequency (Hz)')

        zlabel('spike rate')

        view([-20 60])

        %     view([0 90])

        disp(['max max AN: ' num2str(max(max(PSTH)))])

        title (['firing probability of HSR fibers only. Level= ' ...

            num2str(signalRMSdb,'% 3.0f') ' dB'])

        colorbar('southOutside')

end

%% surface plot of AN spikes

if showMapOptions.surfSpikes ...

    && strcmp(saveAN_spikesOrProbability, 'spikes')

    figure(97), clf

    % select only HSR fibers at the bottom of the matrix

    ANoutput= ANoutput(end-length(savedBFlist)+1:end,:);

    PSTHbinWidth=0.005; % 1 ms bins

    PSTH=UTIL_makePSTH(ANoutput, ANdt, PSTHbinWidth);

    [nY nX]=size(PSTH);

    time=PSTHbinWidth*(1:nX);

    surf(time, savedBFlist, PSTH)

    shading interp

    set(gca, 'yScale','log')

    xlim([0 max(time)])

    ylim([0 max(savedBFlist)])

    %     zlim([0 1000])

    xlabel('time (s)')

    ylabel('best frequency (Hz)')

    zlabel('spike rate')

    view([-20 60])

    %     view([0 90])

    title ([showMapOptions.fileName ':   ' num2str(signalRMSdb,'% 3.0f') ' dB'])

    set(97,'name', 'spikes surface plot')

end

%% figure(98) plot efferent control values as dB

if showMapOptions.showEfferent

    plotInstructions=[];

    plotInstructions.figureNo=98;

    figure(98), clf

    plotInstructions.displaydt=dt;

    plotInstructions.numPlots=4;

    plotInstructions.subPlotNo=1;

    plotInstructions.zValuesRange= [-1 1];

    plotInstructions.title= ['RMS level='...

        num2str(signalRMSdb, '%4.0f') ' dB SPL'];

    UTIL_plotMatrix(savedInputSignal', plotInstructions);

    plotInstructions.subPlotNo=2;

    plotInstructions.zValuesRange=[ -25 0];

    plotInstructions.title= ['AR stapes attenuation (dB); tau='...

        num2str(OMEParams.ARtau, '%4.3f') ' s'];

    UTIL_plotMatrix(20*log10(ARattenuation), plotInstructions);

    % MOCattenuation

    plotInstructions.numPlots=2;

    plotInstructions.subPlotNo=2;

    plotInstructions.yValues= savedBFlist;

    plotInstructions.yLabel= 'dB';

    if strcmp(saveAN_spikesOrProbability,'spikes')

        rate2atten=DRNLParams.rateToAttenuationFactor;

    plotInstructions.title= ['MOC atten; tau=' ...

        num2str(DRNLParams.MOCtau) '; factor='...

        num2str(rate2atten, '%6.4f')];

    else

        rate2atten=DRNLParams.rateToAttenuationFactorProb;

    plotInstructions.title= ['MOC atten; tauProb=' ...

        num2str(DRNLParams.MOCtauProb) '; factor='...

        num2str(rate2atten, '%6.4f')];

    end

    plotInstructions.zValuesRange=[0 -DRNLParams.minMOCattenuationdB+5];

    UTIL_plotMatrix(-20*log10(MOCattenuation), plotInstructions);

    hold on

    [r c]=size(MOCattenuation);

    if r>2

    colorbar('southOutside')

    end

    set(plotInstructions.figureNo, 'name', 'AR/ MOC')

    binwidth=0.1;

    [PSTH ]=UTIL_PSTHmaker(20*log10(MOCattenuation), dt, binwidth);

    PSTH=PSTH*length(PSTH)/length(MOCattenuation);

    t=binwidth:binwidth:binwidth*length(PSTH);

    fprintf('\n\n')

%     UTIL_printTabTable([t' PSTH'])

%     fprintf('\n\n')

end

%% ACF plot if required

if showMapOptions.showACF

    tic

    method.dt=dt;

    method.segmentNo=1;

    method.nonlinCF=savedBFlist;

    minPitch=	80; maxPitch=	4000; numPitches=100;    % specify lags

    pitches=10.^ linspace(log10(minPitch), log10(maxPitch),numPitches);

    pitches=fliplr(pitches);

    filteredSACFParams.lags=1./pitches;     % autocorrelation lags vector

    filteredSACFParams.acfTau=	.003;       % time constant of running ACF

    filteredSACFParams.lambda=	0.12;       % slower filter to smooth ACF

    filteredSACFParams.lambda=	0.01;       % slower filter to smooth ACF

    filteredSACFParams.plotACFs=0;          % special plot (see code)

    filteredSACFParams.plotFilteredSACF=0;  % 0 plots unfiltered ACFs

    filteredSACFParams.plotMoviePauses=.3;          % special plot (see code)

    filteredSACFParams.usePressnitzer=0; % attenuates ACF at  long lags

    filteredSACFParams.lagsProcedure=  'useAllLags';

    % filteredSACFParams.lagsProcedure=  'useBernsteinLagWeights';

    % filteredSACFParams.lagsProcedure=  'omitShortLags';

    filteredSACFParams.criterionForOmittingLags=3;

    filteredSACFParams.plotACFsInterval=200;

    if filteredSACFParams.plotACFs

        % plot original waveform on ACF plot

        figure(13), clf

        subplot(4,1,1)

        t=dt*(1:length(savedInputSignal));

        plot(t,savedInputSignal)

        xlim([0 t(end)])

        title(['stimulus: ' num2str(signalRMSdb, '%4.0f') ' dB SPL']);

    end

    % plot original waveform on summary/smoothed ACF plot

    figure(96), clf

    subplot(2,1,1)

    t=dt*(1:length(savedInputSignal));

    plot(t,savedInputSignal)

    xlim([0 t(end)])

    title(['stimulus: ' num2str(signalRMSdb, '%4.0f') ' dB SPL']);

    % compute ACF

    switch saveAN_spikesOrProbability

        case 'probability'

            inputToACF=ANprobRateOutput.^0.5;

        otherwise

            inputToACF=ANoutput;

    end

    disp ('computing ACF...')

    [P, BFlist, sacf, boundaryValue] = ...

        filteredSACF(inputToACF, method, filteredSACFParams);

    disp(' ACF done.')

    % SACF

    subplot(2,1,2)

    imagesc(P)

    ylabel('periodicities (Hz)')

    xlabel('time (s)')

    title(['running smoothed (root) SACF. ' saveAN_spikesOrProbability ' input'])

    pt=[1 get(gca,'ytick')]; % force top xtick to show

    set(gca,'ytick',pt)

    set(gca,'ytickLabel', round(pitches(pt)))

    tt=get(gca,'xtick');

    set(gca,'xtickLabel', round(100*t(tt))/100)

end

path(restorePath)

%% IC chopper analysis

% global ICrate

% if showMapOptions.ICrates

% [r nEpochs]=size(ICoutput);

% ICrate=zeros(1,length(CNtauGk));

% % convert ICoutput to a 4-D matrix (time, CNtau, BF, fiberType)

% %  NB only one IC unit for any combination.

% y=reshape(ICoutput', ...

%     nEpochs, length(CNtauGk),length(savedBFlist),length(ANtauCas));

% for i=1:length(CNtauGk)

%     ICrate(i)=sum(sum(sum(y(:,i,:,:))))/duration;

%     fprintf('%10.5f\t%6.0f\n', CNtauGk(i), ICrate(i))

% end

% figure(95), plot(CNtauGk,ICrate)

% title ('ICrate'), xlabel('CNtauGk'), ylabel('ICrate')

% end

function ANsmooth = makeANsmooth(ANresponse, sampleRate, winSize, hopSize)

            if nargin < 3

                winSize = 25; %default 25 ms window

            end

            if nargin < 4

                hopSize = 10; %default 10 ms jump between windows

            end

            winSizeSamples = round(winSize*sampleRate/1000);

            hopSizeSamples = round(hopSize*sampleRate/1000);

            % smooth

            hann = hanning(winSizeSamples);

            ANsmooth = [];%Cannot pre-allocate a size as it is unknown until the enframing

            for chan = 1:size(ANresponse,1)

                f = enframe(ANresponse(chan,:), hann, hopSizeSamples);

                ANsmooth(chan,:) = mean(f,2)'; %#ok<AGROW> see above comment

            end

%         end% ------ OF makeANsmooth