BUG: lsm_martin/080618.mdb Import fails

[dzmacdonald]

Cannot import file lsm_martin/080618.mdb from test_images_good

exception:loci.formats.formatexception: LSM files not found.

[jburel]

Moved from sprint 2011-05-19 (12)

[bwzloranger]

Not sure on time for this one. I don't think these files have changed any time recently so this should be importing.. will investigate. (putting in .25 hours for now).

[bwzloranger]

2011-05-23 14:06:52,546 56600      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - FILE_EXCEPTION: /Volumes/ome/data_repo/test_images_good/lsm_martin/080618.mdb
2011-05-23 14:06:52,548 56602      [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - FILE_EXCEPTION: /Volumes/ome/data_repo/test_images_good/lsm_martin/080618.mdb
loci.formats.FormatException: LSM files were not found.
	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:385)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:670)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:248)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:395)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:216)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	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:206)
	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:680)

[Melissa Linkert <melissa@…>]

(In [0e24f2f5dd651596c3f048e833d61e54e7e6919e/bioformats.git]) Be more thorough about finding .lsm files.

If there are multiple .mdb files in the directory and the .mdb file that
we have chosen does not contain valid file references, then look through
all of the other .mdb's and link any orphaned .lsm's to our .mdb.

See #5309.

[Melissa Linkert <melissa@…>]

(In [0e24f2f5dd651596c3f048e833d61e54e7e6919e/bioformats.git]) Be more thorough about finding .lsm files.

If there are multiple .mdb files in the directory and the .mdb file that
we have chosen does not contain valid file references, then look through
all of the other .mdb's and link any orphaned .lsm's to our .mdb.

See #5309.

[mlinkert]

This should be sorted with the above commits - 080618.mdb should have one file linked to it. Passing back to you, Brian, for testing; feel free to reassign to me if there are further problems.

[bwzloranger <bwzloranger@…>]

(In [9aed4512c22b8f1068308c791b0099f1d07a9559/ome.git] on branch develop) Updating to [5a07daaaaadba515bc875a15e8b8fd0b3a62d2c5/bioformats.git]. Fixes #5309

[dzmacdonald]

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x6d86d73a, pid=3444, tid=648
#
# JRE version: 6.0_25-b06
# Java VM: Java HotSpot(TM) Client VM (20.0-b11 mixed mode, sharing windows-x86 )
# Problematic frame:
# V  [jvm.dll+0x7d73a]
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
#

---------------  T H R E A D  ---------------

Current thread (0x026d1800):  VMThread [stack: 0x027a0000,0x027f0000] [id=648]
a
siginfo: ExceptionCode=0xc0000005, reading address 0x00000200

Registers:
EAX=0x1fb75474, EBX=0x353afc20, ECX=0x353afc30, EDX=0x00000000
ESP=0x027ef8f4, EBP=0x027ef90c, ESI=0x00000200, EDI=0x1fb7545c
EIP=0x6d86d73a, EFLAGS=0x00010206

Top of Stack: (sp=0x027ef8f4)
0x027ef8f4:   35446328 000003fe 00000001 353afc30
0x027ef904:   1fb75474 00000003 027ef92c 6d928673
0x027ef914:   1fb75428 6da60ef0 394b4c20 0016ead8
0x027ef924:   00000003 027ef938 027ef938 6d928a42
0x027ef934:   6da60ef0 027ef94c 6d859b94 6da6f138
0x027ef944:   6da60ef0 0016ead8 027ef968 6d856079
0x027ef954:   6da60ef0 00000000 6da60ef0 6da60ef0
0x027ef964:   0016ead8 027ef9a8 6d8504d0 00000001 

Instructions: (pc=0x6d86d73a)
0x6d86d71a:   8b 75 08 8b 43 04 03 fe 8d 04 87 3b f8 89 45 f8
0x6d86d72a:   0f 83 9f 00 00 00 8b 37 85 f6 0f 84 87 00 00 00
0x6d86d73a:   8b 0e 83 e1 03 80 f9 03 74 7d 8b 06 c7 45 fc 03
0x6d86d74a:   00 00 00 8b 55 fc 89 16 8a 0d b9 5b a5 6d 84 c9 


Register to memory mapping:

EAX=0x1fb75474 is an oop
org.apache.xalan.templates.ElemParam 
 - klass: 'org/apache/xalan/templates/ElemParam'
EBX=0x353afc20 is an oop
{instance class} 
 - klass: {other class}
ECX=0x353afc30 is an oop
java.lang.Class 
 - klass: 'java/lang/Class'
EDX=0x00000000 is an unknown value
ESP=0x027ef8f4 is an unknown value
EBP=0x027ef90c is an unknown value
ESI=0x00000200 is an unknown value
EDI=0x1fb7545c is an oop
org.apache.xalan.templates.ElemParam 
 - klass: 'org/apache/xalan/templates/ElemParam'


Stack: [0x027a0000,0x027f0000],  sp=0x027ef8f4,  free space=318k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [jvm.dll+0x7d73a]
V  [jvm.dll+0x138673]
V  [jvm.dll+0x138a42]
V  [jvm.dll+0x69b94]
V  [jvm.dll+0x66079]
V  [jvm.dll+0x604d0]
V  [jvm.dll+0x622b0]
V  [jvm.dll+0x62710]
V  [jvm.dll+0x6129a]
V  [jvm.dll+0x68642]
V  [jvm.dll+0x5ff28]
V  [jvm.dll+0x57acb]
V  [jvm.dll+0x13afb7]
V  [jvm.dll+0x11d903]
V  [jvm.dll+0x11cbce]
V  [jvm.dll+0x11cef0]
V  [jvm.dll+0x11d2f2]
V  [jvm.dll+0x140a8c]
C  [MSVCR71.dll+0x9565]  endthreadex+0xa0
C  [kernel32.dll+0x8e4a5]  BaseThreadInitThunk+0xe
C  [ntdll.dll+0x7d4bd]  RtlCreateUserProcess+0x8c
C  [ntdll.dll+0x7d6cf]  RtlCreateProcessParameters+0x4e

VM_Operation (0x05b0ee48): GenCollectForAllocation, mode: safepoint, requested by thread 0x0522dc00


---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x0522dc00 JavaThread "pool-2-thread-1" [_thread_blocked, id=284, stack(0x05ac0000,0x05b10000)]
  0x0522d400 JavaThread "pool-4-thread-1" [_thread_blocked, id=1368, stack(0x056d0000,0x05720000)]
  0x067d8400 JavaThread "Ice.Timer" [_thread_blocked, id=260, stack(0x07490000,0x074e0000)]
  0x05234800 JavaThread "Ice.SelectorThread" [_thread_in_native, id=1684, stack(0x07400000,0x07450000)]
  0x05234000 JavaThread "Ice.ThreadPool.Client-0" [_thread_in_native, id=3588, stack(0x07370000,0x073c0000)]
  0x05233800 JavaThread "Ice.EndpointHostResolverThread" [_thread_blocked, id=2256, stack(0x072e0000,0x07330000)]
  0x05233400 JavaThread "omero.ClientCallback.ThreadPool-4" [_thread_blocked, id=492, stack(0x07250000,0x072a0000)]
  0x05232c00 JavaThread "omero.ClientCallback.ThreadPool-3" [_thread_blocked, id=3340, stack(0x071c0000,0x07210000)]
  0x05232800 JavaThread "omero.ClientCallback.ThreadPool-2" [_thread_blocked, id=3920, stack(0x07130000,0x07180000)]
  0x05232000 JavaThread "omero.ClientCallback.ThreadPool-1" [_thread_in_native, id=2732, stack(0x070a0000,0x070f0000)]
  0x05231c00 JavaThread "omero.ClientCallback.ThreadPool-0" [_thread_blocked, id=1536, stack(0x07010000,0x07060000)]
  0x05184800 JavaThread "Swing-Shell" daemon [_thread_blocked, id=2704, stack(0x05a30000,0x05a80000)]
  0x04ee3000 JavaThread "TimerQueue" daemon [_thread_blocked, id=2520, stack(0x058a0000,0x058f0000)]
  0x04ecfc00 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=3076, stack(0x05810000,0x05860000)]
  0x04fb2800 JavaThread "AWT-Windows" daemon [_thread_blocked, id=2308, stack(0x05640000,0x05690000)]
  0x04f0cc00 JavaThread "AWT-Shutdown" [_thread_blocked, id=2692, stack(0x055b0000,0x05600000)]
  0x04f0c800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=3436, stack(0x05420000,0x05470000)]
  0x0272bc00 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=2156, stack(0x04c30000,0x04c80000)]
  0x02727800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=2668, stack(0x04ba0000,0x04bf0000)]
  0x02727000 JavaThread "Attach Listener" daemon [_thread_blocked, id=312, stack(0x04b10000,0x04b60000)]
  0x02724800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=3808, stack(0x04a80000,0x04ad0000)]
  0x0270f000 JavaThread "Finalizer" daemon [_thread_blocked, id=2880, stack(0x049f0000,0x04a40000)]
  0x0270d400 JavaThread "Reference Handler" daemon [_thread_blocked, id=3912, stack(0x027f0000,0x02840000)]
  0x026b1800 JavaThread "main" [_thread_blocked, id=3120, stack(0x00080000,0x000d0000)]

Other Threads:
=>0x026d1800 VMThread [stack: 0x027a0000,0x027f0000] [id=648]
  0x0273cc00 WatcherThread [stack: 0x04cc0000,0x04d10000] [id=3548]

VM state:at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
[0x00169508] Threads_lock - owner thread: 0x026d1800
[0x00169918] Heap_lock - owner thread: 0x0522dc00

Heap
 def new generation   total 16576K, used 93K [0x14490000, 0x15680000, 0x1ef30000)
  eden space 14784K,   0% used [0x14490000, 0x14490000, 0x15300000)
  from space 1792K,   5% used [0x154c0000, 0x154d77b8, 0x15680000)
  to   space 1792K,   0% used [0x15300000, 0x15300000, 0x154c0000)
 tenured generation   total 40676K, used 39353K [0x1ef30000, 0x216e9000, 0x34490000)
   the space 40676K,  96% used [0x1ef30000, 0x2159e710, 0x2159e800, 0x216e9000)
 compacting perm gen  total 18688K, used 18583K [0x34490000, 0x356d0000, 0x38490000)
   the space 18688K,  99% used [0x34490000, 0x356b5f40, 0x356b6000, 0x356d0000)
    ro space 10240K,  51% used [0x38490000, 0x389bdc00, 0x389bdc00, 0x38e90000)
    rw space 12288K,  55% used [0x38e90000, 0x3952c300, 0x3952c400, 0x39a90000)

Code Cache  [0x02880000, 0x02bc0000, 0x04880000)
 total_blobs=1966 nmethods=1724 adapters=176 free_code_cache=30153536 largest_free_block=256

Dynamic libraries:
0x00400000 - 0x00432000 	Y:\OMERO.importer-4.3.0-DEV-e7321099\OMERO.importer.exe
0x77080000 - 0x771e0000 	C:\Windows\SysWOW64\ntdll.dll
0x76690000 - 0x767a0000 	C:\Windows\syswow64\kernel32.dll
0x755a0000 - 0x75666000 	C:\Windows\syswow64\ADVAPI32.DLL
0x76bf0000 - 0x76ce0000 	C:\Windows\syswow64\RPCRT4.dll
0x75220000 - 0x75280000 	C:\Windows\syswow64\Secur32.dll
0x74840000 - 0x749de000 	C:\Windows\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.6001.18000_none_5cdbaa5a083979cc\COMCTL32.DLL
0x759c0000 - 0x75a6a000 	C:\Windows\syswow64\msvcrt.dll
0x768d0000 - 0x76960000 	C:\Windows\syswow64\GDI32.dll
0x754a0000 - 0x75570000 	C:\Windows\syswow64\USER32.dll
0x76870000 - 0x768c8000 	C:\Windows\syswow64\SHLWAPI.dll
0x75b80000 - 0x76690000 	C:\Windows\syswow64\SHELL32.DLL
0x769b0000 - 0x76a10000 	C:\Windows\system32\IMM32.DLL
0x767a0000 - 0x76868000 	C:\Windows\syswow64\MSCTF.dll
0x76b90000 - 0x76b99000 	C:\Windows\syswow64\LPK.DLL
0x75b00000 - 0x75b7d000 	C:\Windows\syswow64\USP10.dll
0x6d7f0000 - 0x6da9f000 	c:\program files (x86)\java\jre6\bin\client\jvm.dll
0x74e30000 - 0x74e62000 	C:\Windows\system32\WINMM.dll
0x757a0000 - 0x758e4000 	C:\Windows\syswow64\ole32.dll
0x75a70000 - 0x75afd000 	C:\Windows\syswow64\OLEAUT32.dll
0x74800000 - 0x74839000 	C:\Windows\system32\OLEACC.dll
0x7c340000 - 0x7c396000 	c:\program files (x86)\java\jre6\bin\MSVCR71.dll
0x74c00000 - 0x74c2c000 	C:\Windows\system32\apphelp.dll
0x6d7a0000 - 0x6d7ac000 	c:\program files (x86)\java\jre6\bin\verify.dll
0x6d320000 - 0x6d33f000 	c:\program files (x86)\java\jre6\bin\java.dll
0x75920000 - 0x75927000 	C:\Windows\syswow64\PSAPI.DLL
0x6d7e0000 - 0x6d7ef000 	c:\program files (x86)\java\jre6\bin\zip.dll
0x6d000000 - 0x6d14b000 	C:\Program Files (x86)\Java\jre6\bin\awt.dll
0x74700000 - 0x74742000 	C:\Windows\system32\WINSPOOL.DRV
0x750e0000 - 0x750ec000 	C:\Windows\system32\DWMAPI.DLL
0x74e70000 - 0x74ef0000 	C:\Windows\system32\uxtheme.dll
0x6d230000 - 0x6d27f000 	C:\Program Files (x86)\Java\jre6\bin\fontmanager.dll
0x6d600000 - 0x6d613000 	C:\Program Files (x86)\Java\jre6\bin\net.dll
0x75570000 - 0x7559d000 	C:\Windows\syswow64\WS2_32.dll
0x75280000 - 0x75286000 	C:\Windows\syswow64\NSI.dll
0x74db0000 - 0x74deb000 	C:\Windows\system32\mswsock.dll
0x74e20000 - 0x74e25000 	C:\Windows\System32\wship6.dll
0x6d620000 - 0x6d629000 	C:\Program Files (x86)\Java\jre6\bin\nio.dll
0x75290000 - 0x7541a000 	C:\Windows\syswow64\SETUPAPI.dll
0x74ff0000 - 0x7500e000 	C:\Windows\system32\USERENV.dll
0x74640000 - 0x746fa000 	C:\Windows\system32\PROPSYS.dll
0x75930000 - 0x759b4000 	C:\Windows\syswow64\CLBCatQ.DLL
0x741e0000 - 0x74403000 	C:\Windows\system32\NetworkExplorer.dll
0x74530000 - 0x74637000 	C:\Windows\System32\shdocvw.dll
0x74470000 - 0x74523000 	C:\Windows\system32\WindowsCodecs.dll
0x749e0000 - 0x749f4000 	C:\Windows\system32\MPR.dll
0x75050000 - 0x75058000 	C:\Windows\System32\drprov.dll
0x747c0000 - 0x747d3000 	C:\Windows\System32\ntlanman.dll
0x74ae0000 - 0x74b55000 	C:\Windows\System32\NETAPI32.dll
0x74bc0000 - 0x74bcf000 	C:\Windows\System32\davclnt.dll
0x747f0000 - 0x747fb000 	C:\Windows\system32\cscapi.dll
0x73f70000 - 0x741de000 	C:\Windows\system32\wpdshext.dll
0x73dc0000 - 0x73f6b000 	C:\Windows\WinSxS\x86_microsoft.windows.gdiplus_6595b64144ccf1df_1.0.6001.18175_none_9e7bbe54c9c04bca\gdiplus.dll
0x74780000 - 0x747be000 	C:\Windows\system32\PortableDeviceApi.dll
0x74750000 - 0x7477d000 	C:\Windows\system32\WINTRUST.dll
0x73cc0000 - 0x73db1000 	C:\Windows\system32\CRYPT32.dll
0x74450000 - 0x74462000 	C:\Windows\system32\MSASN1.dll
0x758f0000 - 0x75919000 	C:\Windows\syswow64\imagehlp.dll
0x74410000 - 0x7444f000 	C:\Windows\system32\audiodev.dll
0x73a70000 - 0x73cbb000 	C:\Windows\system32\WMVCore.DLL
0x73a30000 - 0x73a69000 	C:\Windows\system32\WMASF.DLL
0x750d0000 - 0x750d9000 	C:\Windows\system32\LINKINFO.dll
0x74df0000 - 0x74e01000 	C:\Windows\system32\SAMLIB.dll
0x75010000 - 0x7504b000 	C:\Windows\system32\rsaenh.dll
0x74be0000 - 0x74bef000 	C:\Windows\system32\NLAapi.dll
0x75180000 - 0x75199000 	C:\Windows\system32\IPHLPAPI.DLL
0x74c60000 - 0x74c95000 	C:\Windows\system32\dhcpcsvc.DLL
0x74c30000 - 0x74c5c000 	C:\Windows\system32\DNSAPI.dll
0x75170000 - 0x75177000 	C:\Windows\system32\WINNSI.DLL
0x74b80000 - 0x74ba1000 	C:\Windows\system32\dhcpcsvc6.DLL
0x74bd0000 - 0x74bdf000 	C:\Windows\system32\napinsp.dll
0x74b60000 - 0x74b72000 	C:\Windows\system32\pnrpnsp.dll
0x74bb0000 - 0x74bb8000 	C:\Windows\System32\winrnr.dll
0x76960000 - 0x769aa000 	C:\Windows\syswow64\WLDAP32.dll
0x74e10000 - 0x74e15000 	C:\Windows\System32\wshtcpip.dll
0x74bf0000 - 0x74bf6000 	C:\Windows\system32\rasadhlp.dll
0x6d780000 - 0x6d788000 	C:\Program Files (x86)\Java\jre6\bin\sunmscapi.dll

VM Arguments:
jvm_args: -Dexe4j.semaphoreName=y:_omero.importer-4.3.0-dev-e7321099_omero.importer.exe0 -Dexe4j.moduleName=Y:\OMERO.importer-4.3.0-DEV-e7321099\OMERO.importer.exe -Dexe4j.tempDir=C:\Users\donald\AppData\Local\Temp\e4j383C.tmp_dir19566 -Dexe4j.unextractedPosition=173874 -Dexe4j.consoleCodepage=cp0 -Xmx512M 
java_command: <unknown>
Launcher Type: generic

Environment Variables:
PATH=C:\Python26\;C:\Python26\Scripts;C:\Python27\;C:\Python27\Scripts;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;e:\Ice-3.3.1\bin;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\donald\AppData\Roaming\Python\Scripts;c:\program files (x86)\java\jre6\bin
USERNAME=donald
OS=Windows_NT
PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 23 Stepping 6, GenuineIntel



---------------  S Y S T E M  ---------------

OS: Windows Vista Build 6001 Service Pack 1

CPU:total 2 (2 cores per cpu, 1 threads per core) family 6 model 23 stepping 6, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3

Memory: 4k page, physical 2367264k(1003164k free), swap 4981124k(3550240k free)

vm_info: Java HotSpot(TM) Client VM (20.0-b11) for windows-x86 JRE (1.6.0_25-b06), built on Apr 14 2011 01:04:32 by "java_re" with MS VC++ 7.1 (VS2003)

time: Thu May 26 15:20:01 2011
elapsed time: 54 seconds

Bug occurs in vista when importing image.

[jburel]

Moved from sprint 2011-06-02 (13)

[Melissa Linkert <melissa@…>]

(In [d3ee4fd8f7fc63cb2ae27a1f5728a7b31301d3b5/bioformats.git]) Fix .mdb/.lsm file listings on Windows.

This prevents Mac OS X resource files from being read. See #5309.

[Melissa Linkert <melissa@…>]

(In [d3ee4fd8f7fc63cb2ae27a1f5728a7b31301d3b5/bioformats.git]) Fix .mdb/.lsm file listings on Windows.

This prevents Mac OS X resource files from being read. See #5309.

[mlinkert]

I haven't been able to reproduce this exact problem so far, but have noticed several other problems with importing 080618.mdb on Windows. All of the problems that I could find have now been fixed, so could you please test with the latest QA builds and see if the problem persists?

[dzmacdonald]

I can now import it, but it seems to be all white with black line at bottom, is this correct?

[mlinkert]

That sounds correct - the first ~1904 rows are should have pixel values of 15 or 16; the remaining rows have pixel values of 0.