Changing the size info of images per iteration in a for loop

The situation: I'm running a for loop which anaylzes images. Each folder contains separate dataset and all are analyzed using a code that runs on subfolders within a parent folder. In some sub-folders, the Height and Width (H x W) of the images to be analyzed are different.

The problem: I get error whenever the code runs an iteration on a subfolder that contains images of different dimensions (H x W) compared to the sub-folder analyzed in the first iteration (k=1=True). What is missing here such that the code can be executed on images of different dimensions, smoothly?

Here is the relevent lines of the code I have, please read the comments:

for k = 1 : numberOfFolders;

if numberOfImageFiles >= 1600

   %....some code 

for s=InitFrameLast10:StartInt:LastFrameLast10; 
    for t=s:s+ImpFrames; 
         
    fullFileNameLast10=fullfile(thisFolder, baseFileNames{t});
    fprintf('      Now reading %s\n', fullFileNameLast10);

    imageArray_uncropLast10=imread(fullFileNameLast10);

     FigInfo=imfinfo(fullFileNameLast10);
    W=FigInfo.Width;
    H=FigInfo.Height;
   
%I want to assigning W and H (which changes per iteration) to PupilBigLast10
    
    PupilBigLast10(:,:,t)=imageArray_uncropLast10; 
%The line above is where I get the error that Right (not changing--want it to be flexible) and left (changes per folder iteration) are not equal
    
    %....some more code
    end 

end
%....more and more code

[Rik]

Do you want to store the image or only the height and width?

[Lina KORONFEL]

No, I don't want to store the image. All I want to do is to implement the changing H and W to PupilBigLast10(:,:,t), such that its size is equivalent to imageArray_uncropLast10, and the code could proceed further.

[Rik]

You are currently storing the entire content of imageArray_uncropLast10, not just its height and width. You can of course change the size of PupilBigLast10 to make imageArray_uncropLast10 fit inside it. Which of these two would you want to happen?

[Lina Koronfel]

Yes exactly!! How can I change the size of PupilBigLast10 to make the changing dimensions of imageArray_uncropLast10 (which changes per iterartion of "k", or "numberOfFolders") fit inside it? Thank you

Answer 1

[Ameer Hamza]

In MATLAB, it is not possible to create a 3D matrix with a different number of rows and columns in each slice. For such situations, we use cell arrays. You can do something like this:

Add this line at the place where you are initializing PupilBigLast10

PupilBigLast10 = {};

Then, replace the line

PupilBigLast10(:,:,t) = imageArray_uncropLast10;

with

PupilBigLast10{t} = imageArray_uncropLast10; 

[Rik]

Alternatively you could expand the array to make it fit the largest image, which would pad the image with zeros (unless you pad it yourself with something else).

[Lina Koronfel]

That yield the type of PupilBigLast10 as cell and gives it a wrong value (1x64200), 64200 is basically the value of InitFrameLast10, this is wrong and is not what I'm looking for...

imageArray_uncropLast10 is uint8 which value is (H x W), this value changes per k iteration (please see the code above). I want PupilBigLast10 to yield uint8 of (H x W x t), such that H x W are adaptable to the changes...

Again, the issue I'm having now is that the value of H x W of PupilBigLast10 doesn't adapt, so it works for k=1:2, then starting k=3 I get error that the size of PupilBigLast10 and imageArray_uncropLast10 is not equal. I hope I made myself clear. Thank you

[Ameer Hamza]

Lina, If imageArray_uncropLast10 changes size only for different values of k, then you can just reinitialize PupilBigLast10 each time. For example,

for k = 1 : numberOfFolders
    PupilBigLast10 = zeros(H,W,t); % if you know the value of H, W, and t

or if you don't already know then

for k = 1 : numberOfFolders
    PupilBigLast10 = []; % this can be very slow due to dynamic allocation

[Lina Koronfel]

Thank you for the prompt response. There are a couple of problems though. The iterations all yield similar results, which is not what I'm expecting. I placed the command you recommended under the "t" for-loop since this is when the H and W can be identified using imfinfo.

for s=InitFrameLast10:StartInt:LastFrameLast10; 
    for t=s:s+ImpFrames; %Selected frames/trial to be analyzed
         
    fullFileNameLast10=fullfile(thisFolder, baseFileNames{t});
    fprintf('      Now reading %s\n', fullFileNameLast10);
    
    imageArray_uncropLast10=imread(fullFileNameLast10);

   FigInfo=imfinfo(fullFileNameLast10);
   W=FigInfo.Width;
   H=FigInfo.Height;
   
    PupilBigLast10=zeros(H,W,t);
       
    PupilBigLast10(:,:,t)=imageArray_uncropLast10;

    BinaryPupilLast10(:,:,t)=im2bw(PupilBigLast10(:,:,t), 0.4);

    PixelCountLast10(t) = sum(sum(BinaryPupilLast10(:,:,t)));
           
    end 

end

and I also get the same error as before, but now on the following line ( P.S. if I also make BinaryPupilLast10=zeros (H,W,t)) I run out of memory

Unable to perform assignment because the size of the left side is 90-by-160 and the size of the right side is 94-by-160.
Error in BinaryPupilLast10(:,:,t)=im2bw(PupilBigLast10(:,:,t), 0.4);

[Ameer Hamza]

Lina, you should not place this line PupilBigLast10=zeros(H,W,t); inside the 't' for loop. It will initialize the variable at each iteration and overwrite the past values. If it is not possible to identify the dimension in advance, then you can initialize it as empty array PupilBigLast10 = []; outside of this loop.

[Lina Koronfel]

Sorry I didn't copy the full section for the for loop. Here it is

for k = 1 : numberOfFolders;
    close all
    try
	% Get this folder and print it out.
	thisFolder = listOfFolderNames{k};
	fprintf('Processing folder %s\n', thisFolder); 
    
    filePattern = sprintf('%s/*.tif', thisFolder);
	baseFileNames = dir(filePattern);
    baseFileNames= natsortfiles({baseFileNames.name});
    numberOfImageFiles = length(baseFileNames);

if numberOfImageFiles >= 1601
    %some constants
    
for s=InitFrameLast10:StartInt:LastFrameLast10; 
    for t=s:s+ImpFrames; %Selected frames/trial to be analyzed
         
    fullFileNameLast10=fullfile(thisFolder, baseFileNames{t});
    fprintf('      Now reading %s\n', fullFileNameLast10);

    imageArray_uncropLast10=imread(fullFileNameLast10);

       FigInfo=imfinfo(fullFileNameLast10);
       W=FigInfo.Width;
       H=FigInfo.Height;
   
    PupilBigLast10=zeros(H,W,t);
       
    PupilBigLast10(:,:,t)=imageArray_uncropLast10;

    BinaryPupilLast10(:,:,t)=im2bw(PupilBigLast10(:,:,t), 0.4);

    PixelCountLast10(t) = sum(sum(BinaryPupilLast10(:,:,t)));
           
    end 

end

%more code

[Ameer Hamza]

I suggest you add the initialization before the 's' for loop.

BinaryPupilLast10 = [];
for s=InitFrameLast10:StartInt:LastFrameLast10;  

Alternate: Although you mentioned that you don't already know the vaue of H and W but you can just read one file as sample to get their values

fullFileNameLast10 = fullfile(thisFolder, baseFileNames{1}); % just select one file
imageArray_uncropLast10 = imread(fullFileNameLast10);
FigInfo=imfinfo(fullFileNameLast10);
W = FigInfo.Width;
H = FigInfo.Height;
BinaryPupilLast10 = zeros(H,W,t);
for s=InitFrameLast10:StartInt:LastFrameLast10;

Dynamic allocation should be avoided as much as possible.

[Lina KORONFEL]

Thank you so much Ameer!! I tested the code on several folders and it worked everytime with no errors. However, I had to create a zeros matrix for both PupilBig as well as BinaryPupilLast10, and to change the type from double to uint8, which is the type of imageArray_uncropLast10.

Here is the final code as it worked

for k = 1 : numberOfFolders;
    close all
    try
	% Get this folder and print it out.
	thisFolder = listOfFolderNames{k};
	fprintf('Processing folder %s\n', thisFolder); 
    
    filePattern = sprintf('%s/*.tif', thisFolder);
	baseFileNames = dir(filePattern);
    baseFileNames= natsortfiles({baseFileNames.name});
    numberOfImageFiles = length(baseFileNames);
if numberOfImageFiles >= 1601
    %some constants
    fullFileNameOfFolderForDimensionPurpose=fullfile(thisFolder, baseFileNames{1600});
    %imageArrayofFolderForDimensionPurpose=imread(fullFileNameOfFolderForDimensionPurpose);
       FigInfo=imfinfo(fullFileNameOfFolderForDimensionPurpose);
       H=FigInfo.Height;
       W=FigInfo.Width;
       
       %PupilBigLast10=zeros(H,W,k);
       PupilBig=zeros(H,W,k, 'uint8');
       BinaryPupilLast10=zeros(H,W,k, 'uint8');
       
for s=InitFrameLast10:StartInt:LastFrameLast10; 
    for t=s:s+ImpFrames; %Selected frames/trial to be analyzed
         
    fullFileNameLast10=fullfile(thisFolder, baseFileNames{t});
    fprintf('      Now reading %s\n', fullFileNameLast10);
    imageArray_uncropLast10=imread(fullFileNameLast10);

    PupilBigLast10(:,:,t)=imageArray_uncropLast10;
    BinaryPupilLast10(:,:,t)=im2bw(PupilBigLast10(:,:,t), 0.4);
    PixelCountLast10(t) = sum(sum(BinaryPupilLast10(:,:,t)));
           
    end 
end
%more code

Cheers!!

[Ameer Hamza]

Glad to be of help.