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

LIF: fix offset calculation for certain datasets with multiple unstitched files #4222

Merged
merged 1 commit into from
Sep 2, 2024

Conversation

melissalinkert
Copy link
Member

Fixes #3873, fixes #4199.

See files in inbox/qa/31243 and inbox/gh-3873. Without these changes, showinf should throw an ArrayIndexOutOfBoundsException as described in the issues. With these changes, both files should initialize and display images without exception.

ImageJ may be the easiest way to test, as much of this data has small pixel values, so the images may be hard to check with just showinf. Composite color mode may also be useful to more closely match what LAS X shows. Screenshots of LAS X for comparison will be added to the forthcoming config PR.

I'd expect this to be OK for a patch release assuming tests continue to pass.

@sbesson sbesson self-requested a review August 16, 2024 14:52
Copy link
Member

@sbesson sbesson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Tested using the sample files uploaded as part of the corresponding issues.

Without this PR included, the reader initialization fails with an IndexOutOfBoundsException as described and any downstream workflows like importing into OMERO are broken.

With this PR included, the reader initialises without issue for both sample files and the images reading is consistent with the ground truth as shown in the LAS X software.

The nightly CI builds have been passing successfully for the last days with this PR included showing there are no apparent regression for other LIF sample files.

@sbesson sbesson added this to the 8.0.0 milestone Sep 2, 2024
@sbesson sbesson merged commit ce9031f into ome:develop Sep 2, 2024
18 checks passed
@melissalinkert melissalinkert deleted the lif-tile-fix-develop branch September 6, 2024 19:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

LIF Reader: index out of bounds LIF: ArrayIndexOutOfBoundsException when parsing offsets
2 participants