How can I avoid the "out of memory' for the following code?

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I have one set of data that has multiple matrices of 40000x10800. I want to extract those matrices column by column, clear it from zeros values, and the save them in another matrix. but when I ran the following code, it gives the "out of memory" message. Please help me.
r=randi([0 10],40000,10800);
for i=1:1:10800
r_0=r(:,i);
r_0=r_0(r_0~=0);
r_1(:,i)=r_0;
end
Unable to perform assignment because the size of the left side is 36287-by-1 and the size of the right side is 36346-by-1.
I have adjusted the code like above because my dataset is more the 5 Gb, so I couldn't attach it.
  6 Comments
Ranu Ghafour
Ranu Ghafour on 13 Sep 2022
The Bigger picture is that I have data series that has several matrices of 40000x10800 containing numbers. I got this data from a measurement. I want to plot several graphs for statistical analization, but before that I need to remove those cells in each column that has 0 value. However, when I run the code, it gives me an error of either "out of memory" or " size of left side and right size are not equal".

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Accepted Answer

Image Analyst
Image Analyst on 13 Sep 2022
Evidently you have enough memory to hold your variables, you just can't "plot several graphs for statistical analization". Since you can't "remove" zeros, which would leave the matrix with uneven/ragged borders, you should assign them to nan. Then you can use the 'omitnan' in functions like mean(), and functions like plot() will ignore them.
m(m==0) = nan;
% Get mean of matrix:
meanOfM = mean(m(:), 'omitnan');
% or plot each column:
[rows, columns] = size(m);
for col = 1 : columns
plot(m(:, col), '-');
hold on;
end
xlabel('row')
ylabel('Value of m')
grid on;
  1 Comment
Ranu Ghafour
Ranu Ghafour on 13 Sep 2022
Thanks for you kind help. Actually I have to assign those column that I need for my plot or calculation to NaN, otherwise the system still cannot assign zero values of 40000x10800 in one line of code.

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