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+%% ABR analysis script: this script takes the raw recordings and extracts the results
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+% raw recordings are available from last author upon request
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+
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+%% settings
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+fs=19200; % sampling rate after 20-fold resampling
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+bma200_input_gain=10000; % value gained during calibration
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+abr_scale_factor=1/(7e-5*bma200_input_gain); % in mV
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+nboot=500; % number of bootstraps for statistics
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+
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+% set if you want to save the results and bootstrap options (1=on, 0=off)
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+saveon=0;
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+booton=1;
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+
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+% set abr analysis window
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+ana_wind_start=0.001; % offset of rms calculation window
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+ana_wind_dur=0.007; % duration of rms calculation window
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+ana_wind_starts=round(ana_wind_start*fs);
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+ana_wind_stops=round((ana_wind_start+ana_wind_dur)*fs);
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+
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+% define (internal) bat ID, recording date and recording number for analyses
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+dates = {'20170207','20170210','20170817','20191204',...
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+ '20170213','20170223','20170818','20191204',...
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+ '20170217','20170220','20170821','20191205',...
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+ '20170203','20170209','20170817','20191204',...
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+ '20170208','20170216','20170818','20191203',...
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+ '20170306','20170313','20170821','20191205'};
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+
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+reco = {'3','3','3','2','3','3','8','2','3','5','3','2',...
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+ '5','3','7','2','3','3','3','3','3','7','4','2'};
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+
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+animalname = {'3','3','3','3','5','5','5','5','8','8','8','8',...
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+ '2','2','2','2','4','4','4','4','7','7','7','7'};
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+
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+%% data extraction and bootstrap analysis
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+for i=1:24
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+ % choose current bat, date, record number
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+ batid=char(animalname(i));
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+ date=dates(i);
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+ recn=reco(i);
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+
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+ % location of folder with the raw recordings
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+ rootpath=['D:\Documents\Manuskripte\Vocal_development\ABR_recordings\B' batid '\' char(date) '\'];
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+
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+ % circumvent naming error of B2 files
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+ if batid=='2'
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+ recname=['abr_tonepips_ed_b' batid '_m' char(recn) '_'];
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+ else
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+ recname=['abr_tonepips_vpl_b' batid '_m' char(recn) '_'];
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+ end
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+
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+ % access the folder with the recordings
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+ d=dir(rootpath);
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+ filenames=char(d.name); % read in the names of the files in this folder
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+ recnum=0; % set recnum to zero
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+ for fn=3:size(filenames,1) % go through all files in this folder
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+ filename=deblank(filenames(fn,:));
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+ if 1-isempty(strfind(filename,recname))
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+ % extract info from filename
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+ li=strfind(filename,'_l');
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+ fi=strfind(filename,'_fc');
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+ xi=strfind(filename,'_');
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+ xi=xi(min(find(xi>fi)));
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+ if xi>fi+4 % if there is frequency information in the filename
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+ xi=max(xi);
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+ recnum=recnum+1;
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+ lstring=filename(li+2:fi-1);
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+ current_level=str2num(lstring);
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+ fstring=filename(fi+3:xi-1);
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+ current_freq=str2num(fstring);
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+ load([rootpath filename]); % load the file to be analysed
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+ end
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+
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+ mrxin=squeeze(mean(rxin,2)).*abr_scale_factor;
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+ levels(recnum)=current_level;
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+ freqs(recnum)=current_freq/1e3;
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+ rec(recnum,:)=mrxin;
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+
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+ %%% BOOTSTRAPPING ANALYSIS STARTS HERE
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+ if booton==1
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+ data=rxin(ana_wind_starts:ana_wind_stops,:);
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+ datalong=reshape(data,numel(data),1);
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+
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+ % do a bootstrapping analysis
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+ samplesize=size(data,1);
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+ indices=1:(length(datalong)-samplesize);
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+ samplenumber=size(data,2);
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+ originalsignal=mean(data,2);
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+ originalrms=std(originalsignal);
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+
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+ for bn=1:nboot
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+ for rep=1:size(data,2)
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+ bsdata(:,rep)=circshift(data(:,rep),ceil(rand*size(data,1)));
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+ end
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+ bootrms(bn)=std(mean(bsdata,2));
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+ end
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+
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+ confidence=numel(find(originalrms>bootrms))/nboot;
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+ confidences(recnum)=confidence;
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+ end %%% BOOTSTRAP ANALYSIS ENDS HERE
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+ end
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+ end
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+
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+ % organise data for bootstrap plots
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+ all_levels=sort(unique(levels));
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+ all_freqs=sort(unique(freqs));
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+ out=zeros(length(all_levels),length(all_freqs));
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+ for sn=1:length(levels)
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+ cl=levels(sn);
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+ cf=freqs(sn);
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+ li=find(all_levels==cl);
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+ fi=find(all_freqs==cf);
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+ out(li,fi)=std(rec(sn,ana_wind_starts:ana_wind_stops)); % calculate rms from sample 31 because of rec onset irregularities
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+ end
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+ in=[freqs' levels' confidences'];
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+ sort_in=sortrows(in,[1 2]);
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+ ufreqs=unique(freqs);
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+ ulevels=unique(levels);
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+
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+ for fn=1:length(ufreqs)
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+ cfreq=ufreqs(fn);
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+ fconf=sort_in(find(sort_in(:,1)==cfreq),3);
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+ threshold_ind=max(find(fconf<0.95))+1;
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+ if threshold_ind<=length(ulevels) & 1-isempty(threshold_ind)
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+ bootstrap_thresholds(fn)=ulevels(threshold_ind);
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+ else
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+ bootstrap_thresholds(fn)=nan;
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+ end
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+ end
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+
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+ % save results in structures
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+ resultTHRES(i)=struct('uniqueFrequencies',ufreqs','bootstrapThresholds',bootstrap_thresholds');
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+ allCONFI(i)=struct('frequencies',freqs,'levels',levels,'confidences',confidences);
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+ heatRES(i)=struct('all_freqs',all_freqs,'all_levels',all_levels,'out',out);
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+end
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+
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+%% saving of the variables
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+if saveon==1
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+ save('abr_deafening_results.mat','date','resultTHRES','allCONFI');
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+end
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