function output = exp_takanen2013(varargin)
%EXP_TAKANEN2013 Figures from Takanen, Santala, Pulkki (2013a,2013b)
%   Usage: output = exp_takanen2013(flag)
%
%   EXP_TAKANEN2013(flag) reproduces the figure given by flag either from
%   the Takanen et al. (2013) book chapter or the Takanen et al. (2014)
%   manuscript. The format of its output depends on the chosen figure.
%   Optionally, pre-computed cochlear model outputs for the different
%   scenarios can be applied to significantly reduce the required
%   computation time. The pre-computed cochlear model outputs can be 
%   obtained from the authors.
%  
%   The following flags can be specified:
%
%     'binsig'       This option computes the figures from the binaural
%                    signals.
%
%     'cochlea'      This option uses pre-computed cochlea-model outputs
%                    and thus reduces the computation time. (Default).
%
%     'fig8'         Figure 8 from the book chapter Takanen et al. (2013). Binaural activity 
%                    maps obtained with the model for an off-sweet-spot 
%                    listening scenario with different audio coding 
%                    techniques.
%
%     'fig9'         Figure 9 from the book chapter Takanen et al. (2013). Activation
%                    distributions obtained with the model for (a) the 
%                    reference scenario of incoherent pink noise emitted 
%                    from twelve azimuth directions, and (b)-(d) the 
%                    reproduction of such a scenario with an eight-channel
%                    loudspeaker system employing signals obtained with
%                    different audio coding techniques. Additionally, the
%                    the distributions when DirAC is used in audio coding
%                    of 5.0 surround signal having incoherent pink noise
%                    in each channel with (e) the straightforward method 
%                    and (f) the even-layout method.
%
%     'fig7_takanen2014'   Figure 7 from the article Takanen et al. (2014). Binaural activity maps 
%                          for four binaural listening scenarios, namely (a)
%                          HRTF-processed pink noise, (b) pink noise with ITD, 
%                          (c) anti-phasic sinusoidal sweep, and (d) band-
%                          limited noise centered around 500 Hz with an ITD of
%                          1.5 ms.
%
%     'fig8_takanen2014'   Figure 8 from the article Takanen et al. (2014). Binaural activity maps 
%                          for four binaural listening scenarios, namely (a) 
%                          S_pi N_0 with different signal-to-noise ratios, 
%                          (b) binaural interference, (c) precedence effect, and
%                          (d) binaural room impulse response.
%
%   If no flag is given, the function will print the list of valid flags.
%
%   Requirements and installation: 
%   ------------------------------
%
%   1) Functioning model verhulst2012 (see the corresponding requirements)
%
%   2) Data from www.acoustics.hut.fi/publications/papers/AMTool2013-bam/ in amtbase/signals
%
%   3) at least 3 GB of RAM
%
%   Examples:
%   ---------
%
%   To display Figure 8 from the book chapter Takanen et al. (2013) using pre-computed cochlea
%   model outputs use:
%
%     exp_takanen2013('fig8','cochlea');
%
%   To display Figure 9 from the book chapter Takanen et al. (2013) using pre-computed cochlea
%   model outputs use:
%
%     exp_takanen2013('fig9','cochlea');
%
%   To display Figure 7 from the article Takanen et al. (2014) using pre-computed cochlea 
%   model outputs use:
%
%     exp_takanen2013('fig7_takanen2014','cochlea');
%
%   To display Figure 8 the article Takanen et al. (2014) using pre-computed cochlea 
%   model outputs use:
%
%     exp_takanen2013('fig8_takanen2014','cochlea');
%
%   References:
%     M. Takanen, O. Santala, and V. Pulkki. Visualization of functional
%     count-comparison-based binaural auditory model output. Hearing
%     research, 309:147--163, 2014. PMID: 24513586.
%     
%     M. Takanen, O. Santala, and V. Pulkki. Perceptually encoded signals and
%     their assessment. In J. Blauert, editor, The technology of binaural
%     listening. Springer, 2013.
%     
%
%   Url: http://amtoolbox.org/amt-1.4.0/doc/experiments/exp_takanen2013.php


%   #Author: Marko Takanen (2013)
%   #Author: Olli Santala (2013)
%   #Author: Ville Pulkki (2013)

% This file is licensed unter the GNU General Public License (GPL) either 
% version 3 of the license, or any later version as published by the Free Software 
% Foundation. Details of the GPLv3 can be found in the AMT directory "licences" and 
% at <https://www.gnu.org/licenses/gpl-3.0.html>. 
% You can redistribute this file and/or modify it under the terms of the GPLv3. 
% This file is distributed without any warranty; without even the implied warranty 
% of merchantability or fitness for a particular purpose. 

definput.import={'amt_cache'};
definput.flags.type={'missingflag','fig8','fig9','fig7_takanen2014','fig8_takanen2014'};

definput.flags.dataType={'cochlea','binsig'};

[flags,keyvals]  = ltfatarghelper({},definput,varargin);


if flags.do_missingflag
  flagnames=[sprintf('%s, ',definput.flags.type{2:end-2}),...
             sprintf('%s or %s',definput.flags.type{end-1},definput.flags.type{end})];
  error('%s: You must specify one of the following flags: %s.',upper(mfilename),flagnames);
end;

%% Setting of parameters
fs = 48000;
printFigs = 0;
printMap =0;
compType =1;
h = figure;
%% Figure 8 from the book chapter
if flags.do_fig8
    % if the user wishes to compute the cochlear model outputs, binaural
    % input signals are used
    if flags.do_binsig
        data=amt_load('takanen2013','fig8_binsig.mat','testsize');
        for ind=1:data.testsize
            [output,outputMtrx,tit]=amt_cache('get', ['fig8_binsig_' num2str(ind)], flags.cachemode);
            if isempty(output)
                data=amt_load('takanen2013','fig8_binsig.mat',['test' num2str(ind)]);
                tit=data.(['test' num2str(ind)]).case;
                insig=data.(['test' num2str(ind)]).insig;
                clear data
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                nXBins= length(output.levels)*(size(output.colorMtrx,1)-1);
                dim = size(output.activityMap);
                output.colorGains(output.colorGains>1) =1;
                outputMtrx = zeros(dim(1),nXBins,3,'single');
                for colorInd=1:size(output.colorMtrx,1)
                    temp = uint32(find((output.activityMap==(colorInd-1))==1));
                    outputMtrx(temp) = output.colorGains(temp)*output.colorMtrx(colorInd,1);
                    outputMtrx(temp+dim(1)*nXBins) = output.colorGains(temp)*output.colorMtrx(colorInd,2);
                    outputMtrx(temp+2*dim(1)*nXBins) = output.colorGains(temp)*output.colorMtrx(colorInd,3);
                end
                amt_cache('set', ['fig8_binsig_' num2str(ind)], output, outputMtrx, tit);
            end
            g(ind)= subplot(3,2,ind);
            imagesc(output.levels./90,((dim(1)-1):-20:0)/fs,outputMtrx(1:20:end,:,:));
            clear output outputMtrx
            title(tit);
            set(gca,'YTick',.0:.5:2.5);
            set(gca,'YTickLabel',2.5:-0.5:0);
            set(gca,'Xtick',-1:0.4:1);
            xlabel('Activation location');
            ylabel('Time [s]');
        end
        
    end
    %otherwise pre-computed cochlea model outputs are used
    if flags.do_cochlea
        testsize=amt_load('takanen2013','fig8_cochlea.mat','testsize');
        for ind=1:testsize.testsize
            [output,outputMtrx,tit]=amt_cache('get', ['fig8_cochlea_' num2str(ind)], flags.cachemode);
            if isempty(output)
                data=amt_load('takanen2013','fig8_cochlea.mat',['test' num2str(ind)]);
                tit=data.(['test' num2str(ind)]).case;
                insig=data.(['test' num2str(ind)]).cochlear;
                clear data
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                nXBins= length(output.levels)*(size(output.colorMtrx,1)-1);
                dim = size(output.activityMap);
                output.colorGains(output.colorGains>1) =1;
                outputMtrx = zeros(dim(1),nXBins,3,'single');
                for colorInd=1:size(output.colorMtrx,1)
                    temp = uint32(find((output.activityMap==(colorInd-1))==1));
                    outputMtrx(temp) = output.colorGains(temp)*output.colorMtrx(colorInd,1);
                    outputMtrx(temp+dim(1)*nXBins) = output.colorGains(temp)*output.colorMtrx(colorInd,2);
                    outputMtrx(temp+2*dim(1)*nXBins) = output.colorGains(temp)*output.colorMtrx(colorInd,3);
                end
                amt_cache('set', ['fig8_cochlea_' num2str(ind)], output, outputMtrx, tit);
            end
            g(ind)=subplot(3,2,ind);
            imagesc(output.levels./90,((size(output.activityMap,1)-1):-20:0)/fs,outputMtrx(1:20:end,:,:));
            clear output outputMtrx
            title(tit);
            set(gca,'YTick',.0:.5:2.5);
            set(gca,'YTickLabel',2.5:-0.5:0);
            set(gca,'Xtick',-1:0.4:1);
            ylabel('Time [s]');
            xlabel('Activation location');
        end
    end
end
%% Figure 9 from the book chapter
if flags.do_fig9
    probDist = zeros(6,19);
    % if the user wishes to compute the cochlear model outputs, binaural
    % input signals are used
    if flags.do_binsig
        data=amt_load('takanen2013','fig9_binsig.mat', 'testsize');
        for ind=1:data.testsize
            [output,outputMtrx,tit]=amt_cache('get', ['fig9_binsig_' num2str(ind)], flags.cachemode);
            if isempty(output)
                data=amt_load('takanen2013','fig9_binsig.mat',['test' num2str(ind)]);
                tit=data.(['test' num2str(ind)]).case;
                insig=data.(['test' num2str(ind)]).insig;
                clear data
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                for i=1:6
                    probDist(i,:) = sum(output.colorGains(:,i:6:end));
                end
                temp = probDist./(max(probDist,[],2)*ones(1,size(probDist,2)));
                outputMtrx = zeros(size(temp,1),size(temp,2),3,'single');
                for colorInd=2:size(output.colorMtrx,1)
                    outputMtrx(colorInd-1,:,1) = temp(colorInd-1,:)*output.colorMtrx(colorInd,1);
                    outputMtrx(colorInd-1,:,2) = temp(colorInd-1,:)*output.colorMtrx(colorInd,2);
                    outputMtrx(colorInd-1,:,3) = temp(colorInd-1,:)*output.colorMtrx(colorInd,3);
                end
                amt_cache('set', ['fig9_binsig_' num2str(ind)], output, outputMtrx, tit);
            end
            g(ind)= subplot(3,2,ind);
            imagesc(output.levels./90,6:-1:1,outputMtrx);
            clear output outputMtrx
            title(tit);
            set(gca,'YTick',1:6);
            set(gca,'YTickLabel',6:-1:1);
            set(gca,'Xtick',-1:0.4:1);
            ylabel('Frequency area');
            xlabel('Distribution of activation');
        end
    end
    %otherwise pre-computed cochlea model outputs are used
    if flags.do_cochlea
        data=amt_load('takanen2013','fig9_cochlea.mat','testsize');
        for ind=1:data.testsize
            [output,outputMtrx,tit]=amt_cache('get', ['fig9_cochlea_' num2str(ind)], flags.cachemode);
            if isempty(output)
                data=amt_load('takanen2013','fig9_cochlea.mat',['test' num2str(ind)]);
                tit=data.(['test' num2str(ind)]).case;
                insig=data.(['test' num2str(ind)]).cochlear;
                clear data
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                for i=1:6
                    probDist(i,:) = sum(output.colorGains(:,i:6:end));
                end
                temp = probDist./(max(probDist,[],2)*ones(1,size(probDist,2)));
                outputMtrx = zeros(size(temp,1),size(temp,2),3,'single');
                for colorInd=2:size(output.colorMtrx,1)
                    outputMtrx(colorInd-1,:,1) = temp(colorInd-1,:)*output.colorMtrx(colorInd,1);
                    outputMtrx(colorInd-1,:,2) = temp(colorInd-1,:)*output.colorMtrx(colorInd,2);
                    outputMtrx(colorInd-1,:,3) = temp(colorInd-1,:)*output.colorMtrx(colorInd,3);
                end
                amt_cache('set', ['fig9_cochlea_' num2str(ind)], output, outputMtrx, tit);
            end
            g(ind)= subplot(3,2,ind);
            imagesc(output.levels./90,6:-1:1,outputMtrx);
            clear output outputMtrx
            title(tit);
            set(gca,'YTick',1:6);
            set(gca,'YTickLabel',6:-1:1);
            set(gca,'Xtick',-1:0.4:1);
            ylabel('Frequency area');
            xlabel('Distribution of activation');
        end
    end
end
%% Figure 7 from takanen2014
if flags.do_fig7_takanen2014
    % compute the cochlear model outputs, load the binaural input signals
    if flags.do_binsig, s='fig7_takanen2014_binsig'; end
    % otherwise pre-computed cochlea model outputs are used
    if flags.do_cochlea, s='fig7_takanen2014_cochlea'; end

    data=amt_load('takanen2013',[s '.mat']);
    data_tests=data.testsize;
    siglen=zeros(data_tests,1);
    data_tests_Data=zeros(data_tests,1);
    for ind=1:data_tests
      if flags.do_cochlea
        data_tests_Data(ind)=length(data.(['test' num2str(ind)]).cochlearData);
        for caseInd=1:data_tests_Data(ind)
          siglen(ind)=siglen(ind)+length(data.(['test' num2str(ind)]).cochlearData(caseInd).cochlear.velocityLeft);
        end
      end
      if flags.do_binsig
        data_tests_Data(ind)=length(data.(['test' num2str(ind)]).binSignals);
        for caseInd=1:data_tests_Data(ind)
          siglen(ind)=siglen(ind)+length(data.(['test' num2str(ind)]).binSignals(caseInd).insig);
        end
      end          
    end
    clear data % release unused memory
    for ind=1:data_tests
        idx=1;
        %some scenarios consist of multiple test cases that are
        %processed separately
        [levels,activityMap,outputMtrx,scenario,ytickPos,ytickLab,ylab]=amt_cache('get', [s '_' num2str(ind)], flags.cachemode);
        if isempty(levels)
            activityMap=zeros(siglen(ind),114);
            gains=zeros(siglen(ind),114);
            for caseInd=1:data_tests_Data(ind)
                data=amt_load('takanen2013',[s '.mat'],['test' num2str(ind)]);
                if flags.do_cochlea
                  insig=data.(['test' num2str(ind)]).cochlearData(caseInd).cochlear;
                  len=size(insig.velocityLeft,1);
                end
                if flags.do_binsig
                  insig=data.(['test' num2str(ind)]).binSignals(caseInd).insig;
                  len=size(insig,1);
                end            
                ylab=data.(['test' num2str(ind)]).ylab;
                scenario=data.(['test' num2str(ind)]).scenario;
                ytickPos=data.(['test' num2str(ind)]).ytickPos;
                ytickLab=data.(['test' num2str(ind)]).ytickLab(end:-1:1);
                clear data % release unused memory
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                %concatenate the separate activity maps into one map
                activityMap(idx:idx+len-1,:)=output.activityMap;
                gains(idx:idx+len-1,:)=output.colorGains;
                idx=idx+len;
                colorMtrx=output.colorMtrx;
                levels=output.levels;
                clear output insig % release unused memory
            end
            %the anti-phasic sweep contains also frequencies below the
            %frequency range of the model. Hence, the first 0.5 s of the
            %activity map are removed
            if(strcmp('Anti-phasic sinusoidal sweep',scenario)==1)
                activityMap = activityMap(0.5*fs+1:end,:);
                gains = gains(0.5*fs+1:end,:);
            end
            nXBins= length(levels)*(size(colorMtrx,1)-1);
            dim = size(activityMap);
            gains(gains>1) =1;
            outputMtrx = zeros(dim(1),nXBins,3,'single');
            for colorInd=1:size(colorMtrx,1)
                temp = uint32(find((activityMap==(colorInd-1))==1));
                outputMtrx(temp) = gains(temp)*colorMtrx(colorInd,1);
                outputMtrx(temp+dim(1)*nXBins) = gains(temp)*colorMtrx(colorInd,2);
                outputMtrx(temp+2*dim(1)*nXBins) = gains(temp)*colorMtrx(colorInd,3);
            end
            amt_cache('set', [s '_' num2str(ind)], levels, activityMap, outputMtrx, scenario, ytickPos, ytickLab, ylab);
        end
        g(ind)= subplot(2,2,ind);
        imagesc(levels./90,((size(activityMap,1)-1):-20:0)/fs,outputMtrx(1:20:end,:,:));
        clear outputMtrx gains activityMap
        title(scenario);
        set(gca,'YTick',ytickPos);
        set(gca,'YTickLabel',ytickLab);
        set(gca,'Xtick',-1:0.4:1);
        ylabel(ylab);
        xlabel('Activation location');
    end
end
%% Figure 8 from takanen2014
if flags.do_fig8_takanen2014
    % compute the cochlear model outputs, load the binaural input signals
    if flags.do_binsig, s='fig8_takanen2014_binsig'; end
    % otherwise pre-computed cochlea model outputs are used
    if flags.do_cochlea, s='fig8_takanen2014_cochlea'; end

    data=amt_load('takanen2013',[s '.mat']);
    data_tests=data.testsize;
    siglen=zeros(data_tests,1);
    data_tests_Data=zeros(data_tests,1);
    for ind=1:data_tests
      if flags.do_cochlea
        data_tests_Data(ind)=length(data.(['test' num2str(ind)]).cochlearData);
        for caseInd=1:data_tests_Data(ind)
          siglen(ind)=siglen(ind)+length(data.(['test' num2str(ind)]).cochlearData(caseInd).cochlear.velocityLeft);
        end
      end
      if flags.do_binsig
        data_tests_Data(ind)=length(data.(['test' num2str(ind)]).binSignals);
        for caseInd=1:data_tests_Data(ind)
          siglen(ind)=siglen(ind)+length(data.(['test' num2str(ind)]).binSignals(caseInd).insig);
        end
      end          
    end
    clear data % release unused memory
    for ind=1:data_tests
        idx=1;
        %some scenarios consist of multiple test cases that are
        %processed separately
        [levels,activityMap,outputMtrx,scenario,ytickPos,ytickLab,ylab]=amt_cache('get', [s '_' num2str(ind)], flags.cachemode);
        if isempty(levels)
            activityMap=zeros(siglen(ind),114);
            gains=zeros(siglen(ind),114);
            for caseInd=1:data_tests_Data(ind)
                data=amt_load('takanen2013', [s '.mat'], ['test' num2str(ind)]);
                if flags.do_cochlea
                  insig=data.(['test' num2str(ind)]).cochlearData(caseInd).cochlear;
                  len=size(insig.velocityLeft,1);
                end
                if flags.do_binsig
                  insig=data.(['test' num2str(ind)]).binSignals(caseInd).insig;
                  len=size(insig,1);
                end            
                ylab=data.(['test' num2str(ind)]).ylab;
                scenario=data.(['test' num2str(ind)]).scenario;
                ytickPos=data.(['test' num2str(ind)]).ytickPos;
                ytickLab=data.(['test' num2str(ind)]).ytickLab(end:-1:1);
                clear data % release unused memory
                % compute the binaural activity map with the model
                output = takanen2013(insig,fs,compType,printFigs,printMap);
                %concatenate the separate activity maps into one map
                activityMap(idx:idx+len-1,:)=output.activityMap;
                gains(idx:idx+len-1,:)=output.colorGains;
                idx=idx+len;
                colorMtrx=output.colorMtrx;
                levels=output.levels;
                clear output % release unused memory
            end
            %in order to better visualize the clicks in the precedence
            %effect scenario, most of the silent parts of the signal
            %are removed
            if(strcmp('Precedence effect',scenario)==1)
                activityMap = activityMap([1500:3700 4500:6700 7500:9700 10500:12700 13500:15700 16500:18700 20200:22400],:);
                gains = gains([1500:3700 4500:6700 7500:9700 10500:12700 13500:15700 16500:18700 20200:22400],:);
                gains = 2*gains;
            end
            nXBins= length(levels)*(size(colorMtrx,1)-1);
            dim = size(activityMap);
            gains(gains>1) =1;
            outputMtrx = zeros(dim(1),nXBins,3,'single');
            for colorInd=1:size(colorMtrx,1)
                temp = uint32(find((activityMap==(colorInd-1))==1));
                outputMtrx(temp) = gains(temp)*colorMtrx(colorInd,1);
                outputMtrx(temp+dim(1)*nXBins) = gains(temp)*colorMtrx(colorInd,2);
                outputMtrx(temp+2*dim(1)*nXBins) = gains(temp)*colorMtrx(colorInd,3);
            end
            amt_cache('set', [s '_' num2str(ind)], levels,activityMap,outputMtrx,scenario,ytickPos,ytickLab,ylab);
        end
        g(ind)= subplot(2,2,ind);
        imagesc(levels./90,((size(activityMap,1)-1):-20:0)/fs,outputMtrx(1:20:end,:,:));
        clear outputMtrx gains activityMap
        title(scenario);
        set(gca,'YTick',ytickPos);
        set(gca,'YTickLabel',ytickLab);
        set(gca,'Xtick',-1:0.4:1);
        ylabel(ylab);
        xlabel('Activation location');
    end
end
output = g;