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excitanalysissupplsim.m
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excitanalysissupplsim.m
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function excitanalysissupplsim(directory,biftype,threshrange,threshcheck,fftpkcheck,stiffind)
%
% Finds additional metrics on simulated data from bifurcation normal forms.
%
% excitanalysissupplsim(directory,biftype,threshrange,threshcheck,fftpkcheck)
%
% Directory: The directory of the files to be searched e.g. '/Users/.../'
% biftype: bifurcation type to be analyzed e.g. 1
% threshrange: range of thresholds e.g. linspace(0.01,1,100)
% threshcheck: check range of thresholds? (1=yes;0=no) default=1
% fftpkcheck: check FFT? (1=yes;0=no) default=1
%
% Joshua D. Salvi
%
if exist('threshcheck')==0
threshcheck=1;
end
if exist('fftpkcheck')==0
fftpkcheck=1;
end
%Fs = 1/t(2);
dwnspl=1;offset=0;
if biftype ~= 1 && isempty(dir([directory '*-rect-pt' num2str(1) '.mat']))==1
for j = 1:5
files{j} = dir([directory '*-all-pt' num2str(j) '.mat']);
end
elseif biftype == 4
for j = 1:5
files{j} = dir([directory '*-pt' num2str(j) '.mat']);
end
elseif isempty(dir([directory '*-rect-pt' num2str(1) '.mat']))==0
for j = 1:5
files{j} = dir([directory '*-rect-pt' num2str(j) '.mat']);
end
elseif isempty(findstr(directory,'offset')) == 1
for j = 1:5
files{j} = dir([directory '*-pt' num2str(j) '.mat']);
end
else
for j = 1:5
files{j} = dir([directory '*-all-pt' num2str(j) '.mat']);
end
end
%{
if biftype == 4
stiffind = input('Which index in stiffness? (1,2,3,4,5)... ');
end
%}
stiffind2=stiffind;
for m = 1:5
load([directory files{m}.name]);
stiffind=stiffind2;
if m == 1
% Pre-allocate memory
dipsto = zeros(5,length(Xdet),length(Xdet{1}));dipdet = zeros(5,length(Xdet),length(Xdet{1}));
punisto = zeros(5,length(Xdet),length(Xdet{1}));punidet = zeros(5,length(Xdet),length(Xdet{1}));
fftmaxpkstoind = zeros(5,length(Xdet),length(Xdet{1}));fftmaxpkdetind = zeros(5,length(Xdet),length(Xdet{1}));
fftmaxpkheightsto = zeros(5,length(Xdet),length(Xdet{1}));fftmaxpkheightdet = zeros(5,length(Xdet),length(Xdet{1}));
fftmaxpkfreqtsto = zeros(5,length(Xdet),length(Xdet{1}));fftmaxpkfreqtdet = zeros(5,length(Xdet),length(Xdet{1}));
fftmaxpkwidthtdetL = zeros(5,length(Xdet),length(Xdet{1}));fftmaxpkwidthtstoL = zeros(5,length(Xdet),length(Xdet{1}));
fftmaxpkwidthtstoR = zeros(5,length(Xdet),length(Xdet{1}));fftmaxpkwidthtdetR = zeros(5,length(Xdet),length(Xdet{1}));
Xlowsto = zeros(5,length(Xdet),length(Xdet{1}));Xlowdet = zeros(5,length(Xdet),length(Xdet{1}));
Qdet = zeros(5,length(Xdet),length(Xdet{1}));Qsto = zeros(5,length(Xdet),length(Xdet{1}));
Xupsto = zeros(5,length(Xdet),length(Xdet{1}));Xupdet = zeros(5,length(Xdet),length(Xdet{1}));
CVdetpk = cell(5,length(threshrange));CVstopk = cell(5,length(threshrange));
end
if biftype == 1
Xdet1 = Xdet; Xsto1 = Xsto;
clear i;
for j = 1:length(Xdet1)
for k = 1:length(Xdet1{1})
Xdet{j}{k} = Xdet1{j}{k}(1,1:dwnspl:end) + offset; % use only real part
Xsto{j}{k} = Xsto1{j}{k}(1,1:dwnspl:end) + offset;
end
end
clear Xdet1 Xsto1 Hopfdet Hopfsto
elseif biftype == 2
for j = 1:length(Xdet)
for k = 1:length(Xdet{1})
SNICdet=Xdet;SNICsto=Xsto;
Xdet{j}{k} = SNICdet{j}{k}(1:dwnspl:end) + offset;
Xsto{j}{k} = SNICsto{j}{k}(1:dwnspl:end) + offset;
end
end
elseif biftype == 3
Xdet1 = Xdet; Xsto1 = Xsto;
for j = 1:length(Xdet1)
for k = 1:length(Xdet1{1})
Xdet{j}{k} = Xdet1{j}{k}(1,1:dwnspl:end).*sin(Xdet1{j}{k}(2,1:dwnspl:end)) + offset;
Xsto{j}{k} = Xsto1{j}{k}(1,1:dwnspl:end).*sin(Xsto1{j}{k}(2,1:dwnspl:end)) + offset;
end
end
clear Xdet1 Xsto1
elseif biftype == 4
if exist('Xsto')==1
Xsto1=Xsto; Xdet1=Xdet;clear Xdet Xsto;
end
if isempty (findstr([directory files{m}.name],'force')) == 0
mu = F; rt=mu; I=rt;
else
mu = ke; rt=mu; I=rt;
end
sizeX = size(Xdet1);
for j = 1:sizeX(1) % Isolate the appropriate index
for qp = 1:sizeX(3)
Xsto{qp}{j} = Xsto1{j,stiffind,qp}(1,1:dwnspl:end) + offset;
Xdet{qp}{j} = Xdet1{j,stiffind,qp}(1,1:dwnspl:end) + offset;
end
end
elseif biftype == 5
Xsto1=Xsto;Xdet1=Xdet;
clear Xdet Xsto
sizeX = size(Xdet1);
for j = 1:sizeX(1)
for k = 1:sizeX(2)
Xsto{k}{j} = Xsto1{j,k}(1,1:dwnspl:end) + offset;
Xdet{k}{j} = Xdet1{j,k}(1,1:dwnspl:end) + offset;
end
end
else
disp('No bifurcation type chosen');
end
if exist('mu') == 0
if exist('I') == 1
mu = I;
elseif exist('rt') == 1
mu = rt;
else
disp('No control parameter exists');
break;
end
end
if m == 1
for j = 1:5
for k = 1:length(threshrange)
CVdetpk{j,k} = zeros(length(Xdet),length(Xdet{1}));
CVstopk{j,k} = zeros(length(Xdet),length(Xdet{1}));
end
end
end
if threshcheck==1
for n = 1:length(threshrange)
clear trtimedet trtime pkd pks
trtimedet = cell(length(Xdet),length(Xdet{1}));trtime = cell(length(Xdet),length(Xdet{1}));
for j = 1:length(Xdet)
for k = 1:length(Xdet{1})
% Peak finding and CV
pkd{j,k} = PTDetect(Xdet{j}{k},threshrange(n));
pks{j,k} = PTDetect(Xsto{j}{k},threshrange(n));
for l = 2:length(pkd{j,k})
trtimedet{j,k}(l-1) = (pkd{j,k}(l) - pkd{j,k}(l-1));
end
for l = 2:length(pks{j,k})
trtime{j,k}(l-1) = (pks{j,k}(l) - pks{j,k}(l-1));
end
if isempty(trtimedet{j,k})==0
CVdetpk{m,n}(j,k) = std(trtimedet{j,k})/mean(trtimedet{j,k});
else
CVdetpk{m,n}(j,k) = 0;
end
if isempty(trtime{j,k})==0
CVstopk{m,n}(j,k) = var(trtime{j,k})/mean(trtime{j,k});
else
CVstopk{m,n}(j,k) = 0;
end
% Phase distribution
clear xdethilb xstohilb
xdethilb = hilbert(Xdet{j}{k}(round(length(Xdet{j}{k})/2:end)));
xstohilb = hilbert(Xsto{j}{k}(round(length(Xsto{j}{k})/2:end)));
xdetphase = atan2(imag(xdethilb),real(xdethilb));
xstophase = atan2(imag(xstohilb),real(xstohilb));
clear i;
VSdet(m,j,k) = abs(1/length(xdetphase)*sum(exp(i*xdetphase))); % vector strength (det)
VSsto(m,j,k) = abs(1/length(xstophase)*sum(exp(i*xstophase))); % vector strength (sto)
end
end
if mod(n,5)==0
disp(['n = ' num2str(n) '/' num2str(length(threshrange))]);
end
end
end
if exist('t') == 0
Fs=50;
else
Fs = 1/t(2);
end
L = length(Xsto{1}{1});
NFFT = (2^2)*2^nextpow2(L);
nw=10;
XsegL = floor(length(Xsto{1}{1})/nw);
welchwin = round(XsegL);
NPSD = floor(NFFT/nw);
noverlap = 0;
winfunc = hamming(welchwin);
freq = 0.005;
Xsine = sin(2*pi*freq.*t);
[Xsinepsd,fsinepsd] = pwelch(Xsine,winfunc,noverlap,NPSD,Fs);
winpeaknorm = sqrt(max(Xsinepsd).*(2.*Fs.*XsegL.*(sum(abs(winfunc).^2)./XsegL)))./XsegL;
for j = 1:length(Xsto)
for k = 1:length(Xsto{1})
if fftpkcheck==1
clear fftpkspkheight fftpkdpkheight
[Xstofft, fstofft, XstofftCI]= pwelch(Xsto{j}{k},winfunc,noverlap,NPSD,Fs,'ConfidenceLevel',0.999);
[Xdetfft, fdetfft, XdetfftCI]= pwelch(Xdet{j}{k},winfunc,noverlap,NPSD,Fs,'ConfidenceLevel',0.999);
[a1s b1s] = twoclass(Xstofft,1e-4);
[a1d b1d] = twoclass(Xdetfft,1e-4);
pkfs = PTDetect(Xstofft,max([a1s b1s]));
pkfd = PTDetect(Xstofft,max([a1d b1d]));
mxs = 1; mxd = 1;
for q = 1:length(pkfs) % test each peak (stochastic) -> is it statistically distinct from peaks with less then half of its power on both sides?
fhps = find(Xstofft<=(Xstofft(pkfs(q))/2));
testL = sign(XstofftCI(pkfs(q),1)-XstofftCI(fhps(fhps<pkfs(q)),2));
testH = sign(XstofftCI(pkfs(q),1)-XstofftCI(fhps(fhps>pkfs(q)),2));
if sum(testL==1) >= 1 && sum(testH==1) >= 1
fftpkspkheight(q) = Xstofft(pkfs(q));
fftpkspkfreq(q) = fstofft(pkfs(q));
fhpsL = fhps(fhps<pkfs(q));fhpsH = fhps(fhps>pkfs(q));
Lind = fhpsL(testL==1);Lind=Lind(end);
Hind = fhpsH(testH==1);Hind=Hind(1);
fftpkswidth(m,q,1:2) = [fstofft(Lind) fstofft(Hind)];
mxs = mxs+1;
end
end
if mxs > 1
clear ind1
ind1 = find(fftpkspkheight(:)==max(fftpkspkheight(:))); ind1=ind1(1);
if numel(ind1)==0;ind1=1;
end
fftmaxpkstoind(m,j,k) = pkfs(ind1);
fftmaxpkheightsto(m,j,k) = Xstofft(fftmaxpkstoind(m,j,k));
fftmaxpkfreqtsto(m,j,k) = fstofft(fftmaxpkstoind(m,j,k));
fftmaxpkwidthtstoL(m,j,k) = fftpkswidth(m,ind1,1);
fftmaxpkwidthtstoR(m,j,k) = fftpkswidth(m,ind1,2);
Qsto(m,j,k) = fftmaxpkfreqtsto(m,j,k)/(fftmaxpkwidthtstoR(m,j,k)-fftmaxpkwidthtstoL(m,j,k));
else
fftmaxpkheightsto(m,j,k) = 0;
fftmaxpkfreqtsto(m,j,k) = 0;
fftmaxpkwidthtstoL(m,j,k) = 0;
fftmaxpkwidthtstoR(m,j,k) = 0;
Qsto(m,j,k) = 0;
end
for q = 1:length(pkfd) % test each peak (deterministic) -> is it statistically distinct from peaks with less then half of its power on both sides?
fhpd = find(Xdetfft<=(Xdetfft(pkfd(q))/2));
testL = sign(Xdetfft(pkfd(q),1)-XdetfftCI(fhpd(fhpd<pkfd(q)),2));
testH = sign(XdetfftCI(pkfd(q),1)-XdetfftCI(fhpd(fhpd>pkfd(q)),2));
if sum(testL==1) >= 1 && sum(testH==1) >= 1
fftpkdpkheight(q) = Xdetfft(pkfd(q));
fftpkdpkfreq(q) = fdetfft(pkfd(q));
fhpdL = fhpd(fhpd<pkfd(q));fhpdH = fhpd(fhpd>pkfd(q));
Lind = fhpdL(testL==1);Lind=Lind(end);
Hind = fhpdH(testH==1);Hind=Hind(1);
fftpkdwidth(m,q,1:2) = [fdetfft(Lind) fdetfft(Hind)];
mxd = mxd+1;
end
end
if mxd > 1
clear ind1
ind1 = find(fftpkdpkheight(:)==max(fftpkdpkheight(:))); ind1=ind1(1);
if numel(ind1)==0;ind1=1;
end
fftmaxpkdetind(m,j,k) = pkfd(ind1);
fftmaxpkheightdet(m,j,k) = Xdetfft(fftmaxpkdetind(m,j,k));
fftmaxpkfreqtdet(m,j,k) = fdetfft(fftmaxpkdetind(m,j,k));
fftmaxpkwidthtdetL(m,j,k) = fftpkdwidth(m,ind1,1);
fftmaxpkwidthtdetR(m,j,k) = fftpkdwidth(m,ind1,2);
Qdet(m,j,k) = fftmaxpkfreqtdet(m,j,k)/(fftmaxpkwidthtdetR(m,j,k)-fftmaxpkwidthtdetL(m,j,k));
else
fftmaxpkheightdet(m,j,k) = 0;
fftmaxpkfreqtdet(m,j,k) = 0;
fftmaxpkwidthtdetL(m,j,k) = 0;
fftmaxpkwidthtdetR(m,j,k) = 0;
Qdet(m,j,k) = 0;
end
end
if k == 1
disp('Dip test...');
disp([num2str(j) '/' num2str(length(Xsto))])
end
% Find the dip statistic and associated p-value
Nboot = 10^1; % number of bootstraps
%[as bs] = hist(Xsto{j}{k},freedmandiaconis(Xsto{j}{k}));as=as./sum(as);
%[ad bd] = hist(Xsto{j}{k},freedmandiaconis(Xdet{j}{k}));ad=ad./sum(ad);
[dipsto(m,j,k), punisto(m,j,k), Xlowsto(m,j,k), Xupsto(m,j,k)]=HartigansDipSignifTest(Xsto{j}{k},Nboot);
[dipdet(m,j,k), punidet(m,j,k), Xlowdet(m,j,k), Xupdet(m,j,k)]=HartigansDipSignifTest(Xdet{j}{k},Nboot);
if threshcheck ~= 1
if mod(k,25)==0
disp([num2str(k) '/' num2str(length(Xsto{1}))])
end
end
end
end
if threshcheck==1 && fftpkcheck==1
disp(['m = ' num2str(m) '/5']);
disp(['Saving' num2str(m) '...']);
if biftype == 4
save([directory 'stiffind-' num2str(stiffind) '-output' num2str(m) '.mat'],'Qsto','Qdet','VSdet','VSsto','CVdetpk','CVstopk','punisto','punidet','fftmaxpkheightdet','fftmaxpkheightsto','fftmaxpkfreqtdet','fftmaxpkfreqtsto','fstofft','mu','threshrange','dipsto','dipdet');
disp('Finished.');
else
save([directory 'output' num2str(m) '.mat'],'Qsto','Qdet','VSdet','VSsto','CVdetpk','CVstopk','punisto','punidet','fftmaxpkheightdet','fftmaxpkheightsto','fftmaxpkfreqtdet','fftmaxpkfreqtsto','fstofft','mu','threshrange','dipsto','dipdet');
disp('Finished.');
end
end
end
%Pre-allocate memory
mu1d = zeros(length(threshrange),length(Xdet));mu1s = zeros(length(threshrange),length(Xdet));
CV1d = zeros(length(threshrange),length(Xdet));CV1s = zeros(length(threshrange),length(Xdet));
sizeC1 = size(CVdetpk);
sizeC2 = size(CVdetpk{1,1});
if threshcheck ==1 && fftpkcheck ==1
for n = 1:sizeC1(2)
for j = 1:sizeC2(1)
for k = 1:sizeC2(2)
CVdetmean{n}(j,k) = mean([CVdetpk{1,n}(j,k) CVdetpk{2,n}(j,k) CVdetpk{3,n}(j,k) CVdetpk{4,n}(j,k) CVdetpk{5,n}(j,k)]);
CVdetsem{n}(j,k) = std([CVdetpk{1,n}(j,k) CVdetpk{2,n}(j,k) CVdetpk{3,n}(j,k) CVdetpk{4,n}(j,k) CVdetpk{5,n}(j,k)])/sqrt(5);
CVstomean{n}(j,k) = mean([CVstopk{1,n}(j,k) CVstopk{2,n}(j,k) CVstopk{3,n}(j,k) CVstopk{4,n}(j,k) CVstopk{5,n}(j,k)]);
CVstosem{n}(j,k) = std([CVstopk{1,n}(j,k) CVstopk{2,n}(j,k) CVstopk{3,n}(j,k) CVstopk{4,n}(j,k) CVstopk{5,n}(j,k)])/sqrt(5);
Qdetmean(j,k) = mean([Qdet(1,j,k) Qdet(2,j,k) Qdet(3,j,k) Qdet(4,j,k) Qdet(5,j,k)]);
Qdetsem(j,k) = std([Qdet(1,j,k) Qdet(2,j,k) Qdet(3,j,k) Qdet(4,j,k) Qdet(5,j,k)])/sqrt(5);
Qstomean(j,k) = mean([Qsto(1,j,k) Qsto(2,j,k) Qsto(3,j,k) Qsto(4,j,k) Qsto(5,j,k)]);
Qstosem(j,k) = std([Qsto(1,j,k) Qsto(2,j,k) Qsto(3,j,k) Qsto(4,j,k) Qsto(5,j,k)])/sqrt(5);
VSdetmean(j,k) = mean([VSdet(1,j,k) VSdet(2,j,k) VSdet(3,j,k) VSdet(4,j,k) VSdet(5,j,k)]);
VSstomean(j,k) = mean([VSsto(1,j,k) VSsto(2,j,k) VSsto(3,j,k) VSsto(4,j,k) VSsto(5,j,k)]);
VSdetsem(j,k) = std([VSdet(1,j,k) VSdet(2,j,k) VSdet(3,j,k) VSdet(4,j,k) VSdet(5,j,k)])/sqrt(5);
VSstosem(j,k) = std([VSsto(1,j,k) VSsto(2,j,k) VSsto(3,j,k) VSsto(4,j,k) VSsto(5,j,k)])/sqrt(5);
end
CV1d1 = findnearest(CVdetmean{n}(j,:),1);if isempty(CV1d1)==0;CV1d(n,j)=CVdetmean{n}(j,CV1d1(1));else CV1d(n,j)=NaN;end
mu1d(n,j) = mu(CV1d1(1)); % control parameter at which CD ~ 1 (deterministic)
CV1s1 = findnearest(CVstomean{n}(j,:),1);if isempty(CV1s1)==0;CV1s(n,j)=CVstomean{n}(j,CV1s1(1));else CV1s(n,j)=NaN;end
mu1s(n,j) = mu(CV1s1(1)); % control parameter at which CD ~ 1 (stochastic)
end
end
end
if threshcheck==1 && fftpkcheck ==1
if biftype == 4
disp('Saving...');
save([directory 'outputALL-stiffind-' num2str(stiffind) '.mat'],'Qsto','Qdet','VSdet','VSsto','mu1s','mu1d','CVdetmean','CVdetsem','CVstomean','CVstosem','Qstomean','Qstosem','Qdetmean','Qdetsem','VSdetmean','VSdetsem','VSstomean','VSstosem','dipsto','dipdet','punisto','punidet','fftmaxpkheightdet','fftmaxpkheightsto','fftmaxpkfreqtdet','fftmaxpkfreqtsto','fstofft','mu','threshrange','CVdetpk','CVstopk','CV1d','CV1s');
disp('Finished.');
else
disp('Saving...');
save([directory 'outputALL.mat'],'Qsto','Qdet','VSdet','VSsto','mu1s','mu1d','CVdetmean','CVdetsem','CVstomean','CVstosem','Qstomean','Qstosem','Qdetmean','Qdetsem','VSdetmean','VSdetsem','VSstomean','VSstosem','dipsto','dipdet','punisto','punidet','fftmaxpkheightdet','fftmaxpkheightsto','fftmaxpkfreqtdet','fftmaxpkfreqtsto','fstofft','mu','threshrange','CVdetpk','CVstopk','CV1d','CV1s');
disp('Finished.');
end
elseif threshcheck==1 && fftpkcheck ==0
if biftype == 4
disp('Saving...');
save([directory 'output-NOTHRESHCHECK-stiffind-' num2str(stiffind) '.mat'],'VSdet','VSsto','mu1s','mu1d','VSdetmean','VSdetsem','VSstomean','VSstosem','dipsto','dipdet','punisto','punidet','mu','threshrange');
disp('Finished.');
else
disp('Saving...');
save([directory 'output-NOTHRESHCHECK.mat'],'VSdet','VSsto','mu1s','mu1d','VSdetmean','VSdetsem','VSstomean','VSstosem','dipsto','dipdet','punisto','punidet','mu','threshrange');
disp('Finished.');
end
else
if biftype == 4
disp('Saving...');
save([directory 'output-NOTHRESHCHECK-stiffind-' num2str(stiffind) '.mat'],'dipsto','dipdet','punisto','punidet','mu','threshrange');
disp('Finished.');
else
disp('Saving...');
save([directory 'output-NOTHRESHCHECK.mat'],'dipsto','dipdet','punisto','punidet','mu','threshrange');
disp('Finished.');
end
end