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Ticket #365 (closed defect: fixed)

Opened 2009-03-12T14:44:30-05:00

Last modified 2009-03-26T09:05:39-05:00

Error parsing MDB database files: exception in mdb_fetch_row

Reported by:	curtis	Owned by:	melissa
Priority:	major	Milestone:	~~bio-formats-4.1~~
Component:	bio-formats	Severity:	serious
Keywords:		Cc:	GMcNamara@…
Blocked By:		Blocking:

Description

When parsing MDB files, several exceptions are thrown:

curtis@monk:~$ showinf data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.lsm -debug
Debugging at level 1
Checking file format java.io.FileNotFoundException: /Users/curtis/data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.hdr (No such file or directory)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
        at loci.common.RAFile.<init>(RAFile.java:54)
        at loci.common.Location.getHandle(Location.java:152)
        at loci.common.RandomAccessStream.<init>(RandomAccessStream.java:108)
        at loci.formats.in.NiftiReader.isThisType(NiftiReader.java:86)
        at loci.formats.FormatReader.isThisType(FormatReader.java:759)
        at loci.formats.ImageReader.getReader(ImageReader.java:131)
        at loci.formats.ImageReader.getFormat(ImageReader.java:120)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:216)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:59)
        at loci.formats.tools.ImageInfo.main(ImageInfo.java:658)

[Zeiss Laser-Scanning Microscopy]
Initializing reader
java.io.FileNotFoundException: /Users/curtis/data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.hdr (No such file or directory)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
        at loci.common.RAFile.<init>(RAFile.java:54)
        at loci.common.Location.getHandle(Location.java:152)
        at loci.common.RandomAccessStream.<init>(RandomAccessStream.java:108)
        at loci.formats.in.NiftiReader.isThisType(NiftiReader.java:86)
        at loci.formats.FormatReader.isThisType(FormatReader.java:759)
        at loci.formats.ImageReader.getReader(ImageReader.java:131)
        at loci.formats.ImageReader.setId(ImageReader.java:581)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:248)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:59)
        at loci.formats.tools.ImageInfo.main(ImageInfo.java:658)

1236886485809: ZeissLSMReader: ZeissLSMReader.initFile(data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.lsm)
1236886485809: ZeissLSMReader: BaseTiffReader.initFile(data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.lsm)
1236886485809: ZeissLSMReader: MinimalTiffReader.initFile(data/zeiss-lsm/dan/2008-01-14-2channel-zstack.mdb/2channelzstack-noncompressed.lsm)
        Reading IFDs
        Populating metadata
        Removing thumbnails
        Reading LSM metadata
loci.common.ReflectException: Cannot execute method: mdb_fetch_row
        at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:296)
        at loci.formats.in.MDBParser.parseDatabase(MDBParser.java:158)
        at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:796)
        at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:867)
        at loci.formats.FormatReader.setId(FormatReader.java:327)
        at loci.formats.ImageReader.setId(ImageReader.java:581)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:248)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:59)
        at loci.formats.tools.ImageInfo.main(ImageInfo.java:658)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:291)
        ... 8 more
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at mdbtools.libmdb.Data.mdb_copy_ole(Data.java:876)
        at mdbtools.libmdb.Data.mdb_xfer_bound_ole(Data.java:462)
        at mdbtools.libmdb.Data._mdb_attempt_bind(Data.java:415)
        at mdbtools.libmdb.Data.mdb_read_row(Data.java:372)
        at mdbtools.libmdb.Data.mdb_fetch_row(Data.java:91)
        ... 12 more

Initialization took 0.837s

The data/zeiss-lsm/george/63x2x_GFP_ER-Tracker_11_z15um.lsm dataset generates similar exceptions.

Change History

comment:1 Changed 2009-03-12T14:50:19-05:00 by curtis

Milestone set to bio-formats-4.1.0

comment:2 Changed 2009-03-26T09:05:39-05:00 by melissa

Status changed from new to closed
Resolution set to fixed

(In [4945]) Eliminated exceptions when parsing memo and OLE fields from .mdb files. Closes #365.