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2011-03-10 Thursday Meeting

Attending: Brian, Jason, Scott, Colin, Simon, Chris, Jean-Marie, Will, Ola, Melissa, Josh, Carlos, Andrew

Agenda

Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Welcome to Simon Wells

    • Sort out contact info

  2. Accepting minutes from last meeting

  3. Matters Arising (<10 mins)

    • Everyone: Go through the remainer of the unassigned bugs. See: Bug Query
    • Andrew: Send reminder about unassigned bugs
    • Chris: respond to 'connot query LDAP' email - send 'ldap query' documentation - UNKNOWN
    • Changes coming to the infrastructure for hudson/squig/VMs, if you have requrests/changes, speak up!
    • Andrew: Send Jerome the leaflet so he can print out before Tuesday
    • Andrew: For Tuesday: Discuss downgrade transforms. Do they moved to be moved due to licensing
      • Curtis: These should probably live in the java

  4. OMERO 4.1 Web Backport Report (15 mins)

  5. Big Images Report (15 mins)

  6. Generating sprint # (30 mins)

    • What New Tasks were added to old sprint
    • What Tasks are left in old sprint
    • Make new sprint
    • Estimates
    • Close old sprint and move other tasks into new sprint

  7. Email and Forum Review - checked at 12:30 (5 mins)

    • Email -

      • Jerome Avondo - [ome-devel] Python Script: Copy all metadata from one Image to another.
      • Russel - Re: [ome-devel] XMLAnnotations from python (PATCH)

    • Forums -

    • QA -
      link 

      ID  Status  User/email  Type    Created Selected file   Comment Error
3623    new m.tark@uva.n... Insight 4.2.2   2011 03 03  -   -   java.lang.Exception: org....
3622    new unknown Insight 4.3-DEV 2011 03 02  -   -   java.lang.Exception: org....
3621    new harri.jaalin... Importer 4.2.2-r871 2011 03 02  ...--Y02--T0000--Z00--C00.ome.tif   Here's a file that causes prob...   java.lang.NullPointerExce...
3249    new ed@mechanoch... Insight 4.2.2   2011 03 01  -   Running makemovie script    java.lang.Exception: java...

  8. Any other business (<5 mins)

In Attendance

Brian, Jason, Scott, Colin, Simon, Chris, Jean-Marie, Will, Ola, Melissa, Josh, Carlos, Andrew

Notes

  1. Welcome to Simon Wells

    • Sort out contact info - Working on it!

  2. Accepting minutes from last meeting - APPROVED

  3. Matters Arising (<10 mins)

    • Everyone: Go through the remainer of the unassigned bugs. See: Bug Query
      • Still two without owner - have a look!
    • Andrew: Send reminder about unassigned bugs - DONE
    • Chris: respond to 'connot query LDAP' email - send 'ldap query' documentation - REPLIED (awaiting reply)
    • Changes coming to the infrastructure for hudson/squig/VMs, if you have requrests/changes, speak up!
      • Awaiting new hardware
    • Andrew: Send Jerome the leaflet so he can print out before Tuesday
      • Jason: Also a lot of links we can send his way
      • Andrew: leaflet is sent as PDF, waiting for reply
      • Tuesday 2:30 Jerome will present again
    • Andrew: For Tuesday: Discuss downgrade transforms. Do they moved to be moved due to licensing
      • Curtis: These should probably live in the java
      • Stylesheets need to also be available (BSD) in order to encourage uptake
        • Jason: Take the low level code file opening code in BF and move to BSD license
          • Logic is for imageJ file opening, BF will work better and is common architecture
          • Melissa: Also want to be able to move ome-tiff reader into BSD so it can be imbedded into ImageJ
            • Jason: Still some details to work out here, encouraged Curtis to be concrete
            • JMB: This is what Curtis will cover, put code in a branch for us to see
            • JMB: Question is where will the stylesheets live? BSD or GPL (doesn't need answer right now)

  4. OMERO 4.1 Web Backport Report (15 mins)

    • Carlos: Many headed beast, is this OMEROWeb on 4.1? Yes
    • Carlos: Continuous backport is being done weekly, nothing major right now (some major changes coming in the future)
      • Webclient/admin backport being worked on by Ola/Will
      • JMB: Still have screen acquision concept in 4.1? Yes
      • Carlos: Huge list of stuff need to discuss with Ola + JMB
        • Jason: Can happen at Web meeting on Tuesday
        • JMB: will find the fake structure I used previously
    • Josh: Would like to find out about webclient/admin being backported to 4.1
      • Have copied all of OMERO.web over to 4.1 and generated tickets accordingly
      • Carlos: Ola should talk to Josh about getting a full web client on 4.1 (or not)
        • Or do we just need to make this work without fixes and new stuff coming in?
        • Ola: We didn't have the opportunity yet
      • Ola: concern of the deadline
        • Josh: Have had some 4.1 web stuff 'in the wild'. Need minimal funcationality from webAdmin
          • Biggest problem is the group experimenter map differences
        • Ola: Can handle this, let me know timeframe.
          • Jason: Need plate view in webclient. How much work is it?
          • Ola: Few days for WebAdmin. Maximum 1 week. Perhaps 3 days.
          • Jason: Ola, Josh, Carlos have scope discussion after this meeting

  5. Big Images Report (15 mins)

    • Chris: since Tuesday have picked up where Donald left off
      • Investigate JP2000 capabilities for simplifying big images
      • Part 1: translating image data into JP2000 (mostly Jean-Marie)
        • Use bioformats as it exists for doing the testing ("real environment")
        • Didn't have support for custom JP2000 work (configuring tiles, compression aspects)
        • Have adjusted BF and using that infrastructure for testing those features
        • Tiling; Compression and/or resolution levels - levels of the image pyramids
        • Don't have to scale anything. Wavelets encode everything in one file.
        • Changes made to BF JP2000 Writer and the JAI library (since JVM comes with crippled support)
          • Adjusted writer
          • Adjusted library behind writer
          • Adjusted interaction to improve configuration
          • Not finished (80% done): only certain type/size of file supported
          • Still need to make this work with very very large files
          • May use openzoom, waiting to see on results of generating files
          • Problem is that we can only support level 1 JP2000s right now
        • also compressing JP2000
          • investigating tools for compressing files
          • GeoTools: subsectioning, tiling, compressing, ...
      • Part 2: reading JP2000 (70-75% done here) (Chris)
        • Couple good reference libraries been looking at for this (plenty of ISO standards here)
        • Need good/robust support for extracting metadata
        • Currently can't get to the data at the reader right now (have to go to low level library to do this)
          • Going to add this to the reader level
        • Performance: Very very good extraction, compression questionable
        • Hopefully by Friday should have complete flexible infrastructure for reading/writing
        • Based on what we end up using and how it performs, decide on what options we are going to use/keep
        • Note: Can't put multiple images in one JP2 file, will need something to aggrigrate N-dimensional data afterwards
          • Would be nice to have this work applied to all images on the server
        • Jason: Do we have good JP2000 data now? Melissa: SVS files (JP2000 wrapped in a tiff)
          • Chris: Not surprising, level 1 JP2 has no separation so SVS needs this setup, we will probably need something similar
          • Jason: Cloudpack guys are probably using level 3. Chris: This lets lots of n-dimensional stuff and better data-streaming
          • Chris: Screenshot there now with some testing functionality (and testcases listed on milestones page)

  6. Generating sprint # (30 mins)

    • (Reviewing Josh's Sprint Report)

      • Have a nice numerical burn down report, seems like a nice thing to add to the mid-sprint email out
      • Chris: Folks, be aware that putting huge estimates on tickets causes problems, better to estimate low and increasing it (or creating another ticket)
      • Chris: been pushing the documentation ticket for 5 sprints.
        • Question of priority, mad rush at the end of the sprint
        • If we're going to focus on it, but let's commit.

    • Making movies:

      • JMB: Making movies for insight importer for Scott to look at / review
      • Jason: Public is watching!

    • Everyone look at 'generic process' wiki page for process

    • What New Tasks were added to old sprint

    • What Tasks are left in old sprint

    • Make new sprint - DONE

    • Estimates

    • Close old sprint and move other tasks into new sprint

  7. Email and Forum Review - checked at 12:30 (5 mins)

    • Email -

      • Jerome Avondo - [ome-devel] Python Script: Copy all metadata from one Image to another.
        • Same as export, can do parts of this with create image functionality. Chris will look at this again
        • JMB: on par with ome-tiff functionality (Chris will review)
      • Russel - Re: [ome-devel] XMLAnnotations from python (PATCH)
        • Patch needs evaluation (Will reviewed)
        • Chris: version check around an implementation
          • Should not be doing this
          • Carlos: don't feel comfortable going back to specific branches
        • Will: nothing needs doing.
      • change groups
        • Has been requested several times
        • We previously said, "in progress"
        • No longer the case.
        • Also not in Martin's document

    • Forums -

    • QA -
      link 

      ID  Status  User/email  Type    Created Selected file   Comment Error
3623    new m.tark@uva.n... Insight 4.2.2   2011 03 03  -   -   java.lang.Exception: org....
3622    new unknown Insight 4.3-DEV 2011 03 02  -   -   java.lang.Exception: org....
3621    new harri.jaalin... Importer 4.2.2-r871 2011 03 02  ...--Y02--T0000--Z00--C00.ome.tif   Here's a file that causes prob...   java.lang.NullPointerExce...
3249    new ed@mechanoch... Insight 4.2.2   2011 03 01  -   Running makemovie script    java.lang.Exception: java...

  8. Any other business (<5 mins)

    • Java 1.6

      • At least two things popped up which are '1.6-only'. Need plan/consensus on when 1.5 no longer supported.
        • Chris: Would be nice to see which components we could move (server much easier)
        • Melissa: BF 1.5 only, few commits which are not. Some advantages to 1.6, not sure on support costs
        • Josh: 1.5 has been end-of-lifed, so no more backported fixes
          • Need to poll community
          • Jason: Agreed

    • New Start tasks now at http://www.openmicroscopy.org/site/team/process-summary#section-15

    • Desks in Dundee OME Room (only Dundee people required to participate)

    • Backport to 4.2

      • Josh: Everyone who wanted to respond to email, do so?
        • Carlos: Not yet… will handle offline

    • Jason: June 15th weekend confirmed for Paris

      • Josh: Keep in mind if we want core team to come earlier/leave later

Action Items

  • Simon: Add your contact info to the google doc
  • All: Two outstanding bugs without owners (#4545 #4626)
  • JMB: Review docs in #3941 for Colin
  • Goal for end of sprint: all tickets closed (nothing in backlog)
  • JMB: Attach insight importer movie for Scott
  • Chris: Respond to Jerome's email
  • Will: Respond to Russel's email
  • Will: write about changeGroups, saying look at our todos, give us a week to figure out where we are
  • Brian: Move QA ome.tiff file to qa file folder, test
  • Everyone: link visual materials on the milestone page
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