Using Tiff function to save tiff files

Hi everyone,

I am currently trying to save a 3D array into a SINGLE tiff file using the Tiff function as suggested by Matlab. I have found no example showing how to use the Tiff function. Does anyone know? Here is an example of code that needs to be completed:

A = rand(512,512,512);
file = Tiff('myfile.tif','w');
file.write(A)
file.close()

Thank you for you help.

Answer 1

[DGM]

There are at least two ways of doing this.

You can try to just cram everything into a single image. As far as I can tell, I don't see where this is contrary to the TIFF spec, but MATLAB does complain about it. It still works though.

fname = 'fname.tif';

% a MxNx5 3D image
inpict = imread('cameraman.tif');
inpict = repmat(inpict,[1 1 5]);
%warning off

% create the file (you'll get a warning)
write3Dtiff(inpict,fname)

Warning: Sum of Photometric color channels and ExtraSamples does not match the value specified in SamplesPerPixel.
Writing with this configuration will error in a future release. To correct the configuration, define the non-color channels as ExtraSamples.

% read the imate
C(:,:,:) = imread(fname,1);

% test it
size(C) % the size is as expected

ans = 1×3

256 256 5

isequal(C,inpict) % it's the same as the original

ans = logical
   1

Alternatively, you can split the pages of the volumetric image, representing each slice as a frame (a distinct image). This is the more general approach, but reading the file is more verbose.

clearvars
fname = 'fname.tif';

% a MxNx5 3D image
inpict = imread('cameraman.tif');
inpict = repmat(inpict,[1 1 5]);

% reshape the image to be a 4D array
% this presumes that inpict is MxNxFx1
inpict4D = permute(inpict,[1 2 4 3]);

% create the file
write3Dtiff(inpict4D,fname)

% get the information in the multitiff image
info = imfinfo(fname);
nframes = numel(info);

% read images to check that it's the expected size
% this assumes all the frames are the same class and size
C(:,:,:,1) = imread(fname,1);
C = repmat(C,[1 1 1 nframes]);
for f = 2:nframes
    C(:,:,:,f) = imread(fname,f);
end

% permute it back into a 3D array
% this presumes that all frames of C are single-channel
C = permute(C,[1 2 4 3]);

% test it
size(C) % the size is as expected

ans = 1×3

256 256 5

isequal(C,inpict) % it's the same as the original

ans = logical
   1

Choose whichever you feel is suitable. This is an example helper function as is used in both examples above.

function write3Dtiff(array, filename)
    % make sure the vector returned by size() is of length 4
    dims = size(array,1:4);

    % Set data type specific fields
    if isa(array, 'single')
        bitsPerSample = 32;
        sampleFormat = Tiff.SampleFormat.IEEEFP;
    elseif isa(array, 'uint16')
        bitsPerSample = 16;
        sampleFormat = Tiff.SampleFormat.UInt;
    elseif isa(array, 'uint8')
        bitsPerSample = 8;
        sampleFormat = Tiff.SampleFormat.UInt;
    else
        % if you want to handle other numeric classes, add them yourself
        disp('Unsupported data type');
        return;
    end
    
    % Open TIFF file in write mode
    outtiff = Tiff(filename,'w');
    
    % Loop through frames
    for f = 1:dims(4)
        % Set tag structure for each frame
        tagstruct.ImageLength = dims(1);
        tagstruct.ImageWidth = dims(2);
        tagstruct.SamplesPerPixel = dims(3);
        tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
        tagstruct.BitsPerSample = bitsPerSample;
        tagstruct.SampleFormat = sampleFormat;
        
        if any(dims(3) == [3 4]) % assume these are RGB/RGBA
            tagstruct.Photometric = Tiff.Photometric.RGB;
        else % otherwise assume it's I/IA or volumetric
            tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
        end
        
        if any(dims(3) == [2 4]) % assume these are IA/RGBA
            tagstruct.ExtraSamples = Tiff.ExtraSamples.AssociatedAlpha;
        end
        
        % Set the tag for the current frame
        outtiff.setTag(tagstruct);
        
        % Write the frame
        outtiff.write(array(:,:,:,f));
        
        % Create a new directory for the next frame
        if f ~= dims(4)
            outtiff.writeDirectory();
        end
    end
    
    % Close the file
    outtiff.close();
end