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

Add modulo support for LI-FLIM data #1164

Merged
merged 2 commits into from Jul 4, 2014

Conversation

melissalinkert
Copy link
Member

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/12290. Phase and frequency dimensions in LI-FLIM files are now stored in the appropriate Modulo annotation, rather than being stored as separate series/Images.

To test, verify that QA 9236 has two Images when imported - the first should contain 12 planes (for 12 phases), and the second should contain a single plane (the background image).

I would suggest also checking other datasets from the data_repo/from_skyking/li-flim directory, as many of those files are also multi-phase/multi-frequency datasets which have now had their import behavior changed. In all cases, I would expect no more than 2 Images to appear after import.

Phases are added to ModuloT; frequencies are added to ModuloZ.  This is
consistent with how phases/frequencies are handled in other formats.

Fixes #12290.
The series count is now at most 2, so extra bookkeeping to divide
primary images from background images is not necessary.
@joshmoore
Copy link
Member

Relaunched travis (connection reset to maven central)

@mtbc
Copy link
Member

mtbc commented Jun 19, 2014

One query: for from_skyking/li-flim/samples/sample-extended.fli the primary image looks in Insight to have 12 × Z, 5 × T, 12 × t where, for constant T and t, the different Z all look the same. (The background image's 12 × Z look different.) Is that okay?

The 12 planes of QA 9236's primary image come through as 12 × t, so apart from the above query this looks good to merge.

@melissalinkert
Copy link
Member Author

If I open sample-extended.fli in ImageJ, the Z sections are definitely distinct. You might need to zoom in and fiddle with the rendering settings though - there are no identifiable objects in these images and the min/max range is large enough that it's easy not to spot the difference between planes.

@mtbc
Copy link
Member

mtbc commented Jul 4, 2014

@pwalczysko, could you see if you can see a difference on Z for constant T, t? The image is on trout under read-only-1 user-2 in dataset mtbc-pr-1164 as image ID 33551.

(@melissalinkert: I don't know if the CI jobs already reassure that there has been no regression here.)

@pwalczysko
Copy link
Member

Looks like an Insight bug. @mtbc is filing a ticket, thanks.

@mtbc
Copy link
Member

mtbc commented Jul 4, 2014

So, this PR is good to merge.

melissalinkert added a commit that referenced this pull request Jul 4, 2014
Add modulo support for LI-FLIM data
@melissalinkert melissalinkert merged commit d97529d into ome:develop Jul 4, 2014
@melissalinkert
Copy link
Member Author

--rebased-to #1197

@melissalinkert melissalinkert deleted the liflim-modulo branch September 26, 2014 13:35
@sbesson sbesson added this to the 5.1.0-m1 milestone Oct 14, 2014
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

5 participants