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Task #6159 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

Bug: Some Volocity datasets still do not open

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: OMERO-Beta4.3.2
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: dirk.dormann@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-08-04 (2)

Description

See example in data/volocity/dirk/. There should be many, many series (single-plane images), but instead we are given this lovely error message:

Exception in thread "main" java.lang.IllegalArgumentException: Invalid series: 0
	at loci.formats.FormatReader.setSeries(FormatReader.java:778)
	at loci.formats.in.VolocityReader.initFile(VolocityReader.java:547)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:670)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:953)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:986)

Change History (6)

comment:1 Changed 10 years ago by mlinkert

  • Cc dirk.dormann@… added

comment:2 Changed 10 years ago by mlinkert

  • Remaining Time set to 1.5
  • Sprint set to 2011-08-04 (2)

comment:3 Changed 10 years ago by Melissa Linkert <melissa@…>

  • Remaining Time changed from 1.5 to 0
  • Resolution set to fixed
  • Status changed from new to closed

(In [ad97205a55c6c922ace8961b47a7806cc8664e81/bioformats.git]) Aggregate all subviews into a single table.

Previously, subviews beyond the first were ignored, which is obviously
incorrect. Multiple subviews are present in table #1 of Volocity .mvd2
files when many (more than ~30) series are included in the dataset.
Ignoring subviews beyond the first means that essential metadata is
discarded, and so many (or even all) of the series will not be detected.

Closes #6159.

comment:4 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [ad97205a55c6c922ace8961b47a7806cc8664e81/bioformats.git]) Aggregate all subviews into a single table.

Previously, subviews beyond the first were ignored, which is obviously
incorrect. Multiple subviews are present in table #1 of Volocity .mvd2
files when many (more than ~30) series are included in the dataset.
Ignoring subviews beyond the first means that essential metadata is
discarded, and so many (or even all) of the series will not be detected.

Closes #6159.

comment:5 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [b09d051156c9caa3968ebfbc1c89b452f4de5504/bioformats.git]) Aggregate all subviews into a single table.

Previously, subviews beyond the first were ignored, which is obviously
incorrect. Multiple subviews are present in table #1 of Volocity .mvd2
files when many (more than ~30) series are included in the dataset.
Ignoring subviews beyond the first means that essential metadata is
discarded, and so many (or even all) of the series will not be detected.

Closes #6159.
(cherry picked from commit ad97205a55c6c922ace8961b47a7806cc8664e81)

comment:6 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [b09d051156c9caa3968ebfbc1c89b452f4de5504/bioformats.git]) Aggregate all subviews into a single table.

Previously, subviews beyond the first were ignored, which is obviously
incorrect. Multiple subviews are present in table #1 of Volocity .mvd2
files when many (more than ~30) series are included in the dataset.
Ignoring subviews beyond the first means that essential metadata is
discarded, and so many (or even all) of the series will not be detected.

Closes #6159.
(cherry picked from commit ad97205a55c6c922ace8961b47a7806cc8664e81)

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