Task #13112 (closed)
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
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.
Still planning to fix this before the end of March.