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 |
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Priority: | major | Milestone: |
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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.