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Ticket #100 (closed task: fixed)

Opened 2010-06-22T12:04:13-05:00

Last modified 2013-06-07T15:37:54-05:00

Bio-Formats core library split

Reported by: curtis Owned by: curtis
Priority: critical Milestone: imagej2-b3-headless
Component: I/O Version:
Severity: non-issue Keywords:
Cc: Blocked By: #996
Blocking: #9, #101, #102, #1169, #1912

Description (last modified by curtis)

Bio-Formats needs to be split into two halves: 1) SCIFIO: the core API, metadata handling and standard file format readers; and 2) Bio-Formats: the microscopy file format readers.

The SCIFIO library will be BSD licensed, while Bio-Formats will remain GPL. This architecture will allow SCIFIO to become part of ImageJ2, as well as bundled with non-GPL libraries such as VisAD.

Change History

comment:1 Changed 2010-06-22T12:07:13-05:00 by curtis

  • Component changed from other to io

comment:2 Changed 2010-07-20T14:59:34-05:00 by curtis

  • Milestone changed from biweekly-2010: Jul-12 to Jul-23 to biweekly-2010: Jul-26 to Aug-06

comment:3 Changed 2010-08-06T18:06:58-05:00 by curtis

  • Milestone changed from biweekly-2010: Jul-26 to Aug-06 to biweekly-2010: Aug-09 to Aug-20

comment:4 Changed 2010-09-15T11:57:42-05:00 by curtis

  • Milestone changed from biweekly-2010: Sep-07 to Sep-17 to biweekly-2011: Jan-03 to Jan-14

comment:5 Changed 2010-12-09T13:37:11-06:00 by curtis

  • Priority changed from major to critical

comment:6 Changed 2011-02-15T09:34:14-06:00 by curtis

  • Milestone changed from biweekly-2011: Feb-14 to Feb-25 to biweekly-2011: Feb-28 to Mar-11

comment:7 Changed 2011-03-13T21:35:51-05:00 by curtis

  • Milestone changed from biweekly-2011: Feb-28 to Mar-11 to biweekly-2011: Mar-14 to Mar-25

comment:8 Changed 2011-03-28T10:41:11-05:00 by curtis

An initial split is committed to the bf-split branch. More work needs to be done to ensure things are working.

comment:9 Changed 2011-03-28T10:41:24-05:00 by curtis

  • Milestone changed from biweekly-2011: Mar-14 to Mar-25 to biweekly-2011: Mar-28 to Apr-08

comment:10 Changed 2011-04-25T11:25:34-05:00 by curtis

  • Milestone changed from biweekly-2011: Apr-11 to Apr-22 to biweekly-2011: May-23 to Jun-03

Still no time for this yet. Will be needed eventually for ImageJ core I/O though.

comment:11 Changed 2011-06-06T12:43:03-05:00 by curtis

  • Milestone changed from biweekly-2011: May-23 to Jun-03 to biweekly-2011: Jun-20 to Jul-01

comment:12 Changed 2011-07-27T14:50:23-05:00 by curtis

  • Milestone changed from biweekly-2011: Jul-18 to Jul-29 to imagej-2.0-beta1

comment:13 Changed 2011-10-18T14:43:40-05:00 by curtis

Initial version of the split is available in the scifio branch of bio-formats.git. The "scifio" component will be permissively licensed and provide the core I/O infrastructure, while the "bio-formats" component provides the proprietary file format (PFF) readers and is GPL-licensed.

The OME team is planning to discuss the SCIFIO project on next Tuesday, October 25. The plan is to merge the scifio branch onto develop and master after that, then proceed with some major refactoring of the SCIFIO and Bio-Formats projects. But once the initial merge and relicensing is complete, this ticket can be closed.

comment:14 Changed 2011-10-21T11:44:23-05:00 by curtis

See also  ome:#7076 for more on SCIFIO.

comment:15 Changed 2011-11-01T10:46:36-05:00 by curtis

  • Status changed from new to accepted

comment:16 Changed 2011-11-18T12:18:30-06:00 by curtis

Yesterday, the scifio branch was  merged to develop and  then to master. All that remains is to change the copyright blurbs.

comment:17 Changed 2012-02-23T14:43:51-06:00 by curtis

  • Blocking 9 added

comment:18 Changed 2012-02-24T13:38:23-06:00 by curtis

  • Blocking 102 added

comment:19 Changed 2012-02-24T13:39:09-06:00 by curtis

  • Blocking 101 added

comment:18 Changed 2012-02-27T11:09:12-06:00 by curtis

  • Blocked By 996 added

comment:19 Changed 2012-03-29T13:07:08-05:00 by curtis

  • Milestone changed from imagej-2.0-beta1 to imagej-2.0-beta2

Agreeing on the copyright blurb for SCIFIO is taking a very long time to sort out. Unfortunately, this ticket cannot be closed until that is done. Even though the split is done on the technical level, we cannot use SCIFIO as a separate BSD-licensed library in other tools (e.g., VisAD or ITK) until the license is fully sorted out.

For the ImageJ 2.0.0-beta1 release, we will need to add a blurb to the license explaining that while our intention is for the codebase to be BSD-licensed (and ImageJ2 itself is), the entire distribution is technically still a combined work licensed under GPLv2+, because of SCIFIO.

comment:20 Changed 2012-03-29T14:22:39-05:00 by curtis

  • Description modified

comment:21 Changed 2012-04-14T17:59:08-05:00 by curtis

I have submitted  a pull request that updates the licenses for all Bio-Formats and SCIFIO components.

comment:22 Changed 2012-05-14T10:18:47-05:00 by curtis

  • Blocking 1169 added

comment:23 Changed 2012-06-16T23:24:15-05:00 by curtis

  • Status changed from accepted to closed
  • Resolution set to fixed

The license updates have now been merged to the develop branch.

comment:24 Changed 2013-03-26T13:27:59-05:00 by curtis

See also  OME #7405.

comment:25 Changed 2013-06-05T15:10:38-05:00 by bdezonia

  • Blocking 1912 added; 9 removed

comment:26 Changed 2013-06-07T15:37:54-05:00 by curtis

  • Blocking 9 added

(In #9) This ticket is really about improving the infrastructure if I/O for ImageJ2. With SCIFIO, we have now done that. The 2.0.0-beta-7 release is using SCIFIO 0.1.0—File Open and File Save are now extensible—so this ticket is complete.

Remaining tickets about improving the existing I/O mechanism have been migrated to ticket #1920.