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Task #13112 (closed)

Opened 8 years ago

Closed 8 years ago

Last modified 8 years ago

BUG: Leica Lif reader (Pixel data for RGB stacks)

Reported by: bramalingam Owned by: mlinkert
Priority: minor Milestone: B-F-5.2.0
Component: Bio-Formats Version: BIo-Formats-5.1.5
Keywords: LIFReader, external, our-fault Cc: jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

ref: QA 16911,QA16919
https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7932&p=16426#p16426

Testing results:
1) Issue seen with opening thumbnails in ImageJ (after series0):

Reading header
Finding image offsets
Exception in thread "BioFormats-ThumbLoader" java.lang.ArrayIndexOutOfBoundsException: 4
	at loci.formats.FormatTools.openThumbBytes(FormatTools.java:1243)
	at loci.formats.FormatReader.openThumbBytes(FormatReader.java:941)
	at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
	at loci.formats.ChannelSeparator.openThumbBytes(ChannelSeparator.java:234)
	at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
	at loci.formats.DimensionSwapper.openThumbBytes(DimensionSwapper.java:255)
	at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
	at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
	at loci.formats.ReaderWrapper.openThumbBytes(ReaderWrapper.java:361)
	at loci.formats.gui.BufferedImageReader.openThumbImage(BufferedImageReader.java:100)
	at loci.plugins.in.ThumbLoader.loadThumb(ThumbLoader.java:133)
	at loci.plugins.in.ThumbLoader.run(ThumbLoader.java:115)
	at java.lang.Thread.run(Thread.java:745)

2) Issue seen with pixel data for images > series 0 (Multichannel images not stitched correctly)

Change History (3)

comment:1 Changed 8 years ago by mlinkert

  • Keywords LIFReader external our-fault added

Still planning to fix this before the end of March.

comment:2 Changed 8 years ago by mlinkert

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

comment:3 Changed 8 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [6f933af89d7a82f40cfa7d598ed296651f1d0bbe/bioformats.git] on branch develop) Leica LIF: fix multi-dimensional data from color cameras

Fixes #13112.

This fixes the case when a color camera is used (so each plane has 3 RGB
channels), and multiple channels are acquired potentially in addition to
multiple timepoints and/or Z sections.

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