How do I read large set of multi-page TIFF files into tall array using a datastore?

I have a directory of N TIFF files with M pages of resolution _a _x _b_. How can I read these tiff files such the result is an (N * M) x a x b tall array?

The directory has too many images to load all of them into memory at one time.

Answer 1

[MathWorks Support Team]

This task is best separated into two steps. The first step is to import the multi-page TIFF images using a datastore. The second step is create the desired tall array from the datastore.

(1) Import multi-page TIFF images using a datastore

Use 'fileDatastore' with a custom 'ReadFcn' function. The custom function should use the 'Tiff' class to read the multiple pages of the TIFF files. The following code demonstrates how to read a multi-page, monochrome, TIFF file in which each page is the same resolution:

function subimages = readMultipageTiff(filename)
% Read a multipage tiff, assuming each file is the same size
    t = Tiff(filename, 'r');
    subimages(:,:,1) = t.read(); % Read the first image to get the array dimensions correct.
    if t.lastDirectory()
         return; % If the file only contains one page, we do not need to continue.
    end

    % Read all remaining pages (directories) in the file
    t.nextDirectory();
    while true
        subimages(:,:,end+1) = t.read();
        if t.lastDirectory()
            break;
        else
            t.nextDirectory();
        end
    end
end

2) Create a tall array of size M x a x b from the datastore

a x b is the size of each image and M is the number of images. Because the custom read function used in (1) returns matrices such that the first dimension selects a sub-image, 'cell2mat' will produce an M x a x b matrix. This approach will not require loading the entire image set into memory. The following gives an example of this approach:

ds = fileDatastore({'<DirectoryHere>'},'ReadFcn', @readMultipageTiff);
tds = tall(ds);
tds = cell2mat(tds);
write('tds.tall', tds);