% In these supplementary materials, we present the Octave code used to detect
% the clicks in the data set.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                   clicks DETECTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% detection of clicks of dolphins in several files

% inputs : - file ’list.txt’ with the list of all files of the data set
%          - the sound files from the list (.wav)

% outputs : - one file 'Res**.txt' with dates (in s) of each detected click for each sound file
%           - a general file 'balanceTot.txt' with the number of detections by file


% graphics software
graphics toolkit(’gnuplot’)

%%%%%%%%%%%%%%%%%%%%
% GENERAL PARAMETERS

%%%%%%%%%%%%%%%%%%%%

% Files

% Folder of the sound files
Path = ’ adress of the folder of the files .wav ’;

% List of the files
FileName = textread(’list.txt’,’%s’);

% Parameters of click detection
% thresholds to detect the clicks

threshold1=6;
threshold2=1.25;

% Frequency of the high pass filter (Hz)
fcut=100000;

% frecuency of comparation : band [f1;f2] (Hz)
f1=30000;
f2=90000;

% minimal time lap between two clicks (in s)
t_minim=2/1000;

% t_chunk : time of each chunk analyzed (en s)
t_chunk=30;

%%%%%%%%%%%%%%%%%%%%
% Loop on all sound files
%%%%%%%%%%%%%%%%%%%%

fileID = fopen(’balanceTot.txt’,’w’);
fprintf(fileID,'Threshold: %f, coefthreshold %d, bandwidth %d - %d \n', threshold2,threshold1,f1,f2),
fprintf(fileID,’ ’);
fprintf(fileID,’File nb of detections ’);

for k=1:1:length(FileName)

% Reading of the file .wav

   SoundFile = [Path FileName{k}];
   ResultFile = ['Resultats/Res_' FileName{k}(1:15) ’.txt’];

% Reading of the parameters of the sound file

   [Size_total, CHANNELS] = wavread (SoundFile, ”size”);
   [s,fm,dyn] = wavread(SoundFile,[1 10]);
   clear s;

   totaltime=Size_total/fm;
   N=floor(totaltime/t_chunk);
 
% Loop to count the clicks each minute.
   dates_clicks=[];

   for i=1:N
      t_in=(i-1)*t_chunk;
      t_out=t_in+t_chunk;
      beginningN = t_in * fm;
      endingN = t_out * fm;
      extract=wavread(SoundFile,[beginningN endingN]);
      signal = extract(:,1);

% high pass filter
      [butter1,butter2]=butter(5,fcut/(fm/2),’high’);
      signal0=filter(butter1,butter2,signal);
      threshold = std(signal0)*threshold1;

% looking for the moment of the signal when it is larger than the threshold. the number n counts the number of detections higher than the threshold

      n=0;

      while (max(signal0)>threshold)
         [x, ix] = max(signal0);
         spectra=abs(fft(signal(max(ix-255,1):min(ix+256,length(signal)))));
         energyat130 = mean(spectra(120:140));
         energy_bandwidth=mean(spectra(f1/1000:f2/1000));
         if (energyat130>threshold2*energy_bandwidth) 
            dates_clicks=[dates_clicks (i-1)*t chunk+ix/fm];
            n=n+1;
         endif

         signal0(max(1,ix-floor(t_minim*fm)):min(length(signal0),ix+floor(t_minim*fm)))=0;
      endwhile

      numberclicks(i)=n;
      clear signal;
      clear signal0;
   endfor 

% end of the loop on the chunks (i)

% sorting of the dates of the clicks

   Dates_sorted=sort(dates_clicks)’;
   nbclicks= sum(numberclicks)

% writing of the output files

   dlmwrite(ResultFile,Dates_sorted)
   fprintf(fileID,’%s %d', FileName{k}, sum(numeroclicks));
endfor 

% end of the loop on the wav files

fclose(fileID);


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                   clickS PARAMETERS                    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Computation of the parameters of the clicks from the data set

% inputs : - file ’list interesting files.txt’ with the list of all files with detections
%          - sound files from the list

% outputs : - vectors of the parameters for each detected clicks

%%%%%%%%%%%%%%%%%%%
% GLOBAL PARAMETERS
%%%%%%%%%%%%%%%%%%%

% high pass filter

fcut=100000; %cutting freq
order=5; % butterworth filter order

% duration of a chunk of the file opened around a click detection

deltatmicros=500;
deltat=deltatmicros/1000000;

% initialisation clicks count
totalclicks=0;

% Importation of file list
[NameFile] = textread(’list_interesting_files.txt’, ’%s’) ;
N= length(NameFile)

% vectors of parameters
frequencypeak_total=[];
frequencycentr_total=[];
DeltaF_3dB_total=[];
Deltat_10dB_total=[];
DeltaF_10dB_total=[];
Deltat_20dB_total=[];
DeltaF_rms_total=[];
Deltat_rms_total=[];
ICI_total=[];

w=1; % counter of the number of events

%%%%%%%%%%%%%%%%%%%%
% PRINCIPAL LOOP
%%%%%%%%%%%%%%%%%%%%

for i=1:length(NameFile)

% opening of the sound file + extraction parameters

   namefilewav=NameFile{i}
   Path = 'folder of the sound files';
   filewav = [Path namefilewav];
   [totalsize, CHANNELS] = wavread (filewav, ”size”);
   [s,fm,dyn] = wavread(filewav,[1 10]);
   clear s;
   Tm=1/fm;

% opening of the detection file associated to the sound file

   date_and_hour=namefilewav(1:15);
   NameFiledetect=[’Res ’,date_and_hour,’.txt’];
   Path = ’% folder of the detection files ’;
   filedetect = [Path NameFiledetect];
   [date_detection_click] = textread(filedetect, ’%f’) ;
   M=length(date_detection_click)

% test to know if the files are in the same event (less than 20 min of separation)

   if i==1
      msg=’change of event’
      frequencypeak=[];
      frequencycentr=[];
      DeltaF_3dB=[];
      Deltat_10dB=[];
      DeltaF_10dB=[];
      Deltat_20dB=[];
      DeltaF_rms=[];
      Deltat_rms=[];
      ICI=[];
      test=1;
   else   
      hour_raw=str2num(NameFile{i}(10:11));
      min_raw=str2num(NameFile{i}(12:13));
      hour_m1_raw=str2num(NameFile{i-1}(10:11));
      min_m1_raw=str2num(NameFile{i-1}(12:13));
      datemin=hour_raw*60+min_raw;
      datemin_m1=hour_m1_raw*60+min_m1_raw;

      if abs(datemin-datemin m1)>20
         msg=’change of event’
         w=w+1;
         test=1;
      else
         test=0;
      endif
   endif


%%%%%%%%%%%%%%%%%%%%
% second loop on each detected click of the file
%%%%%%%%%%%%%%%%%%%%

   for j=1:M

% ICI computation
      if j>1
         ICI=[ICI date_detection_click(j)-date_detection_click(j-1)];
      endif

% opening of the chunk of sound around the click detection

      t_detect=date_detection_click(j);
      t_entree=t_detect-deltat;
      t_sortie=t_detect+deltat;
      tfinal=t sortie-t entree;
      t=[0:Tm:Tm*floor(tfinal/Tm)]’;
      beginningN = floor(t_entree * fm);
      endingN = beginningN + length(t) - 1;
      extract=wavread(filewav,[beginningN endingN]);
      signal = extract(:,1);

% high pass filter

      [butter1,butter2]=butter(order,fcut/(fm/2),’high’);
      sfiltre=filter(butter1,butter2,signal);
      [val_max imax]=max(sfiltre);
      t0=imax*Tm;
      L=length(sfiltre);

% computation Delta t -10dB

      envelope=abs(hilbert(sfiltre));
      [valmax,indexmax]=max(envelope(200:300));
      indexmax=indexmax+199;
      valplus=valmax;
      incrplus=0;
      while valplus>valmax/sqrt(10)incrplus=incrplus+1;
         valplus=envelope(indexmax+incrplus);
      endwhile
      valmoins=valmax;
      incrmoins=0;
      while valmoins>valmax/sqrt(10)
         incrmoins=incrmoins-1;
         valmoins=envelope(indexmax+incrmoins);
      endwhile
      delta_t_10dB=(incrplus-incrmoins)*Tm;

% computation Delta t -20dB

      envelope=abs(hilbert(sfiltre));
      [valmax,indexmax]=max(envelope(200:300));
      indexmax=indexmax+199;
      valplus=valmax;
      incrplus=0;
      while (valplus>valmax/10) && (incrplus<255)
         incrplus=incrplus+1;
         valplus=envelope(indexmax+incrplus);
      endwhile
      valmoins=valmax;
      incrmoins=0;
      while (valmoins>valmax/10) && (incrmoins>-255)
      incrmoins=incrmoins-1;
      valmoins=envelope(indexmax+incrmoins);
      endwhile
      delta_t_20dB=(incrplus-incrmoins)*Tm;

% delta t rms

      energyt=std(sfiltre);
      MOM2t=sum((t-t0).^2 . ∗ (sfiltre.^2 ));
      delta_t_rms=sqrt(MOM2t/energyt);

% All Delta t
      Deltat_10dB=[Deltat_10dB delta_t_10dB];
      Deltat_20dB=[Deltat_20dB delta_t_20dB];
      Deltat_rms=[Deltat_rms delta t_rms];


%%%%%%%%%%%%%%%%%%%%
% Estimation peak frequency and centroid frequency by FFT

% eventual window
      hamming=0.54-0.46*cos([0:L-1]*2*pi/(L-1));
      window=hamming;

% Fourier transform
      % sfiltre window=sfiltre.*window;
      sfiltre_window=sfiltre;
      Tfourier=fft(sfiltre_window);

% zoom in frequency
      coefzoom=2;
      zoom_Tfourier=Tfourier(1:floor(L/coefzoom));
      f=[1:floor(L/coefzoom)]*fm/L;
      duree=Tm*L;

% Peak frequency
      energy=abs(zoom_Tfourier(90:200));
      [valmax,indexmax]=max(energy);
      fpeak=89000+indexmax*fm/L;

% Centroid frequency
      E=sum(energy.^2);
      extractf=f(90:200);
      MOM1=sum(extractf.*energy’.^2);
      fcentr=MOM1/E;

% Delta f -3bB
      energyplus=valmax;
      incrplus=0;
      while energyplus>valmax/sqrt(2)
         incrplus=incrplus+1;
         energyplus=abs(zoom Tfourier(indexmax+100+incrplus));
      endwhile
      energymoins=valmax;
      incrmoins=0;
      while energymoins>valmax/sqrt(2)
         incrmoins=incrmoins-1;
         energymoins=abs(zoom Tfourier(indexmax+100+incrmoins));
      endwhile
      deltaf 3dB=incrplus-incrmoins;

% Delta f -10bB
      energyplus=valmax;
      incrplus=0;
      while energyplus>valmax/sqrt(10)
         incrplus=incrplus+1;
         energyplus=abs(zoom Tfourier(indexmax+100+incrplus));
      endwhile
      energymoins=valmax;
      incrmoins=0;
      while energymoins>valmax/sqrt(10)
         incrmoins=incrmoins-1;
          energymoins=abs(zoom Tfourier(indexmax+100+incrmoins));
      endwhile
      deltaf 10dB=incrplus-incrmoins;

% Delta f rms
      E=sum(energy.^2);
      MOM2f=sum((extractf-fcentr).^2.*energy’.^2);
      deltaf rms=sqrt(MOM2f/E);

% All frequency and bandwidth
      frequencypeak=[frequencypeak fpeak];
      frequencycentr=[frequencycentr fcentr];
      DeltaF_3dB=[DeltaF_3dB deltaf_3dB];
      DeltaF_10dB=[DeltaF_10dB deltaf_10dB];
      DeltaF_rms=[DeltaF_rms deltaf_rms];
   endfor


   if (test==1) | (i == N )
      frequencypeak_total=[frequencypeak_total frequencypeak];
      frequencycentr_total=[frequencycentr_total frequencycentr];
      DeltaF_3dB_total=[DeltaF_3dB_total DeltaF_3dB];
      Deltat_10dB_total=[Deltat_10dB_total Deltat_10dB];
      DeltaF_10dB_total=[DeltaF_10dB_total DeltaF_10dB];
      Deltat_20dB_total=[Deltat_20dB_total Deltat_20dB];
      DeltaF_rms_total=[DeltaF_rms_total DeltaF_rms];
      Deltat_rms_total=[Deltat_rms_total Deltat_rms];
      ICI_total=[ICI total_ICI];

      frequencypeak=[];
      frequencycentr=[];
      DeltaF_3dB=[];
      Deltat_10dB=[];
      DeltaF_10dB=[];
      Deltat_20dB=[];
      DeltaF_rms=[];
      Deltat_rms=[];
      ICI=[];
   endif

% computation of the total number of clicks
totalclicks=totalclicks+M;

endfor