search

ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
373 stars 241 forks source link

LIFReader: java.lang.IllegalArgumentException when calling openBytes on some multi-series lifext samples #3879

Open sbesson opened 1 year ago

sbesson commented 1 year ago

Using the public samples uploaded as part of the work on #3747, an error occurs when reading the binary data of the last series of the lif/dimension tests LIFs/XYZCS.lifext sample file (from series 16

showinf /uod/idr/repos/curated/leica-xlef-lof/public/lif/dimension\ tests\ LIFs/XYZCS.lifext -series 16
Checking file format [Leica Image File Format]
Initializing reader
LIFReader initializing /uod/idr/repos/curated/leica-xlef-lof/public/lif/dimension tests LIFs/XYZCS.lifext
Reading header
Finding image offsets
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Initialization took 0.22s

Java does not support display of unnormalized floating point data.
Please use the '-normalize' option to avoid receiving a cryptic exception.

Reading core metadata
filename = /uod/idr/repos/curated/leica-xlef-lof/public/lif/dimension tests LIFs/XYZCS.lifext
Series count = 28
Series #0 :

...
Series #27 :
    Image count = 2
    RGB = false (1) 
    Interleaved = false
    Indexed = true (false color)
    Width = 256
    Height = 1
    SizeZ = 1
    SizeT = 1
    SizeC = 2
    Tile size = 256 x 1
    Thumbnail size = 128 x 1
    Endianness = intel (little)
    Dimension order = XYCZT (certain)
    Pixel type = float
    Valid bits per pixel = 32
    Metadata complete = true
    Thumbnail series = false
    -----
    Plane #0 <=> Z 0, C 0, T 0
    Plane #1 <=> Z 0, C 1, T 0

Reading series #16 pixel data (0-9)
Exception in thread "main" java.lang.IllegalArgumentException
    at java.nio.Buffer.position(Buffer.java:244)
    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:650)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:494)
    at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:675)
    at loci.formats.in.LIFReader.openBytes(LIFReader.java:358)
    at loci.formats.FormatReader.openBytes(FormatReader.java:919)
    at loci.formats.ImageReader.openBytes(ImageReader.java:449)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86)
    at loci.formats.tools.ImageInfo.readPixels(ImageInfo.java:821)
    at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1055)
    at loci.formats.tools.ImageInfo.main(ImageInfo.java:1121)

The issue only affects the lifext file. The other lif files in this dataset are detected as multi-images which read without issue.

dgault commented 1 year ago

Another report of this issue was submitted via QA-32456, though it did not contain a sample file.

dgault commented 1 year ago

Two further reports of this issue have been received in Insight Bug-32574 and Insight Bug-32576. There were no sample files included with the bug reports.

The stack traces included with the reports differ from the one posted previously in this issue:

Parameters: {stacktrace=java.lang.IllegalArgumentException: newPosition > limit: (664733 > 664732)
    at java.base/java.nio.Buffer.createPositionException(Buffer.java:318)
    at java.base/java.nio.Buffer.position(Buffer.java:293)
    at java.base/java.nio.ByteBuffer.position(ByteBuffer.java:1094)
    at java.base/java.nio.ByteBuffer.position(ByteBuffer.java:262)
    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:650)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:494)
    at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:675)
    at loci.formats.in.LIFReader.openBytes(LIFReader.java:358)
    at loci.formats.ImageReader.openBytes(ImageReader.java:465)
    at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
    at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
    at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:872)
    at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:803)
    at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:676)
    at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:525)
    at omero.cmd.HandleI.steps(HandleI.java:448)
    at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)
    at omero.cmd.HandleI$2.doWork(HandleI.java:383)
    at omero.cmd.HandleI$2.doWork(HandleI.java:380)
    at jdk.internal.reflect.GeneratedMethodAccessor294.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    at com.sun.proxy.$Proxy81.doWork(Unknown Source)
    at ome.services.util.Executor$Impl.execute(Executor.java:447)
    at omero.cmd.HandleI.run(HandleI.java:379)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
    at ome.services.util.Executor$Impl$1.call(Executor.java:488)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
, message=newPosition > limit: (664733 > 664732)}