Interact with very large Tiff (or rset) images in MATLAB - matlab

Question

I have some very large Tiff images that I am trying to use in a MATLAB GUI application. If I try to load the images using imshow, I get an out-of-memory error. (Yes, I know MATLAB is not the best choice for GUIs or loading large images, but there is good reason for using MATLAB in this case).
I can obviously create a reduced resolution data set (rset file) and use imtool to view the image, but this is not helpful as I want a user to be able to interact with the image by clicking on it to extract (x,y) coords into the application. Imshow does not seem to be directly compatible with rset files. Is there a way for me to load an rset'd image in a panable/zoomable figure, or any other way I can achieve the goal?
I looked at the code for imtool but it seems to be using undocumented classes to read rset files and I can't replicate its behaviour.

Answer 1

You can use low-level file I/O functions of MATLAB to read the entirety or parts of the TIFF image in order to avoid the OOM problem.
fileName = 'LargeTiff.tif';
info = imfinfo(fileName)
% Determine number of frames
nFramesStr= regexp(info.ImageDescription, 'images=(\d*)', 'tokens');
nFrames = str2double(nFramesStr{1}{1});
% Use low-level File I/O functions to read the file
fp = fopen(fileName , 'rb');
% The "StripOffsets" field provides the offset to the first strip.
fseek(fp, info.StripOffsets, 'bof');
% Assume that the image format is 16-bit per pixel and is big-endian
% Also assume that the images are stored one after the other
% For example, read the first 100 frames
frameNum = 100;
imData = cell(1, frameNum);
for cnt = 1 : frameNum
imData{cnt} = fread(fp, [info.Width info.Height], 'uint16', 0, 'ieee-be');
end
fclose(fp);

Answer 2

It looks like my problem is that I simply don't have enough memory to load the whole tiff, and that there is no public specification for the rset files format. So I am going to instead solve the problem by creating my own version of a reduced resolution data set. I should be able to load block sections of the image, resave them and then dynamically load and unload only the needed high-res blocks at zoom, and load a reduced resolution overview when zoomed out.

Answer 3

You can write a callback function to get the pixel co-ordinates (X,Y) from imtool then convert to a tile number and tile index using the code below. You can then utilise the readencodedtile function in matlab
function [tileidx,Tile_num] = getTileInfo(tiffile,X,Y)
A = Tiff(tiffile);
tile_width = A.getTag('TileWidth');
tile_length = A.getTag('TileLength');
SizeA = size(A);
tt = sub2ind(SizeA,X,Y);
% Example only
% X = repmat((1:10)',1,10);
% Y = repmat((1:10),10,1);
% A = reshape(1:100,10,10);
% SizeA = size(A);
% tile_width = 3;
% tile_length = 2;
tileidx = rem(tt-(Y-1)*SizeA(1)-1,tile_length)+1 ...
+ tile_length*rem(Y+tile_width-1,tile_width);
Tile_num = ceil(Y/tile_width)+ ...
(ceil(X/tile_length)-1)*ceil(SizeA(2)/tile_width);