How can I extract and save images from 3D stack images (512x1000x100 double) from a .mat files?
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Chinmay Bepery
on 22 Oct 2023
Commented: Walter Roberson
on 23 Oct 2023
I am trying to extract images and save individual images from a .mat file. The .mat file also consist of a strauct with three filed [images(512x1000x100 double), layerMaps(100x1000x3 double) and age (78)].
At present, I can only show the 100 images by using the following codes:
s=load ("D:\Matlab\1.mat");
D=s.images;
vol = squeeze(D);
[x,y,z] = size(D);
for i=1:z
sliceZ = vol(:,:,i);
cla; % Prevent stuffing too many images into the axes.
imshow(sliceZ, []);
drawnow;
pause(0.25); % Pause for 1/2 second before next frame blows it away.
end
But I can not save those images as individual files and also fail to relate the layerMaps and age with those images. Please share your knowledge in this regards.
3 Comments
Walter Roberson
on 22 Oct 2023
The code in my Answer extracts into separate files.
As you have not given any context, I do not have any guess about what the layerMaps might be for.
Accepted Answer
Chinmay Bepery
on 23 Oct 2023
Edited: Chinmay Bepery
on 23 Oct 2023
1 Comment
Walter Roberson
on 23 Oct 2023
Could you show us
[smallestimg, largestimg] = bounds(vol, 'all')
[smallestdiff, largestdiff] = bounds(diff(unique(vol)))
[smallestlm, largeslm] = bounds(s.LayerMaps, 'all')
More Answers (1)
Walter Roberson
on 22 Oct 2023
s=load ("D:\Matlab\1.mat");
outdir = 'D:\Matlab';
D = s.images;
LM = s.layerMaps;
A = s.age;
z = size(D,3);
for i=1:z
outfile = fullfile(outdir, "image_" + i + ".mat");
savestruct.image = D(:,:,i);
savestruct.layerMap = squeeze(LM(i,:,:));
savestruct.age = A;
save(outfile, "-struct", "savestruct");
end
This will create image_1.mat image_2.mat and so on in the directory named in outdir . Each of the .mat will contain three variables -- "image", "layerMap", and "age" .
2 Comments
Walter Roberson
on 23 Oct 2023
You can imwrite() but they are individually 512 x 1000 . Is that intensity information to be written in grayscale? Or should the layerMaps(100x1000x3 double) be understood to be a 1000 x 3 colormap specific to each image? If it is a per-image colormap then is each image integer values in the range 0 to 999 (or 1 to 1000) that should be understood as the color index?
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