ismember matlab function too slow
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Hi, I would love some help optimizing this piece of code.
In my model i have to go every time instant through all the pixels of an image ( this cannot be changed to solve the equations that I want).
At a given step I want to now if a given pixel corresponds to the list of upetake indexes (uptake_indices) or not. If so I would have a concentration = uptake, else it would be 0.
Currently I am using ismember, but since my arrays are big and the loops are really long, this step delays a lot my code.
Here is a pice of my code.
Thanks for the help!
% list of indexes of my 400x400 image
aux=1;
pareja_indice=zeros(400*400,1);
for i=1:400
for j=1:400
pareja_indice(aux) = sub2ind([400, 400], i, j);
aux=aux+1;
end
end
% Load indexes corresponding to uptake points in the image
load('GABA_uptake_points3.mat');
uptake_indices = sub2ind([400, 400], SourceY, SourceX);
aux=0;
uptake=30;
% initialize concentration matrix
C=zeros(400,400);
for k=1:2000000
% other operations
for i=1:400
for j=1:400
aux=aux+1;
% we should only have uptake at the uptake locations
C_up = uptake * ismember(pareja_indice(aux), uptake_indices);
C(i,j)=C_up;
% ... other operations
end
end
% other operation
end
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Accepted Answer
Hitesh
on 11 Oct 2024
Edited: Hitesh
on 11 Oct 2024
Hi Paula Giménez Mínguez,
From the code snippet, what I understand that you are determining if a pixel index matches an uptake index, which is loaded from the "GABA_uptake_points3.mat" file using the SourceY and SourceX variables. By transforming uptake_indices into a logical array, you can efficiently identify whether each pixel is an uptake point. This method enables direct indexing, offering a significant improvement in elapsed time over repeatedly using ismember.
Refer to the below code :
tic;
% List of indexes of the 400x400 image
pareja_indice = reshape(1:(400*400), [400, 400]);
% Load indexes corresponding to uptake points in the image
load('GABA_uptake_points3.mat');
uptake_indices = sub2ind([400, 400], SourceY, SourceX);
% Create a logical array to identify uptake points
uptake_mask = false(400, 400);
uptake_mask(uptake_indices) = true;
% Initialize concentration matrix
uptake = 30;
C = zeros(400, 400);
for k = 1:2000000
% Only perform operations on uptake points
C(uptake_mask) = uptake;
% ... other operations
end
toc;
For more information on logical array, refer to this MATLAB documentation: https://www.mathworks.com/help/matlab/ref/logical.html
Hope this helps!!
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