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function for compiling images doesn't work
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I try to compile images by using this function but the function is not recalled. what is the problem in this code.
if true
% Pathname="/Users/mohammedabdullah/OneDrive - University at Albany - SUNY/Signals/Signals/April 24 2018_2";
FolderNames= "Cycle 1";
hybs= 8;
Channelstotal= 8;
channelsperhyb= 2;
function offsets = make3channel(PathName, FolderName, hybs, channelstotal, channelsperhyb)
for i = 1:hybs
listing{i} = dir([PathName '\' num2str(i) '\*.tif']);
end
mkdir(PathName,FolderName);
fld = pwd;
Miji;
cd(fld);
k2 = strfind(listing{1}(1).name, 'Pos');
for k = 1:length(listing{1})
roi = listing{1}(k).name(k2(1):k2(1)+4);
mkdir([PathName '\' FolderName],roi);
for i = 0:(hybs/(channelstotal/channelsperhyb))-1
counter = 1;
for j = (i*channelstotal/channelsperhyb)+1:channelstotal/channelsperhyb*(i+1)
Path = ['path=[' PathName '\' num2str(j) '\' listing{j}(k).name ']'];
MIJ.run('Open...', Path);
hybtemp = uint16(MIJ.getCurrentImage);
if mod(j,channelstotal/channelsperhyb) ~=1
regi = cat(3,regi,hybtemp(:,:,4));
c = normxcorr2(regi(:,:,counter),regi(:,:,1));
[~, imax] = max(abs(c(:)));
[ypeak, xpeak] = ind2sub(size(c),imax(1));
offset{i+1,counter} = [(xpeak-size(regi(:,:,1),2)) (ypeak-size(regi(:,:,1),1))];
hybtempreg = imtranslate(hybtemp,offset{i+1,counter});
tform = imregcorr(regi(200:800,200:800,counter),regi(200:800,200:800,1));
hybtempreg = imwarp(hybtemp,tform,'OutputView',imref2d(size(regi(:,:,1))));
hyb = cat(3,hyb, hybtempreg(:,:,1:3));
regireg = cat(3,regireg, hybtempreg(:,:,4));
offsets{i+1,counter} = tform;
else
hyb = hybtemp(:,:,1:3);
regireg = hybtemp(:,:,4);
regi = hybtemp(:,:,4);
end
counter = counter + 1;
MIJ.run('Close All')
end
MIJ.createImage('HYB',hyb,true);
MIJ.run('Stack to Hyperstack...', ['order=xyczt(default) channels=' num2str(channelstotal) ' slices=1 frames=1 display=Grayscale']);
MIJ.run('Save', ['save=[' PathName '\' result '\' roi '\' num2str(i+1) '.tif' ']']);
MIJ.run('Close All')
MIJ.createImage('Regireg',regireg,true);
MIJ.run('Save', ['save=[' PathName '\' FolderName '\' roi '\hyb' num2str(i+1) 'RegistrationCheck.tif' ']']);
MIJ.run('Close All')
end
end
MIJ.exit
end
end
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