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Task #12154 (closed)

Opened 10 years ago

Closed 10 years ago

Bug: units are not correctly parsed from Gatan .dm3 files

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: 5.0.2
Component: Bio-Formats Version: 5.0.0
Keywords: n.a. Cc: ngdias@…, levachevais@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-April/004319.html and QA 8007. The issue is that the reader uses the last stored units value when converting the scale values to micrometers, when it should use the units value stored immediately after the scale value(s) being used.

Change History (3)

comment:1 Changed 10 years ago by bramalingam

QA9172 reporting a similar issue : ​https://www.openmicroscopy.org/qa2/qa/feedback/9172/
Upload completes , but while trying to open an image insight suggests that it is an invalid image.

Warning from the Import log : 



2014-04-15 16:22:44,333 INFO  [              loci.formats.FormatHandler] (l.Server-6) Reading tags
2014-04-15 16:22:44,336 INFO  [              loci.formats.FormatHandler] (l.Server-6) Populating metadata
2014-04-15 16:22:44,336 WARN  [              loci.formats.FormatHandler] (l.Server-6) Not adjusting for unknown units: 
2014-04-15 16:22:44,337 DEBUG [                   loci.formats.Memoizer] (l.Server-6) skipping save memo. elapsed millis: 14
2014-04-15 16:22:44,337 DEBUG [                   loci.formats.Memoizer] (l.Server-6) start[1397575364323] time[13] tag[loci.formats.Memoizer.setId]

comment:2 Changed 10 years ago by bramalingam

  • Cc levachevais@… added

comment:3 Changed 10 years ago by mlinkert

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

Fixed with ​https://github.com/openmicroscopy/bioformats/pull/1079; a new build is not yet available, but this should be included in 5.0.2.

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