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Task #2321 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: LEI import problems

Reported by: omero-qa Owned by: cxallan
Priority: minor Milestone: OMERO-Beta4.2
Component: from QA Version: 4.1
Keywords: n.a. Cc: m.spitaler@…, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2010-06-24 (12)

Description

​http://qa.openmicroscopy.org.uk/qa/feedback/2424/

Comment: again, tried to import Leica SP2 files

java.lang.ArithmeticException: / by zero
	at loci.formats.FormatReader.getRGBChannelCount(FormatReader.java:478)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:395)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:364)
	at loci.formats.in.LeicaReader.initFile(LeicaReader.java:901)
	at loci.formats.FormatReader.setId(FormatReader.java:901)
	at loci.formats.ImageReader.setId(ImageReader.java:588)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:179)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:205)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:344)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:182)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:45)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:97)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)

Change History (14)

comment:1 Changed 9 years ago by cxallan

With the latest version of Bio-Formats in the Beta4.1 branch the exception is:

java.lang.IllegalArgumentException: Invalid series: 0
	at loci.formats.FormatReader.setSeries(FormatReader.java:638)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:414)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:364)
	at loci.formats.in.LeicaReader.initFile(LeicaReader.java:901)
	at loci.formats.FormatReader.setId(FormatReader.java:901)
	at loci.formats.ImageReader.setId(ImageReader.java:588)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:179)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:205)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:337)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:431)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:310)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:209)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:162)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:72)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:389)

comment:2 Changed 9 years ago by cxallan

  • Cc mlinkert-x added

comment:3 Changed 9 years ago by cxallan

  • Milestone changed from Unscheduled to OMERO-Beta4.2
  • Sprint set to 2010-04-30 (8)

comment:4 Changed 9 years ago by jmoore

  • Sprint changed from 2010-04-30 (8) to 2010-05-13 (9)

comment:5 Changed 9 years ago by bwzloranger

comment:6 Changed 9 years ago by bwzloranger

  • Owner changed from bwzloranger to cxallan

comment:7 Changed 9 years ago by cxallan

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

Based on the exception and the data in the QA system it appears that the LEI import was attempted without the corresponding TIFF files. Let us know if you're still experiencing this problem Martin. Closing as invalid, will re-open as necessary.

comment:8 Changed 9 years ago by cxallan

  • Resolution invalid deleted
  • Status changed from closed to reopened

New QA data from Martin:

​http://qa.openmicroscopy.org.uk/qa/feedback/2453/

Martin, can you get us the entire folder somehow? The QA system is failing to pick up the TIFFs and we can't reproduce without them.

Thanks!

-Chris

comment:9 Changed 9 years ago by cxallan

  • Sprint changed from 2010-05-13 (9) to 2010-05-27 (10)

comment:10 Changed 9 years ago by cxallan

  • Sprint changed from 2010-05-27 (10) to 2010-06-10 (11)

comment:11 Changed 9 years ago by jburel

  • Sprint changed from 2010-06-10 (11) to 2010-06-24 (12)

comment:12 Changed 9 years ago by jburel

error with latest version:

2010-06-29 13:28:53,360 26101      [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - Generic error while importing image.
java.lang.IllegalArgumentException: Invalid C size: 0
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:360)
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:321)
	at loci.formats.FormatReader.getZCTCoords(FormatReader.java:943)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:137)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:92)
	at loci.formats.in.LeicaReader.initFile(LeicaReader.java:569)
	at loci.formats.FormatReader.setId(FormatReader.java:1066)
	at loci.formats.ImageReader.setId(ImageReader.java:644)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:476)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:240)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:476)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:476)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:254)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:447)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:384)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)
	at java.lang.Thread.run(Thread.java:613)

comment:13 Changed 9 years ago by mlinkert

Should be fixed in ​bio-formats:r6597.

comment:14 Changed 9 years ago by cxallan

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

(In [7388]) Updating to ​bio-formats:r6600. (Fixes #2321)

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