Task #11873 (closed)
Bug: ND2Reader IndexOutOfBoundsException
| Reported by: | omero-qa | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | 5.0.3 |
| Component: | Bio-Formats | Version: | 4.4.9 |
| Keywords: | ND2Reader | Cc: | lindsay.strotman@… |
| Resources: | n.a. | Referenced By: | https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7799/
% SCIFIO_DEVEL=1 CLASSPATH=./artifacts/loci_tools.jar ./tools/showinf ~/Desktop/7799/Patient\ 67\ from\ 20130812.nd2
Checking file format [Nikon ND2]
Initializing reader
ND2Reader initializing /ome/apache_repo/7799/Patient 67 from 20130812.nd2
Searching for blocks
Parsing block 'ND2 FILE SIG' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageTextInf' 0%
Parsing block 'CustomDataVa' 99%
Parsing block 'ImageAttribu' 99%
Parsing block 'CustomData|A' 99%
Parsing block 'ND2 FILEMAP ' 99%
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:604)
at java.util.ArrayList.get(ArrayList.java:382)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:891)
at loci.formats.FormatReader.setId(FormatReader.java:1360)
at loci.formats.DelegateReader.setId(DelegateReader.java:267)
at loci.formats.ImageReader.setId(ImageReader.java:781)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:993)
at loci.formats.tools.ImageInfo.main(ImageInfo.java:1075)
Change History (6)
comment:1 Changed 10 years ago by rleigh
- Component changed from from QA to Bio-Formats
- Priority changed from minor to major
comment:2 Changed 10 years ago by rleigh
comment:3 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.3
comment:4 Changed 10 years ago by jamoore
- Referenced By set to https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats
comment:5 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:6 Changed 10 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [118f20690d01d8c9e14109c8ee124ddfed1ba90f/bioformats.git] on branch develop) ND2: do not skip bytes at the end of text info blocks
Fixes #11873.
Note: See
TracTickets for help on using
tickets.
You may also have a look at Agilo extensions to the ticket.
Same exception on dev_4_4:
% LOCI_DEVEL=1 SCIFIO_DEVEL=1 CLASSPATH=./artifacts/loci_tools.jar /ome/apache_repo/7799/Patient\ 67\ from\ 20130812.nd2 Checking file format [Nikon ND2] Initializing reader Searching for blocks Parsing block 'ND2 FILE SIG' 0% Parsing block 'ImageCalibra' 0% Parsing block 'ImageMetadat' 0% Parsing block 'ImageTextInf' 0% Parsing block 'CustomDataVa' 99% Parsing block 'ImageAttribu' 99% Parsing block 'CustomData|A' 99% Parsing block 'ND2 FILEMAP ' 99% Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:604) at java.util.ArrayList.get(ArrayList.java:382) at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:888) at loci.formats.FormatReader.setId(FormatReader.java:1244) at loci.formats.DelegateReader.setId(DelegateReader.java:259) at loci.formats.ImageReader.setId(ImageReader.java:727) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1018) at loci.formats.tools.ImageInfo.main(ImageInfo.java:1063)