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iPED/iPED.m
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function [iPED_PDF,converged]=... | |
iPED(imdir,filename,numdig,filetype,resave,dofilter,N,corstep,gausblur,mbf,maf,ensemf,windowz,stradlemod,imstart,bkga) | |
% imdir ='E:\bacteria_data\ecoli\pdf_test\'; | |
% filename='20x_hcb1736_secondaryculture_od0_t'; | |
% numdig= '%04i' | |
% filetype= '.tif' | |
% resave=strcat(imdir,'\results'); | |
% mkdir(resave); | |
% N=100; numebr of images | |
% corstep=1 is the correlation step size | |
% dofilter=1; Edge Tapering gaussian Filter on the whole image | |
% gausblur=0; % Gaussian blur for unresolved particles | |
% mbf=0; %mean subtraction before Gaussian filter | |
% maf=0; %mean subtraction after Gaussianfilter | |
% ensemf=1; %ensemble in Fourier | |
% windowz=64; %window size for gridding | |
% stradlemod=0; %this is for PIV images | |
% imstart=1; %starting image number | |
% bkga % average image of time series to be subtracted from all | |
% images | |
tic | |
h = waitbar(0,'calculating...','Name','Please wait...',... | |
'CreateCancelBtn','setappdata(gcbf,''canceling'',1)'); | |
cropp=1; % window gridding | |
l=0; | |
filter=ones; | |
breakflag=0; | |
kahler=zeros; | |
pid=zeros; | |
straddling=stradlemod; % 1 if frame1 can only be correlated to frame2 | |
convergencecriteria=1; | |
converged=0; | |
FFFF=zeros; | |
eeerrr=zeros; | |
for i=corstep:corstep %% correlations steps | |
% define a whole bunch of parameters, names are self explanatory | |
max_intensity=0; | |
SCC_ensembler=zeros; | |
AC_ensembler=zeros; | |
SCC_ensemblerr=zeros; | |
AC_ensemblerr=zeros; | |
SCC_ensembleFr=zeros; | |
AC_ensembleFr=zeros; | |
SCC_ensembleFrr=zeros; | |
AC_ensembleFrr=zeros; | |
AC=zeros; | |
meannoiselevel=zeros; | |
integrallevel=zeros; | |
L_infinity=zeros; | |
ensgrids=0; | |
% start the PDF calculation | |
for j=imstart:1+straddling:N-i | |
%Read image 1 | |
filenum=num2str(j,numdig) | |
matFilename = strcat(filename,filenum,filetype); | |
[xr1_0,map]=imread([imdir, matFilename]); | |
%if colored images are loaded they will be converted to grey scale | |
%here | |
if size(xr1_0,3)==3 | |
xr1_0=rgb2gray(xr1_0); | |
end | |
% Let's subtract the background | |
xr1_0_m=double(xr1_0)-double(bkga); | |
xr1_0=double(xr1_0); | |
%load image 2 | |
filenum=num2str(j+i,numdig); | |
matFilename = strcat(filename,filenum,filetype); | |
[xr2_0,map]=imread([imdir, matFilename]); | |
if size(xr2_0,3)==3 | |
xr2_0=rgb2gray(xr2_0); | |
end | |
xr2_0_m=double(xr2_0)-double(bkga); | |
xr2_0=double(xr2_0); | |
% for the purpose of image croppings if griding is selceted | |
kmax=size(xr1_0_m,2); | |
for k=1:windowz:kmax-windowz+1 | |
for kk=1:windowz:kmax-windowz+1 | |
% if cropp==1 | |
xr1_m=imcrop(xr1_0_m,[k kk windowz-1 windowz-1]); | |
xr2_m=imcrop(xr2_0_m,[k kk windowz-1 windowz-1]); | |
xr1=imcrop(xr1_0,[k kk windowz-1 windowz-1]); | |
xr2=imcrop(xr2_0,[k kk windowz-1 windowz-1]); | |
% apply gaussian Blur if selected | |
if gausblur==1 | |
xr1_m=imgaussfilt(xr1_m,2); | |
xr2_m=imgaussfilt(xr2_m,2); | |
end | |
%convert uint8 variables to double precision variables so that | |
%they can be used for calculations AND subtract the mean if | |
%selected by the user | |
[X,Y]=meshgrid(1:size(xr1_m,2),1:size(xr1_m,1)); | |
if mbf==1 | |
xr1d_m=double(xr1_m)-mean2(double(xr1_m)); | |
xr2d_m=double(xr2_m)-mean2(double(xr2_m)); | |
else | |
xr1d_m=double(xr1_m); | |
xr2d_m=double(xr2_m); | |
end | |
% Now lets apply the Gauss Edge Tapering filter | |
if dofilter==1 | |
PSF = fspecial('gaussian',30,5); | |
% PSF = fspecial('gaussian',7,1); | |
x1f = edgetaper(xr1d_m,PSF); | |
x2f = edgetaper(xr2d_m,PSF); | |
else | |
x1f=xr1d_m; | |
x2f=xr2d_m; | |
end | |
% if user tuned on the mean subtraction after filter | |
% application | |
if maf==1 | |
x1f=x1f-mean2(x1f); | |
x2f=x2f-mean2(x2f); | |
end | |
%calculate FT of the ROIs | |
F_CC=zeros(size(xr1_m)); | |
G1=fft2(x1f); | |
G2=fft2(x2f); | |
%CC and AC | |
F_CC=G1.*conj(G2); | |
% F_AC=sqrt(G1.*conj(G1).*G2.*conj(G2)); | |
F_AC=0.5*(G1.*conj(G1)+G2.*conj(G2)); | |
%ensemble in Spectral domain? | |
if ensemf==1 | |
SCC_ensembleFrr=SCC_ensembleFrr+(F_CC); | |
AC_ensembleFrr=AC_ensembleFrr+(F_AC); | |
l=l+1; | |
else | |
CC=fftshift(ifft2(F_CC)); | |
AC=fftshift(ifft2(F_AC)); | |
l=l+1; | |
SCC_ensembler=SCC_ensembler+CC; | |
AC_ensembler=AC_ensembler+AC; | |
end | |
%calculate GCC-SCOT and L infinity of the PDF | |
if ensemf==1 | |
ensgrids=ensgrids+1; | |
GCC_ensemble=(fftshift(ifft2(SCC_ensembleFrr./abs(SCC_ensembleFrr)))); | |
SCC_ensembler=fftshift(ifft2(SCC_ensembleFrr)); | |
AC_ensembler=fftshift(ifft2(AC_ensembleFrr)); | |
iPED_PDF=(fftshift(ifft2(fft2(SCC_ensembler)./fft2(AC_ensembler)))); | |
L_infinity(ensgrids)=norm(iPED_PDF, inf); | |
if L_infinity(ensgrids)==inf || isnan(L_infinity(ensgrids)) | |
try | |
L_infinity(ensgrids)=L_infinity(ensgrids-1); | |
catch | |
L_infinity(ensgrids)=1 | |
end | |
end | |
%convergence check using L_infinity | |
if convergencecriteria==1 && ensgrids>50 &&converged==0 | |
% L_infinity(ensgrids); | |
convx=(1:ensgrids); % Explanatory variable | |
f = @(F,x) F(1)./sqrt(x)+F(2); | |
lb = [0,0]; | |
ub = [inf,inf]; | |
beta0 = [10,10]; | |
opts = optimset('Display','off'); | |
[FFF,resnorm] =lsqcurvefit(f,beta0,convx,L_infinity,lb,ub,opts); | |
eeerrr(ensgrids)=abs(L_infinity(ensgrids)-FFF(2))/FFF(2)*100; | |
FFFF(ensgrids)=FFF(2); | |
if mean(eeerrr(ensgrids-49:ensgrids))<10 && std(FFFF(ensgrids-49:ensgrids))<0.1*mean(FFFF(ensgrids-49:ensgrids)) | |
converged=j | |
figure | |
y_predicted=f(FFF,convx); | |
plot(1:ensgrids,L_infinity(1:ensgrids),'*'); | |
hold on | |
plot(convx,y_predicted,'g','LineWidth',3); | |
plot([ensgrids ensgrids],[0 max(max(L_infinity),max(y_predicted))],'k','LineWidth',3) | |
axis tight | |
legend('data','fit','convergence') | |
% set(gca,'XScale','log') | |
pltname=strcat(resave,'/timelag',num2str(i),'convergence',num2str(j),'.fig') | |
saveas(gcf,pltname) | |
break | |
end | |
if converged | |
breakflag=1 | |
break | |
end | |
end | |
else | |
%store everything | |
iPED_PDF=(fftshift(ifft2(fft2(SCC_ensembler)./fft2(AC_ensembler)))); | |
meannoiselevel(j)=mean(abs(iPED_PDF(:))); | |
integrallevel(j)=trapz(iPED_PDF(:)); | |
L_infinity(j)=norm(iPED_PDF, inf); | |
end | |
end | |
if getappdata(h,'canceling') | |
breakflag=1; | |
end | |
if converged | |
breakflag=1 | |
break | |
end | |
if getappdata(h,'canceling') | |
breakflag=1; | |
break | |
end | |
end | |
if getappdata(h,'canceling') | |
breakflag=1; | |
break | |
end | |
if converged | |
breakflag=1 | |
break | |
end | |
waitbar(j/(N),h,strcat('Image ', {' '}, num2str(j),{' '}, 'out of ',{' '},num2str(N-i),{' '},' .'))%{sprintf('/n')} | |
end | |
% savemeannoise = strcat(resave,'/meannoise',num2str(j+i),'window',num2str(windowz),'_',num2str(i)); | |
% save(savemeannoise,'meannoiselevel','integrallevel','L_infinity') | |
% | |
if ensemf==1 | |
SCC_ensembler=fftshift(ifft2(SCC_ensembleFrr)); | |
AC_ensembler=fftshift(ifft2(AC_ensembleFrr)); | |
end | |
SCC_ensemble = SCC_ensembler; | |
AC_ensemble = AC_ensembler; | |
iPED_PDF=(fftshift(ifft2(fft2(SCC_ensemble)./fft2(AC_ensemble)))); | |
%save everything | |
savecor = strcat(resave,'/SCC_',num2str(j+i),'window',num2str(windowz),'_',num2str(i)); | |
save(savecor,'SCC_ensemble') | |
savecor = strcat(resave,'/AC_',num2str(j+i),'window',num2str(windowz),'_',num2str(i)); | |
save(savecor,'AC_ensemble') | |
savecor = strcat(resave,'/iPED_PDF_',num2str(j+i),'window',num2str(windowz),'_',num2str(i)); | |
save(savecor,'iPED_PDF') | |
if breakflag==1 | |
delete(h) | |
break | |
end | |
end | |
toc | |
end | |