annotate utilities/UTIL_showMAP.m @ 35:25d53244d5c8

latest parameters

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