Tiff file corrupted when using Imwrite

Dear all,

I'm using for a while the imwrite function to create, save and append data to a tiff file:

...  

ind_rand = randperm(nb_frames) ;
for f = 1:nb_frames
    if(f==1)
        imwrite(x_UINT16,name_stk_file,'WriteMode', 'overwrite','Compression','none');
    else
        imwrite(x_UINT16,name_stk_file,'WriteMode', 'append','Compression','none');
    end%if       
end

The file is created but when I try to open it with ImageJ for example, the file is corrupted even if its size is correct.

When I open it and display it with Matlab (fopen -> imshow), the file is OK.

Could you help me please?

There is no Matlab error, just the file can not be opened and ImageJ displays this error:

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 596MB of 98096MB (<1%)

java.lang.NegativeArraySizeException

at ij.io.ImageReader.readCompressed16bitImage(ImageReader.java:164)

at ij.io.ImageReader.read16bitImage(ImageReader.java:105)

at ij.io.ImageReader.readPixels(ImageReader.java:785)

at ij.io.FileOpener.readPixels(FileOpener.java:587)

at ij.io.FileOpener.open(FileOpener.java:86)

at ij.io.FileOpener.openImage(FileOpener.java:53)

at ij.io.Opener.openTiff2(Opener.java:1118)

at ij.io.Opener.openTiff(Opener.java:917)

at ij.io.Opener.openImage(Opener.java:335)

at ij.io.Opener.openImage(Opener.java:241)

at ij.io.Opener.open(Opener.java:104)

at ij.io.Opener.openAndAddToRecent(Opener.java:310)

at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:194)

at ij.plugin.DragAndDrop.run(DragAndDrop.java:160)

at java.lang.Thread.run(Thread.java:750)

[Sébastien MAILFERT]

When I read the file information in Matlab

imageinfo('E:\R2022a\Compilation\HD_perf_two_particles_20220711\for_redistribution_files_only\HD_two_part_bg0.tif');

I don't see the number of images winthin the file (should be 8752).

[Abderrahim. B]

Seems like your question is answered here.

[Sébastien MAILFERT]

That's interesting but the file has a size of 200 Mo and I created other files with a size > 4Go that can be opened by ImageJ.

[Jan]

"readCompressed16bitImage" from the error message sounds strange for an uncompressed image.

Answer 1

[Siraj]

Hi!

I understand that you've created a TIFF file with multiple images using MATLAB, and it opens fine within MATLAB. However, when you try to open it in "ImageJ," it doesn't work.

The error message indicates that the TIFF file is of a large size, and a big TIFF file is not the same as a normal TIFF file. Not all software readers are optimized for reading large TIFF files. MATLAB, on the other hand, can handle both regular and big TIFF files seamlessly.

You may want to consider this potential solution. First, try creating a TIFF object in MATLAB using the "Tiff" function, and make sure to set the access type appropriately as either "w8" or "a." You can refer to this link to learn more about the "Tiff" function and how to specify the file access type.

https://www.mathworks.com/help/matlab/ref/tiff.html

Next, append your images to this object. When saving a large TIFF file, consider adjusting the default "RowsPerStrip" value to a smaller setting. This may help address the issue you're encountering when opening the file in other software.

You can refer to the provided code snippet to see how to create and write TIFF objects while also configuring and setting their associated tags.

% Prompt the user to select a folder containing PNG files 
ImFolder = "Images"; 

% List all PNG files in the selected directory 
pngFiles = dir(fullfile(ImFolder, '*.png')); 

% Create a TIFF file named "test.tif" and open it for writing 
t = Tiff("test.tif", "w8"); 

% Read the first PNG image to get its size and metadata 
image = imread(fullfile(ImFolder, pngFiles(1).name)); 

% Loop through each PNG file in the folder 
for i = 1:length(pngFiles) 
    % Read the current PNG image 
    image = imread(fullfile(ImFolder, pngFiles(i).name)); 
    
    % Set TIFF tags for the current image 
    setTag(t,'Photometric',Tiff.Photometric.RGB); 
    setTag(t,'PlanarConfiguration',Tiff.PlanarConfiguration.Chunky); 
    setTag(t,'BitsPerSample',8); 
    setTag(t,'SamplesPerPixel',3); 
    setTag(t,'ImageLength',size(image ,1)); 
    setTag(t,'ImageWidth',size(image ,2));   
    
    % Write the current image data to the TIFF file 
    write(t, image); 
    
    % Create a new directory (frame) in the TIFF file for the next image 
    writeDirectory(t); 
    
end 

% Close the TIFF file to save it 
close(t); 

Hope this helps.