how to modify the variables for changing FOR loop to PARFOR loop??
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I have a code described here which takes lot of time to run on my 32 cores machine. I tried to use all cores by changing for loop by parfor loop. I get an error about in final_lmatrix which ccannot be classied.
CC = bwconncomp(B_fill_slice);
L = labelmatrix(CC);
numObjects = CC.NumObjects;
prev_regions = 0; %initialize
new_regions = numObjects;
disp('init_regions')
disp(new_regions);
iter = 1;
while ((new_regions - prev_regions)>0)
disp('sub');
disp(new_regions - prev_regions);
prev_regions = new_regions;
disp('iter');
disp(iter);
new_num = 0;
final_lmatrix = zeros(r,c,p, 'uint8'); % preallocation
for n = 1:new_regions
region = (L==n);
l = water(region); %compute watershed and return labelmatrix
if (n~=1)
l = reassign_label(uint8(l),r,c,p,new_num);
end
final_lmatrix = l+final_lmatrix; %contains the updated label matrix to be used for the next iteration
new_num = max(final_lmatrix(:));
end %end for loop
new_regions = new_num;
L = final_lmatrix;
disp('new_regions');disp(new_regions);
iter = iter+1;
end %end while loop
thanks
댓글 수: 3
Rik
2022년 7월 25일
Every iteration should independent. That means you can only use n as an index. If you don't have memory issues, that means you should use final_lmatrix(:,:,:,n) inside the loop.
답변 (2개)
Jan
2022년 7월 25일
What is the bottleneck of your code? Use the profiler to find it. If it is the water() command, parallelize this command:
lArray = zeros(r,c,p, new_regions, 'uint8')
parfor n = 1:new_regions
lArray(:, :, :, n) = water(L == n);
end
Does this work? Then the re-assigning of the lables runs in a separate sequential loop, or you can create a more efficient method.
Bruno Luong
2022년 7월 25일
편집: Bruno Luong
2022년 7월 25일
Could you try this inner loop (EDIT fix issue with 0 label):
final_lmatrix = 0;
parfor n = 1:new_regions
region = (L==n);
lbn = water(region); %compute watershed and return labelmatrix
m = max(lbn);
LUT = [0, (1-2*2^-n)+2^-n*((1:m)/m)];
lbn = LUT(lbn); % I don't know what is your reassign_label function does
final_lmatrix = final_lmatrix + lbn;
end %end for loop
[~,~,final_lmatrix] = unique(final_lmatrix);
final_lmatrix = final_lmatrix - 1;
댓글 수: 5
Bruno Luong
2022년 7월 25일
편집: Bruno Luong
2022년 7월 25일
So it looks like your label is higher for n small (pushed up by later iterations).
I did the opposite since I didn't know the detail of your function.
It's really not hard to change to match your labeling convention.
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