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usvseg09r2.m
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usvseg09r2.m
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function varargout = usvseg09r2(action)
% usvseg09r2
%
% by R.O. Tachibana (rtachi@gmail.com)
% May 23, 2020
% update:
% - changed structure of global variable
% gv.gui / gv.dat / gv.prm
% - output duration is now in milliseconds but not seconds
% - added "meanfreq" and "cvfreq" as output feature
% - deleted "whitening" and "hanntaperspec" functions for comparison
% - parallel computeing (parfor) is now working only for batch processing
% global variable
global gv;
% Initiation ------------------------------------------------------
if nargin==0
% version
usevsegver = 'USVSEG ver 0.9 (rev 2)';
fftsize = 1024;
% load parameters
prmfile = [fileparts(mfilename('fullpath')) filesep 'usvseg_prm.mat'];
if exist(prmfile)==2, l=load(prmfile); gv.prm = l.prm;
else % default values
prm.timestep = 0.0005; prm.freqmin = 30000; prm.freqmax = 120000;
prm.threshval = 4.5; prm.durmin = 0.005; prm.durmax = 0.3;
prm.gapmin = 0.030; prm.margin = 0.015; prm.wavfileoutput = 1;
prm.imageoutput = 1; prm.imagetype = 0; prm.traceoutput = 0;
prm.readsize = 10; prm.mapL = 1000; prm.mapH = 6000;
gv.prm = prm;
end
gv.usevsegver = usevsegver;
gv.prm.fftsize = fftsize; % FFT size = window size
gv.dat.pth = cd;
% make GUI
makegui;
cla(gv.gui.haxes(1)); cla(gv.gui.haxes(2)); cla(gv.gui.haxes(3));
return
end
% open ----------------------------------------------------------------
if strcmp(action,'open')
% clear axes
cla(gv.gui.haxes(1)); cla(gv.gui.haxes(2)); cla(gv.gui.haxes(3));
% unable
set([gv.gui.hpush_thrs gv.gui.hpush_dtct gv.gui.hpush_save gv.gui.hpush_sgmt gv.gui.hpush_play gv.gui.hpush_swav],'Enable','Off');
% fetch parameters from GUI
fetchparams;
timestep = gv.prm.timestep;
readsize = gv.prm.readsize;
fftsize = gv.prm.fftsize;
% get file
[fn,pth] = uigetfile([gv.dat.pth filesep '*.wav']);
% show file name
set(gv.gui.htext_fnam,'string',['File: ' pth fn]);
busytoggle(1);
% read wav
ai = audioinfo([pth fn]);
fs = ai.SampleRate;
wav = audioread([pth fn],[1 min(readsize*fs,ai.TotalSamples)]);
% show fs
set(gv.gui.htext_fsvl,'string',num2str(fs/1000));
% multitaper spectrogram
step = round(timestep*fs);
mtsp = multitaperspec(wav,fs,fftsize,timestep,0);
mtsimrng = median(mtsp(:)) + [0 40];
fvec = [0; (1:(fftsize/2))'/fftsize*fs];
tvec = ((0:(size(mtsp,2)-1))*step+fftsize/2)/fs;
% default view range : 2 seconds
xl = [0 2];
yl = [0 max(fvec)/1000];
% save in global variable
gv.dat.fn = fn; gv.dat.pth = pth;
gv.dat.fs = fs; gv.dat.wav = wav; gv.dat.step = step;
gv.dat.mtsp = mtsp; gv.dat.mtsimrng = mtsimrng;
gv.dat.fvec = fvec; gv.dat.tvec = tvec;
gv.dat.xl = xl; gv.dat.yl = yl;
% draw mtsp
drawmtsp;
% enable
set(gv.gui.hpush_flat,'Enable','On');
busytoggle(0);
return;
end
% flattening ------------------------------------------------------------
if strcmp(action,'flat')
busytoggle(1);
% clear axes
cla(gv.gui.haxes(2)); cla(gv.gui.haxes(3));
% flattening
fltnd = flattening(gv.dat.mtsp);
fltndimrng = [0 30];
% save
gv.dat.fltnd = fltnd;
gv.dat.fltndimrng = fltndimrng;
% draw fltnd
drawfltnd;
% enable
set(gv.gui.hpush_thrs,'Enable','On');
busytoggle(0);
return;
end
% thresholding ------------------------------------------------------------
if strcmp(action,'thrs')
% clear axes
cla(gv.gui.haxes(3));
% fetch
fetchparams;
freqmin = gv.prm.freqmin; freqmax = gv.prm.freqmax; threshval = gv.prm.threshval;
fs = gv.dat.fs; fvec = gv.dat.fvec; tvec = gv.dat.tvec; fltnd = gv.dat.fltnd;
busytoggle(1);
% threshold calculation with threshval*sigma (SD) of background noise
thresh = estimatethresh(fltnd,fs,freqmin,freqmax,threshval);
% thresholding
thrshd = thresholding(fltnd,fs,freqmin,freqmax,thresh);
% draw
set(0,'CurrentFigure',gv.gui.hfig);
set(gv.gui.hfig,'CurrentAxes',gv.gui.haxes(3));
imagesc(tvec,fvec/1000,thrshd); axis xy
colormap(gca,gray);
set(gca,'tickdir','out'); box off;
ylabel('Frequency (kHz)');
set(gv.gui.haxes,'xlim',gv.dat.xl,'ylim',gv.dat.yl);
drawnow;
% enable
set(gv.gui.hpush_dtct,'Enable','On');
% save
gv.dat.thrshd = thrshd; gv.dat.thresh = thresh;
busytoggle(0);
return;
end
% detection ------------------------------------------------------------
if strcmp(action,'dtct')
busytoggle(1);
% clear axes
cla(gv.gui.haxes(3));
% fetch
fetchparams;
fs = gv.dat.fs; timestep = gv.prm.timestep;
freqmin = gv.prm.freqmin; freqmax = gv.prm.freqmax;
durmin = gv.prm.durmin; durmax = gv.prm.durmax;
gapmin = gv.prm.gapmin; margin = gv.prm.margin;
mtsp = gv.dat.mtsp; fltnd = gv.dat.fltnd; thrshd = gv.dat.thrshd;
% onset/offset detection
[onoffset,onoffsetm] = detectonoffset(thrshd,fs,timestep,gapmin,durmin,durmax,margin);
% peak tracking
[freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq] = specpeaktracking(mtsp,fltnd,fs,timestep,freqmin,freqmax,onoffset,margin);
% save
gv.dat.onoffset = onoffset; gv.dat.onoffsetm = onoffsetm;
gv.dat.freqtrace = freqtrace; gv.dat.amptrace = amptrace;
gv.dat.maxampval = maxampval; gv.dat.maxfreq = maxfreq; gv.dat.maxampidx = maxampidx;
gv.dat.meanfreq = meanfreq; gv.dat.cvfreq = cvfreq;
% draw trace
drawtrace;
% enable
set(gv.gui.hpush_save,'Enable','On');
set(gv.gui.hpush_sgmt,'Enable','On');
set(gv.gui.hpush_play,'Enable','On');
busytoggle(0);
return;
end
% save ----------------------------------------------------------------
if strcmp(action,'save')
busytoggle(0);
% fetch
onoffset = gv.dat.onoffset;
maxampval = gv.dat.maxampval; maxfreq = gv.dat.maxfreq;
meanfreq = gv.dat.meanfreq; cvfreq = gv.dat.cvfreq;
dur = diff(onoffset,[],2);
[~,prefix,~] = fileparts(gv.dat.fn);
% save CSV
[fn,pth] = uiputfile([gv.dat.pth filesep prefix '_dat.csv'],'file name');
fid = fopen([pth fn],'wt');
fprintf(fid,'#,start,end,duration,maxfreq,maxamp,meanfreq,cvfreq\n');
if ~isempty(onoffset)
for n=1:size(onoffset,1)
fprintf(fid,'%d,%.04f,%.04f,%.1f,%.03f,%.02f,%.03f,%.04f\n',n,onoffset(n,1),onoffset(n,2),dur(n)*1000,maxfreq(n)/1000,maxampval(n),meanfreq(n)/1000,cvfreq(n));
end
end
fclose(fid);
busytoggle(1);
return;
end
% segment -------------------------------------------------------------
if strcmp(action,'sgmt')
busytoggle(0);
% fetch
fetchparams;
margin = gv.prm.margin; timestep = gv.prm.timestep;
wavflg = gv.prm.wavfileoutput; imgflg = gv.prm.imageoutput;
fltflg = gv.prm.imagetype; trcflg = gv.prm.traceoutput;
wav = gv.dat.wav; fs = gv.dat.fs; mtsp = gv.dat.mtsp; fltnd = gv.dat.fltnd;
tvec = gv.dat.tvec; onoffset = gv.dat.onoffset;
freqtrace = gv.dat.freqtrace;amptrace = gv.dat.amptrace;
fltndimrng = gv.dat.fltndimrng; mtsimrng = gv.dat.mtsimrng;
% file name
[~,prefix,~] = fileparts(gv.dat.fn);
outp = uigetdir(gv.dat.pth);
% output
startid = 1;
if fltflg==1, inputimg = fltnd; imrng = fltndimrng;
else, inputimg = mtsp; imrng = mtsimrng; end
segfun(startid,outp,prefix,inputimg,imrng,wav,fs,timestep,margin,onoffset,tvec,amptrace,freqtrace,wavflg,imgflg,trcflg);
busytoggle(0);
return;
end
% play ----------------------------------------------------------------
if strcmp(action,'play')
playfs = 44100;
% fetch
fetchparams;
mapL = gv.prm.mapL; mapH = gv.prm.mapH;
fs = gv.dat.fs; tvec = gv.dat.tvec;
freqtrace = gv.dat.freqtrace; amptrace = gv.dat.amptrace;
% audible sound synthesis
synthsnd = soundsynthesis(freqtrace(:,1),amptrace(:,1),tvec,fs,playfs,[mapL mapH]);
% get range
rng = max(1,round(gv.dat.xl(1)*playfs)):min(length(synthsnd),round(gv.dat.xl(2)*playfs));
% play
ap = audioplayer(synthsnd(rng),playfs);
playblocking(ap);
delete(ap);
set(gv.gui.hpush_swav,'Enable','On');
% save
gv.dat.playfs = playfs;
gv.dat.synthsnd = synthsnd;
return;
end
% save wav ----------------------------------------------------------------
if strcmp(action,'swav')
newfn = [gv.dat.fn(1:end-4) '_syn.wav'];
[f,p] = uiputfile([gv.dat.pth newfn]);
audiowrite([p f],gv.dat.synthsnd,gv.dat.playfs);
return;
end
% long ----------------------------------------------------------------
if strcmp(action,'long')
% fetch parameter
fetchparams;
timestep = gv.prm.timestep; margin = gv.prm.margin; durmax = gv.prm.durmax;
wavflg = gv.prm.wavfileoutput; imgflg = gv.prm.imageoutput;
fltflg = gv.prm.imagetype; trcflg = gv.prm.traceoutput;
readsize = gv.prm.readsize; fftsize = gv.prm.fftsize;
% clear axes
cla(gv.gui.haxes(1)); cla(gv.gui.haxes(2)); cla(gv.gui.haxes(3));
% disable
set(gv.gui.hpush_open,'enable','on');
set(gv.gui.hpush_dtct,'enable','off');
set(gv.gui.hpush_save,'enable','off');
set(gv.gui.hpush_sgmt,'enable','off');
set(gv.gui.hpush_long,'enable','on');
% get long wavfile
busytoggle(1);
[fn,pth] = uigetfile([gv.dat.pth filesep '*.wav']);
fp = [pth fn];
ainfo = audioinfo(fp);
wavsize = ainfo.TotalSamples;
fs = ainfo.SampleRate;
nreadsize= round(readsize*fs);
nread = ceil(wavsize/nreadsize);
fvec = [0; (1:(fftsize/2))'/fftsize*fs];
step = round(timestep*fs);
yl = [0 max(fvec)/1000];
gv.dat.fs = fs;
gv.dat.yl = yl;
% show fs
set(gv.gui.htext_fsvl,'string',num2str(fs/1000));
% CSV setting
[~,prefix,~] = fileparts(fn);
[sfn,spth] = uiputfile([pth filesep prefix '_dat.csv'],'save file name');
savefp = [spth sfn];
fid = fopen(savefp,'wt');
fprintf(fid,'#,start,end,duration,maxfreq,maxamp,meanfreq,cvfreq\n');
fclose(fid);
% segmentation setting
outp = uigetdir(spth,'output directory');
% start
prevn = 0;
prevlast = 0;
med = [];
thresh = [];
for r=1:nread
set(gv.gui.htext_fnam,'string',['File: ' fp ' ... (' num2str(r) '/' num2str(nread) ' blocks)']);
busytoggle(1);
% read
rng = [prevlast+1 min(r*nreadsize,wavsize)];
if diff(rng)<fftsize*2, break; end
[wav,fs] = audioread(fp,rng);
% process
[mtsp,fltnd,onoffset,onoffsetm,freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq,thresh,med,contflg] = procfun(wav,fs,fftsize,gv.prm,med,thresh);
busytoggle(0);
dur = diff(onoffset,[],2);
ronoffset = onoffset+(prevlast+1)/fs;
ronoffsetm = onoffsetm+(prevlast+1)/fs;
nstep = size(mtsp,2);
tvec = ((0:(nstep-1))*step+fftsize/2)/fs;
rtvec = tvec+(prevlast+1)/fs;
mtsimrng = median(mtsp(:)) + [0 40];
fltndimrng = [0 30];
% save to global
gv.dat.tvec = rtvec; gv.dat.fvec = fvec; gv.dat.mtsp = mtsp; gv.dat.fltnd = fltnd;
gv.dat.onoffset = ronoffset; gv.dat.onoffsetm = ronoffsetm;
gv.dat.freqtrace = freqtrace; gv.dat.amptrace = amptrace;
gv.dat.maxampval = maxampval; gv.dat.maxampidx = maxampidx; gv.dat.maxfreq = maxfreq;
gv.dat.meanfreq = meanfreq; gv.dat.cvfreq = cvfreq;
gv.dat.mtsimrng = mtsimrng; gv.dat.fltndimrng = fltndimrng;
gv.dat.xl = [min(rtvec) max(rtvec)];
% draw MTSP
drawmtsp;
% draw Flattened
drawfltnd;
% draw trace
drawtrace;
% save CSV
fid = fopen(savefp,'at');
if ~isempty(ronoffset)
for n=1:size(ronoffset,1)
fprintf(fid,'%d,%.04f,%.04f,%.1f,%.03f,%.02f,%.03f,%.04f\n',n+prevn,ronoffset(n,1),ronoffset(n,2),dur(n)*1000,maxfreq(n)/1000,maxampval(n),meanfreq(n)/1000,cvfreq(n));
end
end
fclose(fid);
% segmentation
if fltflg==1, inputimg = fltnd; imrng = fltndimrng;
else, inputimg = mtsp; imrng = mtsimrng; end
segfun(prevn+1,outp,prefix,inputimg,imrng,wav,fs,timestep,margin,onoffset,rtvec,amptrace,freqtrace,wavflg,imgflg,trcflg)
% calc
prevn = size(onoffset,1)+prevn;
if contflg==1
if isempty(onoffset)
prevlast = rng(2) - durmax * fs;
else
prevlast = round(onoffset(end,2)*fs)+prevlast;
end
else
prevlast = rng(2);
end
end
msgbox('Done!');
return;
end
% folder (multiple files) ----------------------------------------------------------------
if strcmp(action,'fldr')
set(gv.gui.htext_fnam,'string','');
% clear axes
cla(gv.gui.haxes(1)); cla(gv.gui.haxes(2)); cla(gv.gui.haxes(3));
% disable
set(gv.gui.hpush_open,'enable','on');
set(gv.gui.hpush_dtct,'enable','off');
set(gv.gui.hpush_save,'enable','off');
set(gv.gui.hpush_sgmt,'enable','off');
set(gv.gui.hpush_long,'enable','on');
% fetch parameters
fetchparams;
timestep = gv.prm.timestep; margin = gv.prm.margin; durmax = gv.prm.durmax;
wavflg = gv.prm.wavfileoutput; imgflg = gv.prm.imageoutput;
fltflg = gv.prm.imagetype; trcflg = gv.prm.traceoutput;
readsize = gv.prm.readsize; fftsize = gv.prm.fftsize;
% get reading path and files
pth = uigetdir(gv.dat.pth);
gv.dat.pth = pth;
d = dir([pth filesep '*.wav']);
fns = {d.name};
nfile = length(fns);
for f=1:nfile
% get wavfile
fp = [pth filesep fns{f}];
ainfo = audioinfo(fp);
wavsize = ainfo.TotalSamples;
fs = ainfo.SampleRate;
nreadsize= round(readsize*fs);
nread = ceil(wavsize/nreadsize);
fvec = [0; (1:(fftsize/2))'/fftsize*fs];
step = round(timestep*fs);
yl = [0 max(fvec)/1000];
gv.dat.fs = fs;
gv.dat.yl = yl;
% show fs
set(gv.gui.htext_fsvl,'string',num2str(fs/1000));
% CSV setting
[~,prefix,~] = fileparts(fns{f});
sfn = [prefix '_dat.csv'];
savefp = [pth filesep sfn];
% if we already did this, continue
if exist(savefp,'file'), continue; end
fid = fopen(savefp,'wt');
fprintf(fid,'#,start,end,duration,maxfreq,maxamp,meanfreq,cvfreq\n');
fclose(fid);
% segmentation setting
%{
mkdir(pth,prefix);
outp = [pth filesep prefix];
%}
% start
prevn = 0;
prevlast = 0;
med = [];
thresh = [];
for r=1:nread
% read
set(gv.gui.htext_fnam,'string',sprintf('File: %s ... (%d/%d blocks) [%d/%d files]',fp,r,nread,f,nfile));
busytoggle(1);
rng = [prevlast+1 min(r*nreadsize,wavsize)];
if diff(rng)<fftsize*2, break; end
[wav,fs] = audioread(fp,rng);
% process
[mtsp,fltnd,onoffset,onoffsetm,freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq,thresh,med,contflg] =...
procfun(wav,fs,fftsize,gv.prm,med,thresh);
dur = diff(onoffset,[],2);
ronoffset = onoffset+(prevlast+1)/fs;
ronoffsetm = onoffsetm+(prevlast+1)/fs;
nstep = size(mtsp,2);
tvec = ((0:(nstep-1))*step+fftsize/2)/fs;
rtvec = tvec+(prevlast+1)/fs;
mtsimrng = median(mtsp(:)) + [0 40];
fltndimrng = [0 30];
busytoggle(0);
% save to global
gv.dat.tvec = rtvec; gv.dat.fvec = fvec; gv.dat.mtsp = mtsp; gv.dat.fltnd = fltnd;
gv.dat.onoffset = ronoffset; gv.dat.onoffsetm = ronoffsetm;
gv.dat.freqtrace = freqtrace; gv.dat.amptrace = amptrace;
gv.dat.maxampval = maxampval; gv.dat.maxampidx = maxampidx; gv.dat.maxfreq = maxfreq;
gv.dat.meanfreq = meanfreq; gv.dat.cvfreq = cvfreq;
gv.dat.mtsimrng = mtsimrng; gv.dat.fltndimrng = fltndimrng;
gv.dat.xl = [min(rtvec) max(rtvec)];
% draw MTSP
drawmtsp;
% draw Flattened
drawfltnd;
% draw trace
drawtrace;
% save CSV
fid = fopen(savefp,'at');
if ~isempty(ronoffset)
for n=1:size(ronoffset,1)
fprintf(fid,'%d,%.04f,%.04f,%.1f,%.03f,%.02f,%.03f,%.04f\n',n+prevn,ronoffset(n,1),ronoffset(n,2),dur(n)*1000,maxfreq(n)/1000,maxampval(n),meanfreq(n)/1000,cvfreq(n));
end
end
fclose(fid);
% segmentation
%{
if fltflg==1, inputimg = fltnd; imrng = fltndimrng;
else, inputimg = mtsp; imrng = mtsimrng; end
segfun(prevn+1,outp,prefix,inputimg,imrng,wav,fs,timestep,margin,onoffset,rtvec,amptrace,freqtrace,wavflg,imgflg,trcflg);
% calc
prevn = size(onoffset,1)+prevn;
if contflg==1
if isempty(onoffset)
prevlast = rng(2) - durmax * fs;
else
prevlast = round(onoffset(end,2)*fs)+prevlast;
end
else
prevlast = rng(2);
end
%}
end
end
msgbox('Done!');
return;
end
% zoom -----------------------------------------------------
if strcmp(action,'z')
set(gcf,'Pointer','crosshair')
waitforbuttonpress;
p1 = get(gca,'currentpoint');
rbbox;
p2 = get(gca,'currentpoint');
newxl = sort([p1(1,1) p2(1,1)]);
newyl = sort([p1(1,2) p2(1,2)]);
set(gcf,'Pointer','arrow')
gv.dat.xl = newxl;
gv.dat.yl = newyl;
set([gv.gui.haxes],'xlim',gv.dat.xl,'ylim',gv.dat.yl);
return;
end
% zoom in -----------------------------------------------------
if strcmp(action,'i')
xl = get(gca,'XLim');
center = xl(1)+diff(xl)/2;
newxl = center + [-diff(xl)/2 diff(xl)/2]*0.75;
gv.dat.xl = newxl;
set([gv.gui.haxes],'xlim',gv.dat.xl);
return;
end
% zoom out -----------------------------------------------------
if strcmp(action,'o')
xl = get(gca,'XLim');
center = xl(1)+diff(xl)/2;
newxl = center + [-diff(xl)/2 diff(xl)/2]*1.25;
gv.dat.xl = newxl;
set([gv.gui.haxes],'xlim',gv.dat.xl);
return;
end
% zoom in veritcal --------------------------------------------------
if strcmp(action,'u')
yl = get(gca,'ylim');
center = yl(1)+diff(yl)/2;
newyl = center + [-diff(yl)/2 diff(yl)/2]*0.75;
gv.dat.yl = newyl;
set([gv.gui.haxes],'ylim',gv.dat.yl);
return;
end
% zoom out vertical ---------------------------------------------------
if strcmp(action,'j')
yl = get(gca,'ylim');
center = yl(1)+diff(yl)/2;
newyl = center + [-diff(yl)/2 diff(yl)/2]*1.25;
gv.dat.yl = newyl;
set([gv.gui.haxes],'ylim',gv.dat.yl);
return;
end
% slide forward ----------------------------------------------
if double(action)==29 % ->
xl = get(gca,'xlim');
newxl = xl+diff(xl)*0.05;
gv.dat.xl = newxl;
set([gv.gui.haxes],'xlim',gv.dat.xl);
return;
end
% slide back --------------------------------------------------
if double(action)==28 % <-
xl = get(gca,'xlim');
newxl = xl-diff(xl)*0.05;
gv.dat.xl = newxl;
set([gv.gui.haxes],'xlim',gv.dat.xl);
return;
end
% slide up ----------------------------------------------
if double(action)==30 % up
yl = get(gca,'ylim');
newyl = yl+diff(yl)*0.1;
gv.dat.yl = newyl;
set([gv.gui.haxes],'ylim',gv.dat.yl);
return;
end
% slide down --------------------------------------------------
if double(action)==31 % down
xl = get(gca,'ylim');
newyl = xl-diff(xl)*0.1;
gv.dat.yl = newyl;
set([gv.gui.haxes],'ylim',gv.dat.yl);
return;
end
% save PDF file ------------------------------------------------
if strcmp(action,'p')
[f,p] = uiputfile([gv.dat.pth filesep '*.pdf']);
set(gcf,'renderer','painters','PaperOrientation','landscape','PaperUnits','normalized','PaperPosition',[0 0 1 1])
print([p f],'-dpdf');
return;
end
% help --------------------------------------------------
if strcmp(action,'h')
msg = {
'i ... zoom in horizontal'
'o ... zoom out horizontal'
'u ... zoom in vertical'
'j ... zoom out vertical'
'right ... slide to right'
'left ... slide to left'
'up ... slide to upper'
'down ... slide to lower'
'p ... save PDF file'
'h ... help'
};
msgbox(msg,'Key Command List');
return;
end
% for other things --------------------------------------
if length(action)==1
return;
end
% for internal functions --------------------------------------
if length(action)>5
varargout{1} = eval(['@' action]);
return;
end
% ////////////////////////////////////////////////////////////////////////
function drawmtsp
global gv;
set(0,'CurrentFigure',gv.gui.hfig);
set(gv.gui.hfig,'CurrentAxes',gv.gui.haxes(1));
imagesc(gv.dat.tvec,gv.dat.fvec/1000,gv.dat.mtsp); axis xy
set(gca,'tickdir','out'); box off
ylabel('Frequency (kHz)');
colormap(flipud(gray));
caxis(gv.dat.mtsimrng);
set(gv.gui.haxes,'xlim',gv.dat.xl,'ylim',gv.dat.yl);
drawnow;
% ////////////////////////////////////////////////////////////////////////
function drawfltnd
global gv;
% fetch
fetchparams;
freqmin = gv.prm.freqmin;
freqmax = gv.prm.freqmax;
fvec = gv.dat.fvec;
tvec = gv.dat.tvec;
fltnd = gv.dat.fltnd;
fltndimrng = gv.dat.fltndimrng;
% draw
set(0,'CurrentFigure',gv.gui.hfig);
set(gv.gui.hfig,'CurrentAxes',gv.gui.haxes(2));
imagesc(tvec,fvec/1000,fltnd); axis xy
set(gca,'tickdir','out'); box off;
caxis(fltndimrng);
hls = line([min(tvec) max(tvec); min(tvec) max(tvec)]',[freqmax freqmax;freqmin freqmin]'/1000); set(hls,'color','r','linestyle','--');
ylabel('Frequency (kHz)');
set(gv.gui.haxes,'xlim',gv.dat.xl,'ylim',gv.dat.yl);
drawnow;
% ////////////////////////////////////////////////////////////////////////
function drawtrace
global gv;
% fetch
fvec = gv.dat.fvec;
tvec = gv.dat.tvec;
fltnd = gv.dat.fltnd;
fltndimrng = gv.dat.fltndimrng;
freqtrace = gv.dat.freqtrace;
onoffset = gv.dat.onoffset;
onoffsetm = gv.dat.onoffsetm;
maxampidx = gv.dat.maxampidx;
maxfreq = gv.dat.maxfreq;
margin = gv.prm.margin;
fs = gv.dat.fs;
% draw
set(0,'CurrentFigure',gv.gui.hfig);
set(gv.gui.hfig,'CurrentAxes',gv.gui.haxes(3));
imagesc(tvec,fvec/1000,fltnd); axis xy
if ~isempty(onoffset)
nonsylzone = [[0 onoffsetm(1,1)]; [onoffsetm(1:end-1,2) onoffsetm(2:end,1)]; [onoffsetm(end,2) max(tvec)]];
temp = [[onoffset(:,1)-margin onoffset(:,1)]; [onoffset(:,2) onoffset(:,2)+margin]];
[~,sid] = sort(temp(:,1));
margzone = temp(sid,:);
idx = find((margzone(2:end,1)-margzone(1:end-1,2))>0);
ons = [margzone(1,1);margzone(idx+1)];
offs = [margzone(idx,2);margzone(end,2)];
margzone = [ons offs];
else
nonsylzone = [0 tvec(end)];
margzone = [0 0];
end
set(0,'CurrentFigure',gv.gui.hfig);
set(gv.gui.hfig,'CurrentAxes',gv.gui.haxes(3));
hp1 = patch(margzone(:,[1 2 2 1])',repmat([0 0 fs fs]/2000,size(margzone,1),1)',1);
hp2 = patch(nonsylzone(:,[1 2 2 1])',repmat([0 0 fs fs]/2000,size(nonsylzone,1),1)',1);
set(hp1,'linestyle','none','facecolor','k','facealpha',0.1);
set(hp2,'linestyle','none','facecolor','k','facealpha',0.3);
hlf = line(tvec,freqtrace(:,1:3)/1000);
set(hlf,'linestyle','none','marker','.','color','b');
hlm = line(tvec(maxampidx),maxfreq/1000);
set(hlm,'linestyle','none','marker','+','color','r');
colormap(gca,flipud(gray));
caxis(fltndimrng);
set(gca,'tickdir','out'); box off;
ylabel('Frequency (kHz)');
xlabel('Time (s)');
set(gv.gui.haxes,'xlim',gv.dat.xl,'ylim',gv.dat.yl);
drawnow;
% ////////////////////////////////////////////////////////////////////////
function makegui
global gv
% figure
hfig = figure;
set(hfig,'MenuBar','none','NumberTitle','off','ToolBar','none','Name',gv.usevsegver);
set(hfig,'KeyPressFcn','usvseg09r2(get(gcf,''CurrentCharacter''));');
set(hfig,'DeleteFcn',@finishfunc);
% axes
haxes(1) = axes;
haxes(2) = axes;
haxes(3) = axes;
set(haxes,'tickdir','out')
% uicontrol
hpush_open = uicontrol(hfig,'style','pushbutton');
hpush_flat = uicontrol(hfig,'style','pushbutton');
hpush_thrs = uicontrol(hfig,'style','pushbutton');
hpush_dtct = uicontrol(hfig,'style','pushbutton');
hpush_save = uicontrol(hfig,'style','pushbutton');
hpush_sgmt = uicontrol(hfig,'style','pushbutton');
hpush_play = uicontrol(hfig,'style','pushbutton');
hpush_swav = uicontrol(hfig,'style','pushbutton');
hpush_long = uicontrol(hfig,'style','pushbutton');
hpush_fldr = uicontrol(hfig,'style','pushbutton');
hedit_step = uicontrol(hfig,'style','edit');
hedit_fmin = uicontrol(hfig,'style','edit');
hedit_fmax = uicontrol(hfig,'style','edit');
hedit_thre = uicontrol(hfig,'style','edit');
hedit_dmin = uicontrol(hfig,'style','edit');
hedit_dmax = uicontrol(hfig,'style','edit');
hedit_gmin = uicontrol(hfig,'style','edit');
hedit_marg = uicontrol(hfig,'style','edit');
htggl_wavo = uicontrol(hfig,'style','toggle');
htggl_imgo = uicontrol(hfig,'style','toggle');
htggl_imgt = uicontrol(hfig,'style','toggle');
htggl_trac = uicontrol(hfig,'style','toggle');
hedit_read = uicontrol(hfig,'style','edit');
hedit_mapL = uicontrol(hfig,'style','edit');
hedit_mapH = uicontrol(hfig,'style','edit');
htext_fnam = uicontrol(hfig,'style','text');
htext_fslb = uicontrol(hfig,'style','text');
htext_fsvl = uicontrol(hfig,'style','text');
htext_step = uicontrol(hfig,'style','text');
htext_fmin = uicontrol(hfig,'style','text');
htext_fmax = uicontrol(hfig,'style','text');
htext_dmin = uicontrol(hfig,'style','text');
htext_dmax = uicontrol(hfig,'style','text');
htext_gmin = uicontrol(hfig,'style','text');
htext_thre = uicontrol(hfig,'style','text');
htext_marg = uicontrol(hfig,'style','text');
htext_wavo = uicontrol(hfig,'style','text');
htext_imgo = uicontrol(hfig,'style','text');
htext_imgt = uicontrol(hfig,'style','text');
htext_trac = uicontrol(hfig,'style','text');
htext_maps = uicontrol(hfig,'style','text');
htext_read = uicontrol(hfig,'style','text');
% busy mark
hpanl_busy = uipanel(hfig);
set(hpanl_busy,'backgroundcolor',[0.6 0.6 0.6]);
% strings
set(hpush_open,'string','open');
set(hpush_flat,'string','flatten');
set(hpush_thrs,'string','threshold');
set(hpush_dtct,'string','detect');
set(hpush_save,'string','save csv');
set(hpush_sgmt,'string','segment');
set(hpush_play,'string','play');
set(hpush_swav,'string','save');
set(hpush_long,'string','long file');
set(hpush_fldr,'string','multiple files');
set(htext_fnam,'string','');
set(hedit_step,'string',num2str(gv.prm.timestep*1000));
set(hedit_fmin,'string',num2str(gv.prm.freqmin/1000));
set(hedit_fmax,'string',num2str(gv.prm.freqmax/1000));
set(hedit_thre,'string',num2str(gv.prm.threshval));
set(hedit_dmin,'string',num2str(gv.prm.durmin*1000));
set(hedit_dmax,'string',num2str(gv.prm.durmax*1000));
set(hedit_gmin,'string',num2str(gv.prm.gapmin*1000));
set(hedit_marg,'string',num2str(gv.prm.margin*1000));
set(hedit_read,'string',num2str(gv.prm.readsize));
set(hedit_mapL,'string',num2str(gv.prm.mapL/1000));
set(hedit_mapH,'string',num2str(gv.prm.mapH/1000));
set(htext_fslb,'string',{'sampling', '(kHz)'});
set(htext_fsvl,'string','-');
set(htext_step,'string',{'time step','(ms)'});
set(htext_fmin,'string',{'freq min','(kHz)'});
set(htext_fmax,'string',{'freq max','(kHz)'});
set(htext_thre,'string',{'threshold','(SD)'});
set(htext_dmin,'string',{'dur min','(ms)'});
set(htext_dmax,'string',{'dur max','(ms)'});
set(htext_gmin,'string',{'gap min','(ms)'});
set(htext_marg,'string',{'margin','(ms)'});
set(htext_wavo,'string',{'wavfile','output'});
set(htext_imgo,'string',{'image','output'});
set(htext_imgt,'string',{'image','type'});
set(htext_trac,'string',{'trace','output'});
set(htext_maps,'string',{'map','(kHz)'});
set(htext_read,'string',{'read size','(s)'});
set(htext_fnam,'string','File: filename');
% toggle
str1 = {'off','on'};
str2 = {'orig','flat'};
set(htggl_wavo,'value',gv.prm.wavfileoutput,'string',str1{gv.prm.wavfileoutput+1});
set(htggl_imgo,'value',gv.prm.imageoutput,'string',str1{gv.prm.imageoutput+1});
set(htggl_imgt,'value',gv.prm.imagetype,'string',str2{gv.prm.imagetype+1});
set(htggl_trac,'value',gv.prm.traceoutput,'string',str1{gv.prm.traceoutput+1});
set(htggl_wavo,'callback','str={''off'',''on''}; set(gco,''string'',str{get(gco,''value'')+1});');
set(htggl_imgo,'callback','str={''off'',''on''}; set(gco,''string'',str{get(gco,''value'')+1});');
set(htggl_imgt,'callback','str={''orig'',''flat''}; set(gco,''string'',str{get(gco,''value'')+1});');
set(htggl_trac,'callback','str={''off'',''on''}; set(gco,''string'',str{get(gco,''value'')+1});');
% callbacks
set(hpush_open,'callback','usvseg09r2(''open'');');
set(hpush_flat,'callback','usvseg09r2(''flat'');');
set(hpush_thrs,'callback','usvseg09r2(''thrs'');');
set(hpush_dtct,'callback','usvseg09r2(''dtct'');');
set(hpush_save,'callback','usvseg09r2(''save'');');
set(hpush_sgmt,'callback','usvseg09r2(''sgmt'');');
set(hpush_play,'callback','usvseg09r2(''play'');');
set(hpush_swav,'callback','usvseg09r2(''swav'');');
set(hpush_long,'callback','usvseg09r2(''long'');');
set(hpush_fldr,'callback','usvseg09r2(''fldr'');');
% text set
set(htext_fnam,'horizontalalign','left');
% set position
set(hfig,'position',[10 80 1000 750]);
hts = [htext_fslb,htext_step,htext_fmin,htext_fmax,htext_thre,htext_dmin,htext_dmax,htext_gmin,htext_marg,htext_wavo,htext_imgo,htext_imgt,htext_trac,htext_read];
hed = [htext_fsvl,hedit_step,hedit_fmin,hedit_fmax,hedit_thre,hedit_dmin,hedit_dmax,hedit_gmin,hedit_marg,htggl_wavo,htggl_imgo,htggl_imgt,htggl_trac,hedit_read];
for n=1:length(hts)
set(hts(n),'units','normalized','position',[0.02 0.94-(n-1)*0.035 0.06 0.035]);
set(hed(n),'units','normalized','position',[0.08 0.94-(n-1)*0.035 0.04 0.035]);
end
set(hpush_open,'units','normalized','position',[0.02 0.42 0.10 0.04]);
set(hpush_flat,'units','normalized','position',[0.02 0.38 0.10 0.04]);
set(hpush_thrs,'units','normalized','position',[0.02 0.34 0.10 0.04]);
set(hpush_dtct,'units','normalized','position',[0.02 0.30 0.10 0.04]);
set(hpush_save,'units','normalized','position',[0.02 0.26 0.10 0.04]);
set(hpush_sgmt,'units','normalized','position',[0.02 0.22 0.10 0.04]);
set(htext_maps,'units','normalized','position',[0.02 0.16 0.04 0.04]);
set(hedit_mapL,'units','normalized','position',[0.06 0.16 0.03 0.04]);
set(hedit_mapH,'units','normalized','position',[0.09 0.16 0.03 0.04]);
set(hpush_play,'units','normalized','position',[0.02 0.12 0.05 0.04]);
set(hpush_swav,'units','normalized','position',[0.07 0.12 0.05 0.04]);
set(hpush_long,'units','normalized','position',[0.02 0.06 0.10 0.04]);
set(hpush_fldr,'units','normalized','position',[0.02 0.02 0.10 0.04]);
% filename and axis
set(hpanl_busy,'units','normalized','position',[0.175 0.955 0.02 0.025]);
set(htext_fnam,'units','normalized','position',[0.20 0.96 0.77 0.02]);
set(haxes(1), 'units','normalized','position',[0.20 0.68 0.77 0.25]);
set(haxes(2), 'units','normalized','position',[0.20 0.38 0.77 0.25]);
set(haxes(3), 'units','normalized','position',[0.20 0.08 0.77 0.25]);
% disable
set(hpush_open,'enable','on');
set(hpush_flat,'enable','off');
set(hpush_thrs,'enable','off');
set(hpush_dtct,'enable','off');
set(hpush_save,'enable','off');
set(hpush_sgmt,'enable','off');
set(hpush_play,'enable','off');
set(hpush_swav,'enable','off');
set(hpush_long,'enable','on');
set(hpush_fldr,'enable','on');
% save handles
gv.gui.hfig = hfig;
gv.gui.haxes = haxes;
gv.gui.hpush_open = hpush_open;
gv.gui.hpush_flat = hpush_flat;
gv.gui.hpush_thrs = hpush_thrs;
gv.gui.hpush_dtct = hpush_dtct;
gv.gui.hpush_save = hpush_save;
gv.gui.hpush_sgmt = hpush_sgmt;
gv.gui.hpush_play = hpush_play;
gv.gui.hpush_swav = hpush_swav;
gv.gui.hpush_long = hpush_long;
gv.gui.hpush_fldr = hpush_fldr;
gv.gui.htext_fnam = htext_fnam;
gv.gui.htext_fsvl = htext_fsvl;
gv.gui.hedit_step = hedit_step;
gv.gui.hedit_fmin = hedit_fmin;
gv.gui.hedit_fmax = hedit_fmax;
gv.gui.hedit_thre = hedit_thre;
gv.gui.hedit_dmin = hedit_dmin;
gv.gui.hedit_dmax = hedit_dmax;
gv.gui.hedit_gmin = hedit_gmin;
gv.gui.hedit_marg = hedit_marg;
gv.gui.hedit_read = hedit_read;
gv.gui.hedit_mapL = hedit_mapL;
gv.gui.hedit_mapH = hedit_mapH;
gv.gui.htggl_wavo = htggl_wavo;
gv.gui.htggl_imgo = htggl_imgo;
gv.gui.htggl_imgt = htggl_imgt;
gv.gui.htggl_trac = htggl_trac;
gv.gui.hpanl_busy = hpanl_busy;
% delete function
function finishfunc(~,~)
global gv
prmname = [fileparts(mfilename('fullpath')) filesep 'usvseg_prm.mat'];
fetchparams;
prm = gv.prm;
save(prmname,'prm');
clearvars -global gv;
disp('bye!')
% ////////////////////////////////////////////////////////////////////////
function busytoggle(num)
global gv
if num==1
set(gv.gui.hpanl_busy,'backgroundcolor',[1 0 0]);
drawnow;
else
set(gv.gui.hpanl_busy,'backgroundcolor',[0 1 0]);
drawnow;
end
% ////////////////////////////////////////////////////////////////////////
function fetchparams
global gv
prm.fftsize = gv.prm.fftsize;
prm.timestep = str2num(get(gv.gui.hedit_step,'string'))/1000;
prm.freqmin = str2num(get(gv.gui.hedit_fmin,'string'))*1000;
prm.freqmax = str2num(get(gv.gui.hedit_fmax,'string'))*1000;
prm.threshval = str2num(get(gv.gui.hedit_thre,'string'));
prm.durmin = str2num(get(gv.gui.hedit_dmin,'string'))/1000;
prm.durmax = str2num(get(gv.gui.hedit_dmax,'string'))/1000;
prm.gapmin = str2num(get(gv.gui.hedit_gmin,'string'))/1000;
prm.margin = str2num(get(gv.gui.hedit_marg,'string'))/1000;
prm.wavfileoutput= get(gv.gui.htggl_wavo,'value');
prm.imageoutput = get(gv.gui.htggl_imgo,'value');
prm.imagetype = get(gv.gui.htggl_imgt,'value');
prm.traceoutput = get(gv.gui.htggl_trac,'value');
prm.readsize = str2num(get(gv.gui.hedit_read,'string'));
prm.mapL = str2num(get(gv.gui.hedit_mapL,'string'))*1000;
prm.mapH = str2num(get(gv.gui.hedit_mapH,'string'))*1000;
gv.prm = prm;
% ////////////////////////////////////////////////////////////////////////
function [mtsp,fltnd,onoffset,onoffsetm,freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq,thresh,med,contflg] = procfun(wav,fs,fftsize,params,med,thresh)
timestep = params.timestep;
gapmin = params.gapmin;
durmin = params.durmin;
durmax = params.durmax;
margin = params.margin;
freqmin = params.freqmin;
freqmax = params.freqmax;
% multitaper spec
mtsp = multitaperspec(wav,fs,fftsize,timestep,0);
% flattening
[fltnd,med] = flattening(mtsp,med);
% threshold calculation with n*sigma (SD) of background noise
if isempty(thresh)
thresh = estimatethresh(fltnd,fs,freqmin,freqmax,params.threshval);
end
% thresholding
thrshd = thresholding(fltnd,fs,freqmin,freqmax,thresh);
% onset/offset detection
[onoffset,onoffsetm,~,contflg] = detectonoffset(thrshd,fs,timestep,gapmin,durmin,durmax,margin);
% peak tracking
[freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq] = specpeaktracking(mtsp,fltnd,fs,timestep,freqmin,freqmax,onoffset,margin);
% ////////////////////////////////////////////////////////////////////////
function segfun(startid,outp,prefix,inputimg,imrng,wav,fs,timestep,margin,onoffset,tvec,amptrace,freqtrace,wavflg,imgflg,trcflg)
fftsize = (size(inputimg,1)-1)*2;
step = round(timestep*fs);
onset = onoffset(:,1);
offset = onoffset(:,2);
im = flipud(uint8((inputimg-imrng(1))/(imrng(2)-imrng(1))*64));
cm = flipud(gray(64));
for n=1:length(onset)
rng = [max(round((onset(n)-margin)*fs),1) min(round((offset(n)+margin)*fs),length(wav))];
rngs = round((rng-fftsize/2)/step);
rng2 = [max(rngs(1),1) min(rngs(2),size(im,2))];
% wave write
if wavflg==1
fname = sprintf('%s_%04d.wav',prefix,n+startid-1);
audiowrite([outp filesep fname],wav(rng(1):rng(2)),fs);
end
% jpg write
if imgflg==1
imseg = im(:,rng2(1):rng2(2));
fname = sprintf('%s_%04d.jpg',prefix,n+startid-1);
imwrite(imseg,cm,[outp filesep fname]);
end
% trace write
if trcflg==1
af = [amptrace(:,1) freqtrace(:,1) amptrace(:,2) freqtrace(:,2) amptrace(:,3) freqtrace(:,3)];
dat = [tvec(rng2(1):rng2(2))' af(rng2(1):rng2(2),:)];
% CSV file
fname = sprintf('%s_%04d.csv',prefix,n+startid-1);
dlmwrite([outp filesep fname],dat,'precision',6);
end
end
% ////////////////////////////////////////////////////////////////////////
function [freqtrace,amptrace,maxampval,maxampidx,maxfreq,meanfreq,cvfreq] = specpeaktracking(mtsp,fltnd,fs,timestep,freqmin,freqmax,onoffset,margin)
if isempty(onoffset)
freqtrace = nan(size(mtsp,2),4);
amptrace = nan(size(mtsp,2),4);
maxampval = [];
maxampidx = [];
maxfreq = [];
meanfreq = [];
cvfreq = [];
return;
end
fftsize = (size(fltnd,1)-1)*2;
step = round(fs*timestep);
% spectral peak saliency
spcsal = spectralsaliency(fltnd);
% get peak and reorganize
bandwidth = 9;
ncandidates = 4;
contmin = 10;
ampthr = 0;
nstep = size(fltnd,2);
fnmin = floor(freqmin/fs*fftsize)+1;
fnmax = ceil(freqmax/fs*fftsize)+1;
onidx = round((onoffset(:,1)-margin)*fs/step); % add margin
offidx = round((onoffset(:,2)+margin)*fs/step); % add margin
onidx(1) = max(1,onidx(1));
offidx(end) = min(nstep,offidx(end));
freqmat = nan(nstep,ncandidates);
ampmat = nan(nstep,ncandidates);
maxampval = nan(length(onoffset(:,1)),1);
maxampidx = ones(length(onoffset(:,1)),1);
maxampfreq = nan(size(onoffset,1),1);
meanfreq = nan(size(onoffset,1),1);
cvfreq = nan(size(onoffset,1),1);
for n=1:size(onoffset,1)
idx = onidx(n):offidx(n);
[peakfreq,peakamp] = searchpeak(spcsal(fnmin:fnmax,idx),fltnd(fnmin:fnmax,idx),ncandidates,bandwidth);
[peakfreqsg,peakampsg] = segregatepeak(peakfreq+fnmin-1,peakamp,contmin,ampthr);
freqmat(idx,:) = peakfreqsg;
ampmat(idx,:) = peakampsg;
if any(~isnan(peakampsg(:)))
[mvC,miC] = max(peakampsg,[],2);
[~,miR] = max(mvC);
maxampidx(n) = miR+idx(1)-1;
maxampfreq(n) = peakfreqsg(miR,miC(miR));
if ~isnan(maxampfreq(n))
maxampval(n) = mtsp(round(maxampfreq(n)),maxampidx(n));
end