Minimise memory requirements when importing many images

I am using imread to read in 430 monochrome (16-bit) images of resolution 1024x1280. I apply a common mask to each image, which is a 1024x1280 logical array. I also dispose of any pixels with values outside the range 50-60000.

I'm storing the processed images as layers of a 3-d array:

cube1 = zeros(1024,1280,430);
for k=1:430
    image = double(imread (myImageFiles(k).name)));
    image(~mask) = NaN;
    image(image<50 | image>60000) = NaN; % replace 'bad' pixels outside limits with NaN
    cube1(:,:,k) = image;
end

The image is cast as a double because I want to replace certain pixels with NaNs. If i just read in as uint16 then these pixels are stored as zeros. I also want to create a second cube in the same way and divide the elements in cube1 by the corresponding elements in cube2.

newCube = cube1./cube2;

However, I am coming up against 'out of memory' issues (system has 8GB RAM). I can reduce memory by not casting as a double but lose the NaN feature. Please could someone advise on a way to tackle this? I've tried saving as a .mat file, but each cube array is over 4GB (before any compression).

[Adam Danz]

Some ideas

1. Use single instead of double.
2. Since you're doing element-wise division, do you need to load all 430 images into the same array? Can you load image 1 from cube1 and then load image 1 from cube2, and then store the result of division, then get rid of the two image data sets and repeat for the next pair of images?

[Steve Francis]

Thanks, Adam. I will give this a try.

Answer 1

[Catalytic]

Why is it better to use NaNs instead of zeros? A value of 0 doesn't conflict with anything because all of your nontrivial values lie between 50 and 60000.

cube = zeros(1024,1280,430,'single');

for k=1:430

    image1 = imread (myFiles1(k).name));
    image2 = imread (myFiles2(k).name));
    
    image1(image1<50 | image1>60000) = 0; 
    image2(image2<50 | image2>60000) = 0; 
    
    image3 = single(image1)./single(image2);
    image3(~isfinite(image3))=0;
    
    cube(:,:,k)=image3;
end