Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Change in tiff reading since 0.3.5 #111

Open
warnerwarner opened this issue Jul 3, 2024 · 1 comment
Open

Change in tiff reading since 0.3.5 #111

warnerwarner opened this issue Jul 3, 2024 · 1 comment
Labels

Comments

@warnerwarner
Copy link

Hi,

I've been using OMETIFF with Images to read in some ome.tiff files. I initially had been using v0.3.5 which was correctly reading my files in. However, I recently updated to v0.4.5 which seems to read all of my data values as close to 0s? I replicated my environment but with OMETIFF downgraded and it worked correctly again.

Here is my example code :
using Images tiff_file = "example_tiff.ome.tiff" ome = Images.load(tiff_file); img = Float64.(ome.data); img[1:10, 100, 50, 20, 2]
Which the output with OMETIFF = 0.3.5 is:
0.0
0.0
9.9402579968e10
2.27090563072e11
3.4585493504e11
3.74746185728e11
3.22445049856e11
1.2199846912e10
0.0
0.0

Which I validated was correct with another ome.tiff viewer.

However, if I repeat this same code in an enviroment with OMETIFF=0.4.5 I get the following output:
0.0
0.0
1.816473723e-314
2.733680534326e-312
4.766792508506e-312
1.361377490515e-312
1.375216308147e-312
6.86310032404e-313
0.0
0.0

The only differences with my environments is the version of OMETIFF:

(working_env) pkg> status Project viewer_3d v0.1.0 Status ~/Documents/Github/3d_volumes/viewer_3d/Project.toml [e9467ef8] GLMakie v0.10.4 [916415d5] Images v0.26.1 ⌃ [2d0ec36b] OMETIFF v0.3.14 Info Packages marked with ⌃ have new versions available and may be upgradable.

(not_working_env) pkg> status Status ~/Documents/Github/3d_volumes/viewer_3d_BIG/Project.toml [e9467ef8] GLMakie v0.10.4 [916415d5] Images v0.26.1 [2d0ec36b] OMETIFF v0.4.5

I'd appreciate any guidance. I'm not super familiar with this kind of work, but because the 0s are still being correctly read as 0s, I'm guessing its misinterpreting the bit values?

@tlnagy tlnagy added the bug label Jul 5, 2024
@warnerwarner
Copy link
Author

Hi,

Just to add, I'm pretty certain its the little vs big Endian read - if I use bswap on the values I get the correct values. A fix for now is just to bswap.(img) but it would be good to include this somewhere.

Thanks

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

2 participants