rharkes/fast_tiff_write

A fast multi-image tiff writer for Matlab

fast_tiff_write's Issues

how to support int16 image

My data is int16 tif

In Matlab 2023b, Fast_Tiff_Write vs Tifflib

Using Fast_Tiff_Write to save large TIFF files takes approximately half the time compared to saving with the Tiff library. The time difference between the two is not more than ten times greater than stated in Readme.
only change the tags in code.

tf.setTag('Photometric',Tiff.Photometric.MinIsBlack);
tf.setTag('Compression',Tiff.Compression.None);
tf.setTag('BitsPerSample',16);
tf.setTag('SamplesPerPixel',1);
tf.setTag('SampleFormat',Tiff.SampleFormat.UInt);
tf.setTag('ImageLength',size(IM,1));
tf.setTag('ImageWidth',size(IM,2));
tf.setTag('ResolutionUnit',3);
tf.setTag('PlanarConfiguration',Tiff.PlanarConfiguration.Chunky);

My Computer is Thinkbook 16+ 2023,CPU is AMD R7480H, GPU is GTX 4050

how to support custom tiff tag

like XResolution, YResolution, and ResolutionUnit

The resulting tiff is not valid - cannot be opened by ImageJ nor MATLAB imread

I used MATLAB R2019a Update 6 (on macOS Sierra 10.12.6) to run the included test_fTiff.m. The resulting test.tif cannot be read by ImageJ (only the first frame is recognized). MATLAB 'imread' gives the following error:
Unable to read TIFF file "test.tif". File is corrupt or image does not contain any readable strips.

XResolution and YResolution could be set separately

Consider that the aspect ratio of the image is not 1:1

rows and columns appear switched

It's fast and mostly reliable, it helps a lot for writing large image stacks. Thanks.

However, the written images appear to be rotated and flipped (x and y axes are swapped)

Here is a bit of code to show this:

% fast Tiff test

testImg = [1,2;3,4;5,6];
testImg = im2uint16(rescale(testImg));

imwrite(testImg,'tiff-imwrite.tif');

fTIFF = Fast_Tiff_Write('tiff-fTIFF.tif',1,0);
fTIFF.WriteIMG(testImg); %% this does not work for some reason
% fTIFF.WriteIMG(permute(testImg,[2,1])); %% this does work
fTIFF.close;

subplot(1,3,1);
imagesc(testImg);
axis equal tight
title('original image')

subplot(1,3,2)
imagesc(imread('tiff-imwrite.tif'));
axis equal tight
title('read after imwrite')

subplot(1,3,3)
imagesc(imread('tiff-fTIFF.tif'));
axis equal tight
title('read after fTIFF.WriteIMG')

This produces this result:

In case OS and Matlab version are relevant: '9.6.0.1214997 (R2019a) Update 6' on 'PCWIN64' (Windows 10).

A simple workaround is to permute the image before writing (as in the commented-out line 10), but perhaps there is a way to not have to do this.

(Or perhaps I'm missing something obvious, that's also quite possible).