2007-06-14 Project-wide 3:45 BST
Attending: Alexa, Andrew, Brian, Cat, Chris, Curtis, Jason, David
Agenda
Review of last project-wide ConferenceCall 2007-05-31 if necessary- News and Updates
- Bio-Formats status
- OME-XML Evolution status
- OMERO.server Beta2 Summary
- OMERO client Beta2 Summary
- Jean-Marie (in absentia)
- Fixed timeout problem related to thumbnail service.
- Fixed minor bugs reported by people here in Homburg.
- TODO: See big files issue reported during user sessions on tuesday. I will have a look at it asap.
- I put a new Beta 2 version of the client for testing users.openmicroscopy.org.uk/~jburel/build/build_macOSX/beta2 or users.openmicroscopy.org.uk/~jburel/build/build/beta2
- Jean-Marie (in absentia)
- Review of who is doing what
- Other
- Bob Freeman's issues (Josh)
Notes
- bio-formats
- maint. and bugfixes. release notes cover it.
- issues with email.
- added logging
- melissa half-time on ome-notes
- jrs: formats? cr: ?
- jrs: ? reformatting the webpage?
- cr: working on it as a whole reworking
- main thing we talked about was a level-of-supported with thermoeter graphic. work along with ome-xml.org. bioformats could definitely go on ome-xml.org. not visbio, etc.
- chris: issue 1
- problems merging things into loci.* Mostly solved
- reading tiffs. All ifd into memory. For Leica, large table consumes memory
- question: how do we handle this since everything depends on ifd's being read out.
- curtis: exclude list? so that they aren't parse. only if you don't need that info.
- brian: basically the color table.
- curtis: used?
- chris: don't know. brian: don't think we do.
- brian: and can we get it back after being excluded?
- curtis: do we need it?
- curtis: reason for long initialization is to make each plane short. (visualization use-case)
- brian: excludes are happy medium with lazy loading
- chris: threshold on the ifd's in memory with cache.
- curtis: worried about the complexity of caching (at several layers)
- chris: objectizing ifd?
- curtis: good idea. plus yes-or-no lazy. leave LRU to the application code.
- chris: if object hierarchy small, and have ifd factory then each app-dev can set things up as desired.
- curtis: makes sense. you taking a stab at it?
- chris: need to see how complicated. if too bad, just add exclude list (or based on size) @
- curtis: complicated
- brian: we really need it. should also help visbio.
- brian: problems with totally white channels
- curtis: try with command line and via imagej to see if it produces the same results
- brian: possibly due to omero's conversions
- brian: stk files. being supported?
- curtis: ask melissa
- jason: nd file support status
- brian: may be working. let me check @
- importer
- some optimizations re: TiffTools (openByte) couple of quirks
- all of the series stuff is working. tested with leica. Full leica support.
- stks working.
- not ome-xml working. need changes to our system. not as easy as expected.
- jason: priority xml or tiff?
- curtis: should be the same
- brian: correct
- beta2: leica, metamorphs, pics, lsms, dvs, full-tiffs (w/o raw file)
- server
- chris: whole bunch of IO optimizations. thumbnail retrieval and PGI calculations
- issue: if channel mapped to compound color. last kicker before beta2 to the world. @
- monday: successfully deployed omero in homburg (AIX 8cpus/16gigs ram)
- jason: problems with importing very large files (multi-gig)?
- brian: fixed a while ago. need to upgrade to beta2. there was no upgrade. will check with user.
- chris: upgrade should be relatively straightforward. just upgrade, but old clients should work (just don't download files). need new importers.
- chris: whole bunch of IO optimizations. thumbnail retrieval and PGI calculations
- clients
- package java clients together
- moving to web admin
- chris: for beta3 need shoola/insight more deployment friendly. (use built-in user directories. eases importer/insight deployment. dmgs and exe)
- then should be able to ship as dmg?
- jean-marie's summary
- donald's not here
- jason: cat, user comments for beta2 minor?
- cat: yes. roi's mostly.
- on schedule.
- release
- beta2 testing next week (Monday). on issues, wait on brian for thursday.
- beta2.1 in 2 weeks.
- misc
- need list of formats from lars. @
- ome-xml
- some feedback from chris and curtis. on the tiki
- next week is putting together website
- next week after that is putting together a validator (min. specs)
- curtis: validator in python? andrew: for integration...
- chris: goal is to get a command line script to validate xml and produce a report. then xslt to transform xml report into html. integrate into a turbogears application. bundle download: A) CLI validator or B) small turbogears that you can start up and visualize the report.
- curtis: sweet.
- feedback period is coming to an end.
- ome-xml.org a trac? Still plan? (python script can also be plugged into script)
- curtis: bioformats content to ome-xml.org?
- chris: then you lose a lot of the power of trac
- chris: use interwiki links.
"Every day is OME day" (T-shirt @)
- Alexa
- ldap: things working automatically without rewrites.
- adding trac page on server development doc deficienies
- Brian: 2.0 has WebAdmin release? documentation?
- David & CruiseControl
- two builds currently running
- slight difficulties due to svn:externals
- test reports are published
- email sent to a distribution list: josh, david, chris, alexa, brian?, jason?