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Task #2372 (closed)

Opened 9 years ago

Closed 9 years ago

Bug:importing OME-TIFF

Reported by: jburel Owned by: cxallan
Priority: blocker Milestone: OMERO-Beta4.2
Component: Import Version: n.a.
Keywords: n.a. Cc: mlinkert, ajpatterson, bwzloranger
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2010-06-10 (11)

Description

4d-series.ome.tif

    ome.formats.importer.gui.GuiImporter  - java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:546)
	at java.util.ArrayList.get(ArrayList.java:321)
	at ome.xml.r201004.Pixels.getChannel(Pixels.java:473)
	at loci.formats.ome.OMEXMLMetadataImpl.getChannelSamplesPerPixel(OMEXMLMetadataImpl.java:943)

Change History (11)

comment:1 Changed 9 years ago by cxallan

  • Status changed from new to assigned

comment:2 Changed 9 years ago by cxallan

  • Owner changed from bwzloranger to cxallan
  • Status changed from assigned to new

comment:3 Changed 9 years ago by wmoore

Just in case this isn't the same bug - here's the "Debug Text" when I tried to import the ome-tiffs from test-images-good

2010-05-25 09:27:44,428 101006     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Creating root!
2010-05-25 09:27:44,957 101535     [entQueue-0] INFO   me.formats.importer.gui.FileQueueHandler  - Scheduling candidate calculations(3)=[/Users/will/Documents/biology-data/test_images_good/multi_ome-tif]
2010-05-25 09:27:44,958 101536     [1-thread-1] INFO   me.formats.importer.gui.FileQueueHandler  - Background: calculating candidates(3)=[/Users/will/Documents/biology-data/test_images_good/multi_ome-tif]
2010-05-25 09:27:44,958 101536     [1-thread-1] INFO      ome.formats.importer.ImportCandidates  - Depth: 4 Metadata Level: MINIMUM
2010-05-25 09:27:44,961 101539     [1-thread-1] ERROR     ome.formats.importer.ImportCandidates  - Error on ome.formats.importer.gui.FileQueueHandler[,0,0,1195x626,invalid,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=] with ome.formats.importer.ImportCandidates$SCANNING@5db507
2010-05-25 09:27:44,995 101573     [1-thread-1] DEBUG  importer.gui.ErrorHandler$MyErrorHandler  - UNKNOWN_FORMAT: /Users/will/Documents/biology-data/test_images_good/multi_ome-tif/test_setup.ini
2010-05-25 09:27:45,663 102241     [1-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - FILE_EXCEPTION: /Users/will/Documents/biology-data/test_images_good/multi_ome-tif/tubhiswt_C1.ome.tif
2010-05-25 09:27:45,665 102243     [1-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-05-25 09:27:45,665 102243     [1-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-05-25 09:27:45,762 102340     [1-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - FILE_EXCEPTION: /Users/will/Documents/biology-data/test_images_good/multi_ome-tif/tubhiswt_C2.ome.tif
2010-05-25 09:27:45,786 102364     [1-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-05-25 09:27:45,787 102365     [1-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-05-25 09:27:45,817 102395     [1-thread-1] DEBUG  me.formats.importer.gui.FileQueueHandler  - SCANNING: Depth:0 Num:    4 Tot:    4 File: od/multi_ome-tif
2010-05-25 09:27:45,817 102395     [1-thread-1] INFO      ome.formats.importer.ImportCandidates  - 4 file(s) parsed into 0 group(s) with 3 call(s) to setId in 746ms. (859ms total) [1 unknowns]
2010-05-25 09:27:45,820 102398     [entQueue-0] INFO   me.formats.importer.gui.FileQueueHandler  - Handling import containers(3)=[/Users/will/Documents/biology-data/test_images_good/multi_ome-tif]
2010-05-25 09:28:13,377 129955     [3-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - KeepAlive ping

comment:4 Changed 9 years ago by cxallan

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

comment:5 Changed 9 years ago by cxallan

(In [7126]) Updating to ​bio-formats:r6414; general OME-XML and OME-TIFF changes. (See #2372, #2376)

comment:6 Changed 9 years ago by cxallan

(In [7160]) Updating to ​bio-formats:r6440; fixes for OME-TIFF (See #2372)

comment:7 Changed 9 years ago by cxallan

  • Cc mlinkert-x ajpatterson bwzloranger added; cxallan removed
  • Status changed from new to assigned

After upgrade to ​bio-formats:r6440 in r7160 and the addition of Xalan JARs to the CLASSPATH in r7161 we've got one failing file:

2010-06-02 16:45:36,854 125115     [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - FILE_EXCEPTION: /Users/Zapgun/Documents/_Work/data_repo/test_images_good/ome-tiff/8x binning int 125x50 286fps_1.ome.tif
loci.formats.FormatException: loci.common.services.ServiceException: java.lang.NumberFormatException: For input string: "4294967295"
        at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:251)
        at loci.formats.FormatReader.setId(FormatReader.java:1066)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:220)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:240)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:426)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:367)
        at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
        at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
        at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:637)
Caused by: loci.common.services.ServiceException: java.lang.NumberFormatException: For input string: "4294967295"
        at loci.formats.services.OMEXMLServiceImpl.createRoot(OMEXMLServiceImpl.java:218)
        at loci.formats.services.OMEXMLServiceImpl.createOMEXMLMetadata(OMEXMLServiceImpl.java:170)
        at loci.formats.services.OMEXMLServiceImpl.createOMEXMLMetadata(OMEXMLServiceImpl.java:162)
        at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:245)
        ... 21 more
Caused by: java.lang.NumberFormatException: For input string: "4294967295"
        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
        at java.lang.Integer.parseInt(Integer.java:461)
        at java.lang.Integer.valueOf(Integer.java:554)
        at ome.xml.r201004.Channel.update(Channel.java:195)
        at ome.xml.r201004.Channel.<init>(Channel.java:147)
        at ome.xml.r201004.Pixels.update(Pixels.java:257)
        at ome.xml.r201004.Pixels.<init>(Pixels.java:144)
        at ome.xml.r201004.Image.update(Image.java:326)
        at ome.xml.r201004.Image.<init>(Image.java:141)
        at ome.xml.r201004.OME.update(OME.java:237)
        at ome.xml.r201004.OME.<init>(OME.java:126)
        at loci.formats.services.OMEXMLServiceImpl.createRoot(OMEXMLServiceImpl.java:213)
        ... 24 more

comment:8 Changed 9 years ago by cxallan

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

comment:9 Changed 9 years ago by cxallan

(In [7293]) Updating to ​bio-formats:r6540; update to 2010-06 schema OME-XML translation. (See #2372, #2376)

comment:10 Changed 9 years ago by cxallan

(In [7296]) Removed Experimenter and ExperimenterGroup? object population from the client side metadata store; resolves OME-XML related issues. (See #2372, #2376)

comment:11 Changed 9 years ago by cxallan

  • Remaining Time set to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [7297]) Updating to ​bio-formats:r6548; final version of 2010-06 aware Bio-Formats JARs. (Fixes #2372, #2376)

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