Homec4science
Diffusion Motion correction paper (cluster_pipeline) Browse

R6289/code/process_w.m
678da7fa12b2cluster_pipeline

Last Change
Raw File

process_w.m
View Options

function process_w()
parfor idx = 1:lxg
tic;
fnIJ='/home/aymanns/registration/ij.jar'; % Path to "ij.jar"
fnMIJ='/home/aymanns/registration/mij.jar'; % Path to "mij.jar"
javaaddpath(fnIJ);
javaaddpath(fnMIJ);
colorFlow=zeros(size(seqRescale,1),size(seqRescale,2),3,size(seqRescale,3)-1);
vectorFlow=zeros(512,512,size(seqRescale,3)-1);
for t = 1:N-1
colorFlow(:,:,:,t) = flowToColor(w(:,:,:,t,idx));
vectorFlow(:,:,t) = flowToVectorImage(w(:,:,:,t,idx),[18,18],[512,512],idx*10^N+t,tmpdir);
end
dlmwrite([char(outdir(idx)),'/wx_frame',num2str(t),'.dat'],w(:,:,1,t,idx));
dlmwrite([char(outdir(idx)),'/wy_frame',num2str(t),'.dat'],w(:,:,2,t,idx));
seqWarped=seq;
seqwWarped=seqW;
seqWarped(:,:,t+1)=warpImg(seq(:,:,t+1),w(:,:,1,t,idx),w(:,:,2,t,idx));
seqwWarped(:,:,t+1)=warpImg(seqW(:,:,t+1),w(:,:,1,t,idx),w(:,:,2,t,idx));
[cY1, mY1, ng1] = motion_metrics(seqWarped);
[cY2, mY2, ng2] = motion_metrics(seqwWarped);
fnOut1=[char(outdir(idx)),'/warped1.tif']; % Sequence fnIn1 warped
fnOut2=[char(outdir(idx)),'/warped2.tif']; % Sequence fnIn2 warped
fnColor=[char(outdir(idx)),'/color_flow.tif']; % Color visualization of the motion field
fnVector=[char(outdir(idx)),'/vectors.tif'];
mijwrite_stack(single(seqWarped),fnOut1);
mijwrite_stack(single(seqwWarped),fnOut2);
mijwrite_stack(single(colorFlow),fnColor,1);
mijwrite_stack(single(vectorFlow),fnVector);
dlmwrite([char(outdir(idx)),'/cY_Out1.dat'],cY1);
dlmwrite([char(outdir(idx)),'/cY_Out2.dat'],cY2);
dlmwrite([char(outdir(idx)),'/mY_Out1.dat'],mY1);
dlmwrite([char(outdir(idx)),'/mY_Out2.dat'],mY2);
dlmwrite([char(outdir(idx)),'/ng_Out1.dat'],ng1);
dlmwrite([char(outdir(idx)),'/ng_Out2.dat'],ng2);
fprintf(['parfor loop over idx ',num2str(idx),' finished in ',num2str(toc)]);
end
c4science · Help