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Task #4168 (closed)

Opened 9 years ago

Closed 8 years ago

BUG: Slidebook pixel data is not always correct

Reported by: mlinkert Owned by: mlinkert
Priority: blocker Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: marjolijnmertz@…, bopohob@…, glenmac@…, vbindoka@…, kris@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-06-19 (17)

Description

See files in data/slidebook/marjolijn, data/slidebook/roman and data/slidebook/glen/Loci sld/.

Change History (57)

comment:1 Changed 9 years ago by jmoore

imported from bio-formats:#592

comment:2 Changed 9 years ago by mlinkert

  • Keywords sprint-1 removed
  • Remaining Time set to 3
  • Sprint set to 2011-02-10 (5)

comment:3 Changed 9 years ago by mlinkert

  • Status changed from new to accepted

comment:4 Changed 9 years ago by mlinkert

  • Remaining Time changed from 3 to 2.5

comment:5 Changed 9 years ago by mlinkert

  • Remaining Time changed from 2.5 to 2

comment:6 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [d77992b7d0d6d4e2929b7e53ee9f6f6f34d9da72/bioformats.git]) Fixed Slidebook reader so that most spool files can be opened again.

See #4168.

comment:7 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [fe7039413747b5a240e0dcb314a3053d07e917fa/bioformats.git]) A few more fixes to Slidebook pixel reading. See #4168.

comment:8 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [b605a01ae92752c5ff5464380f1ef33c81901cd2/bioformats.git]) Yet another fix for Slidebook pixel data reading. See #4168.

comment:9 Changed 9 years ago by mlinkert

  • Remaining Time changed from 2 to 1.5

comment:10 Changed 9 years ago by jburel

  • Sprint changed from 2011-02-10 (5) to 2011-02-24 (6)

Moved from sprint 2011-02-10 (5)

comment:11 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [aa6ad8695b97addf5f45c2f0d5388b46e080e761/bioformats.git]) One more X/Y dimension fix in Slidebook reader. See #4168.

comment:12 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [ce3406ef97977f37913d59a5579e613624c86590/bioformats.git]) One of many necessary fixes to the Slidebook reader's pixel data offset logic.

See #4168.

comment:13 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [d77992b7d0d6d4e2929b7e53ee9f6f6f34d9da72/bioformats.git]) Fixed Slidebook reader so that most spool files can be opened again.

See #4168.

comment:14 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [fe7039413747b5a240e0dcb314a3053d07e917fa/bioformats.git]) A few more fixes to Slidebook pixel reading. See #4168.

comment:15 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [b605a01ae92752c5ff5464380f1ef33c81901cd2/bioformats.git]) Yet another fix for Slidebook pixel data reading. See #4168.

comment:16 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [aa6ad8695b97addf5f45c2f0d5388b46e080e761/bioformats.git]) One more X/Y dimension fix in Slidebook reader. See #4168.

comment:17 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [ce3406ef97977f37913d59a5579e613624c86590/bioformats.git]) One of many necessary fixes to the Slidebook reader's pixel data offset logic.

See #4168.

comment:18 Changed 9 years ago by mlinkert

  • Remaining Time changed from 1.5 to 1.0

comment:19 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [317ea420c373281c323af709d9759525f6d8808a/bioformats.git]) Removed XY dimension calculation hack, in which X == Y == sqrt(plane size).

See #4168.

comment:20 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [a0a3b1d2c00f8752132b301359f7218e6bb5b445/bioformats.git]) Fix for 2-channel files whose SizeX is too large.

See #4168.

comment:21 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [aba505a064feafc1a5b798b33330da58d1ecb7f1/bioformats.git]) Fixed various problems with reading > 2 GB spool files.

See #4168.

comment:22 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [317ea420c373281c323af709d9759525f6d8808a/bioformats.git]) Removed XY dimension calculation hack, in which X == Y == sqrt(plane size).

See #4168.

comment:23 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [a0a3b1d2c00f8752132b301359f7218e6bb5b445/bioformats.git]) Fix for 2-channel files whose SizeX is too large.

See #4168.

comment:24 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [aba505a064feafc1a5b798b33330da58d1ecb7f1/bioformats.git]) Fixed various problems with reading > 2 GB spool files.

See #4168.

comment:25 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [0372066139a51d61ea431128ee0bc791e809a6f0/bioformats.git]) Better Z size calculation for 4D and 5D datasets.

See #4168.

comment:26 Changed 9 years ago by mlinkert

  • Remaining Time changed from 1.0 to 0.6

comment:27 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [0372066139a51d61ea431128ee0bc791e809a6f0/bioformats.git]) Better Z size calculation for 4D and 5D datasets.

See #4168.

comment:28 Changed 9 years ago by jburel

  • Sprint changed from 2011-02-24 (6) to 2011-03-10 (7)

Moved from sprint 2011-02-24 (6)

comment:29 Changed 9 years ago by mlinkert

  • Owner mlinkert-x deleted
  • Status changed from accepted to new

comment:30 Changed 9 years ago by mlinkert

  • Owner set to mlinkert-x

comment:31 Changed 9 years ago by jburel

  • Sprint changed from 2011-03-10 (7) to 2011-03-24 (8)

Moved from sprint 2011-03-10 (7)

comment:32 Changed 9 years ago by mlinkert

  • Sprint 2011-03-24 (8) deleted

comment:33 Changed 9 years ago by mlinkert

  • Sprint set to 2011-04-21 (10)

comment:34 Changed 9 years ago by mlinkert

  • Sprint changed from 2011-04-21 (10) to 2011-05-05 (11)

comment:35 Changed 9 years ago by mlinkert

  • Sprint changed from 2011-05-05 (11) to 2011-05-19 (12)

comment:36 Changed 9 years ago by mlinkert

  • Summary changed from Slidebook pixel data is not always correct to BUG: Slidebook pixel data is not always correct

comment:37 Changed 9 years ago by mlinkert

  • Sprint changed from 2011-05-19 (12) to 2011-06-02 (13)

comment:38 Changed 9 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3 to OME-5.0
  • Priority changed from critical to major
  • Remaining Time 0.6 deleted
  • Sprint 2011-06-02 (13) deleted

A lot of progress has been made on this, but there are still a couple of files that don't open correctly. We're in the process of receiving some additional information that, once reviewed, will make it much easier to sort out the Slidebook pixel data problems once and for all. Unfortunately, that's not going to happen until well after the 4.3 release deadline.

comment:39 Changed 8 years ago by mlinkert

  • Cc kris@… added

comment:40 Changed 8 years ago by mlinkert

  • Sprint set to 2012-01-17 (6)

comment:41 Changed 8 years ago by mlinkert

  • Remaining Time set to 5

comment:42 Changed 8 years ago by jburel

  • Sprint changed from 2012-01-17 (6) to 2012-01-31 (7)

Referencing ticket #7716 has changed sprint.

comment:43 Changed 8 years ago by jmoore

  • Sprint changed from 2012-01-31 (7) to 2012-02-14 (8)

Moved from sprint 2012-01-31 (7)

comment:44 Changed 8 years ago by jburel

  • Sprint changed from 2012-02-14 (8) to 2012-02-28 (9)

Moved from sprint 2012-02-14 (8)

comment:45 Changed 8 years ago by jburel

  • Sprint changed from 2012-02-28 (9) to 2012-03-13 (10)

Moved from sprint 2012-02-28 (9)

comment:46 Changed 8 years ago by jburel

  • Sprint changed from 2012-03-13 (10) to 2012-03-27 (11)

Moved from sprint 2012-03-13 (10)

comment:47 Changed 8 years ago by jburel

  • Sprint changed from 2012-03-27 (11) to 2012-04-10 (12)

Moved from sprint 2012-03-27 (11)

comment:48 Changed 8 years ago by mlinkert

  • Remaining Time changed from 5 to 2

This is a lot closer to being ready with recent commits on https://github.com/melissalinkert/bioformats/tree/slidebook

There are still a few directories that need attention:

  • jcb
  • kate
  • roman
  • vytas

comment:49 Changed 8 years ago by jburel

  • Sprint changed from 2012-04-10 (12) to 2012-04-24 (13)

Moved from sprint 2012-04-10 (12)

comment:50 Changed 8 years ago by jburel

  • Sprint changed from 2012-04-24 (13) to 2012-05-08 (14)

Moved from sprint 2012-04-24 (13)

comment:51 Changed 8 years ago by jburel

  • Sprint changed from 2012-05-08 (14) to 2012-05-22 (15)

Moved from sprint 2012-05-08 (14)

comment:52 Changed 8 years ago by mlinkert

  • Remaining Time changed from 2 to 1.5

(A new build is not yet available; the amount of time to completion is just being reduced to reflect recent progress.)

comment:53 Changed 8 years ago by jburel

  • Sprint changed from 2012-05-22 (15) to 2012-06-05 (16)

Moved from sprint 2012-05-22 (15)

comment:54 Changed 8 years ago by mlinkert

  • Priority changed from major to blocker

Increasing priority; a new build with these fixes is not yet available.

comment:55 Changed 8 years ago by jburel

  • Sprint changed from 2012-06-05 (16) to 2012-06-19 (17)

Moved from sprint 2012-06-05 (16)

comment:56 Changed 8 years ago by mlinkert

  • Remaining Time changed from 1.5 to 0.5

Tons of progress made with this commit:

https://github.com/melissalinkert/bioformats/commit/013826bf4f50f4bf28e0f7c5bf73bd561d254ecc

A new build is not yet available, but we're now in the home stretch and shouldn't have much trouble to get the rest of the testing sorted out later in the day on Wednesday.

comment:57 Changed 8 years ago by mlinkert

  • Remaining Time changed from 0.5 to 0
  • Resolution set to fixed
  • Status changed from new to closed

New build not available, but should now all be sorted out for the upcoming 4.4 release.

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