Task #10966 (closed)
Opened 11 years ago
Closed 11 years ago
Bug: CZI does not support multiple file reading
Reported by: | omero-qa | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | 5.0.0-beta1 |
Component: | Bio-Formats | Version: | n.a. |
Keywords: | n.a. | Cc: | lorenzmaier@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | FS demo 4.4 |
Description
Multi-file support does not appear to work correctly:
https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7271/
http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20130523/57117226/attachment.html
% CLASSPATH=artifacts/loci_tools.jar LOCI_DEVEL=1 ./tools/showinf /ome/apache_repo/7271/bioformats_multifile.czi Checking file format [Zeiss CZI] Initializing reader Unknown segment type: DELETED Unknown segment type: DELETED Unknown segment type: ZISRAWATTDIR Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.RangeCheck(ArrayList.java:547) at java.util.ArrayList.get(ArrayList.java:322) at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:386) at loci.formats.FormatReader.setId(FormatReader.java:1183) at loci.formats.ImageReader.setId(ImageReader.java:727) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:992) at loci.formats.tools.ImageInfo.main(ImageInfo.java:1035)
Change History (7)
comment:1 Changed 11 years ago by rleigh
- Component changed from from QA to Bio-Formats
comment:2 Changed 11 years ago by mlinkert
- Owner changed from mlinkert-x to mlinkert
comment:3 Changed 11 years ago by mlinkert
comment:4 Changed 11 years ago by rleigh
From Lorenz Maier:
I've just uploaded a new set of multi-file images (QA 7276, "Experiment-297.czi"), because even the original Zeiss "Zen blue" software has problems opening the first set of files since I renamed them to bioformats_multifile.czi.
The exception noted in Ticket 10966 remains the same as before.
I was already referring to the new set of files when I wrote to the mailing list about the expected dimensions.
On the QA site I've also tried to note this, but I get a "CSRF verification failed" message when I'm not logged in. I tried registering and logging in, but then it does not accept my password (on 2 accounts I tried).
comment:5 Changed 11 years ago by mlinkert
- Milestone changed from Unscheduled to OMERO-5
- Sprint set to FS Demo 4.3
comment:6 Changed 11 years ago by jburel
- Sprint changed from FS Demo 4.3 to FS demo 4.4
Moved from sprint FS Demo 4.3
comment:7 Changed 11 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
See https://github.com/openmicroscopy/bioformats/pull/562
The forthcoming 5.0.0-beta1 builds will contain these changes.
See also https://www.openmicroscopy.org/qa2/qa/feedback/7276/