Task #2372 (closed)
Opened 14 years ago
Closed 14 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 14 years ago by cxallan
- Status changed from new to assigned
comment:2 Changed 14 years ago by cxallan
- Owner changed from bwzloranger to cxallan
- Status changed from assigned to new
comment:3 Changed 14 years ago by wmoore
comment:4 Changed 14 years ago by cxallan
- Sprint changed from 2010-05-13 (9) to 2010-05-27 (10)
comment:5 Changed 14 years ago by cxallan
(In [7126]) Updating to bio-formats:r6414; general OME-XML and OME-TIFF changes. (See #2372, #2376)
comment:6 Changed 14 years ago by cxallan
(In [7160]) Updating to bio-formats:r6440; fixes for OME-TIFF (See #2372)
comment:7 Changed 14 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 14 years ago by cxallan
- Sprint changed from 2010-05-27 (10) to 2010-06-10 (11)
comment:9 Changed 14 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 14 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 14 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)
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