Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #12268 (closed)

Opened 10 years ago

Closed 9 years ago

Bug: bfconvert fails to save z sections other than zero

Reported by: rleigh Owned by: mlinkert
Priority: minor Milestone: 5.1.0
Component: Bio-Formats Version: 5.0.1
Keywords: n.a. Cc: Sabine.Fischer@…, l.maier@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

bfconvert -z 6 ~/code/bioformats-examples/cpp/glview/vessels.ome.tiff test.ome.tiff
/home/rleigh/code/bioformats-examples/cpp/glview/vessels.ome.tiff
OMETiffReader initializing /home/rleigh/code/bioformats-examples/cpp/glview/vessels.ome.tiff
Reading IFDs
Populating metadata
[OME-TIFF] -> test.ome.tiff [OME-TIFF]
Exception in thread "main" loci.formats.FormatException: Plane index:12 must be < 2
        at loci.formats.FormatWriter.checkParams(FormatWriter.java:325)
        at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:170)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:197)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:183)
        at loci.formats.FormatWriter.saveBytes(FormatWriter.java:126)
        at loci.formats.ImageWriter.saveBytes(ImageWriter.java:201)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:547)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:483)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:677)

The same applies to any section number other than zero. This is a 2C 144Z image, but appears to fail with any image with z>0. Tested with C=1, and still the same. Looks like the saved image isn't using indexes based from zero but might be using unconverted indexes from the source image?

Change History (2)

comment:1 Changed 10 years ago by rleigh

  • Cc l.maier@… added

comment:2 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.0
  • Resolution set to fixed
  • Status changed from new to closed
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.63759 sec.)

We're Hiring!