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Task #6099 (closed)

Opened 13 years ago

Closed 12 years ago

Some JPEG-2000 files do not open correctly

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: klinedd@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-06-05 (16)

Description

See data/jpeg2000/david/multichannel-2d test.jp2. This is a 12-bit, 3 channel file - it opens correctly in ImageMagick?, but opens very incorrectly in Bio-Formats. The min/max pixel values are reported as 0-1280, 1-1241, and 1-65535; the red and green channels are subtly incorrect (should be ~146-1476 and ~181-2054, respectively), but the blue channel is very wrong (should be ~160-2088) as there is no way that a 12-bit image should have pixel values greater than 4095.

Bio-Formats is picking up the correct channel count and bit depth, so I suspect that this is something broken deep inside JAI.

Change History (6)

comment:1 Changed 13 years ago by mlinkert

  • Cc klinedd@… added

comment:2 Changed 13 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3.2 to OME-5.0

comment:3 Changed 12 years ago by mlinkert

  • Remaining Time set to 0.001
  • Sprint set to 2012-05-08 (14)
  • Status changed from new to accepted

Fixed with: ​https://github.com/melissalinkert/bioformats/commit/57af1d2ba9227c860f91e5d5070386629fa7b14f

A new build that contains the fix is not yet available.

comment:4 Changed 12 years ago by jburel

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

Moved from sprint 2012-05-08 (14)

comment:5 Changed 12 years ago by jburel

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

Moved from sprint 2012-05-22 (15)

comment:6 Changed 12 years ago by mlinkert

  • Remaining Time changed from 0.001 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

Fixed in latest build.

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