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Task #2374 (closed)

Opened 14 years ago

Closed 14 years ago

BUG: importing nrrd

Reported by: jburel Owned by: cxallan
Priority: critical Milestone: OMERO-Beta4.2
Component: Import Version: n.a.
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2010-05-13 (9)

Description

  • Select files in test_images_good/nrrd
  • File unreadable. I assume the files will be valid.

Change History (7)

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 mlinkert-x
  • Status changed from assigned to new

Exception with ​bio-formats:r6301:

2010-05-18 15:39:34,451 1008860    [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - I/O error while importing image.
java.io.FileNotFoundException: /Volumes/ome/data_repo/test_images_good/nrrd/average-goodbr (No such file or directory)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
        at loci.common.Location.getHandle(Location.java:196)
        at loci.common.Location.getHandle(Location.java:167)
        at loci.formats.ImageReader.getReader(ImageReader.java:148)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.in.NRRDReader.initFile(NRRDReader.java:259)
        at loci.formats.FormatReader.setId(FormatReader.java:1012)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
        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:213)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
        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)

comment:3 Changed 14 years ago by mlinkert

Should be fixed in ​bio-formats:r6333.

comment:4 Changed 14 years ago by cxallan

With ​bio-formats:r6340 there's now a file not found exception:

2010-05-19 08:09:04,404 34916      [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - I/O error while importing image.
java.io.FileNotFoundException: /Users/callan/testimages/nrrd/average-goodbrains-warp40-5_e1e-2.PIC (No such file or directory)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
        at loci.common.Location.getHandle(Location.java:196)
        at loci.common.Location.getHandle(Location.java:167)
        at loci.formats.ImageReader.getReader(ImageReader.java:148)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.in.NRRDReader.initFile(NRRDReader.java:257)
        at loci.formats.FormatReader.setId(FormatReader.java:1012)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
        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:213)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
        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)

comment:5 Changed 14 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan

comment:6 Changed 14 years ago by cxallan

Working fine with correct datasets. Missing files uploaded to test_images_good.

comment:7 Changed 14 years ago by cxallan

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