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
  3 Comments
Rik
Rik on 25 Jul 2022
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.

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Answers (2)

Jan
Jan on 25 Jul 2022
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.
  1 Comment
Rizwan Khan
Rizwan Khan on 25 Jul 2022
Yes, water ( ) command is the bottleneck but issue I am getting with the function of re-assigning lables. We have to update the label numbers in the subsequest regions.
Purpose of reassign label function: I am applying my own watershed transform locally on the 3D image. Suppose region 1st has 5 labels numbering 1 to 5 and region 2nd has 3 labels which gives lables as 1 to 3 and therefore I ressign the lables to start as 6,7, and 8 to avoid overwriting and son on.

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Bruno Luong
Bruno Luong on 25 Jul 2022
Edited: Bruno Luong on 25 Jul 2022
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;
  5 Comments
Bruno Luong
Bruno Luong on 25 Jul 2022
Edited: Bruno Luong on 25 Jul 2022
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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