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)
Welcome to Simon Wells
- Sort out contact info
Accepting minutes from last meeting
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
OMERO 4.1 Web Backport Report (15 mins)
Big Images Report (15 mins)
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
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 -
linkID 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...
Any other business (<5 mins)
- Java 1.6
- 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)
In Attendance
Brian, Jason, Scott, Colin, Simon, Chris, Jean-Marie, Will, Ola, Melissa, Josh, Carlos, Andrew
Notes
Welcome to Simon Wells
- Sort out contact info - Working on it!
Accepting minutes from last meeting - APPROVED
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)
-
Jason: Take the low level code file opening code in BF and move to BSD license
-
Everyone: Go through the remainer of the unassigned bugs. See: Bug Query
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
-
Josh: Have had some 4.1 web stuff 'in the wild'. Need minimal funcationality from webAdmin
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)
-
Chris: since Tuesday have picked up where Donald left off
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
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
-
Jerome Avondo - [ome-devel] Python Script: Copy all metadata from one Image to another.
Forums -
- Re: OMERO.web Basket - Ola sorted this
QA -
linkID 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...
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
-
At least two things popped up which are '1.6-only'. Need plan/consensus on when 1.5 no longer supported.
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
-
Josh: Everyone who wanted to respond to email, do so?
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