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 #12257 (new)

Opened 10 years ago

Last modified 8 years ago

netCDF cannot open certain large .ims files

Reported by: mlinkert Owned by:
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: 5.0.1
Keywords: ImarisHDFReader, hdf, netcdf Cc: l.maier@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See QA 9217 and ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-May/004407.html. Attempting to read the file throws an IllegalArgumentException? during setId, which is coming from deep within NetcdfFile?.open. This is a > 1GB file, but e have successfully opened larger .ims files so size alone is likely not the issue.

libhdf5 seems to read the file correctly - at least, 'h5ls' and 'h5dump' show more or less what I would expect.

Change History (1)

comment:1 Changed 8 years ago by mlinkert

  • Owner mlinkert deleted

See follow-up on parent ticket: ​https://trac.openmicroscopy.org/ome/ticket/9651#comment:1

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: 0.65597 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!