Empty windows on Ubuntu with 3D effects

[Michael Doube]

Hi all

Some time ago I asked the list about a bug where the contents of ImageJ
windows are not rendered when ImageJ is running on Ubuntu with 3D
desktop effects enabled.  I had a couple of useful replies from the list
and submitted an issue to Sun, which has received a bit of attention
over the last couple of days.

At the moment, it appears that the empty window bug is fixed in JRE7,
which you can download and test:
https://jdk7.dev.java.net/
(it is buggy at the moment - I keep on getting windows that are locked
so I can't close them)

But the second part of the bug is not fixed:  ImageJ windows are missing
from the panel / Awn list.

I'm hopeful that this will be resolved, so will keep you informed of
progress.

Cheers

Mike

[Gabriel Lapointe]

This trick worked for me in 7.04

http://ubuntuforums.org/showthread.php?t=506686

Good luck

Michael Doube wrote:

> Hi all
>
> Some time ago I asked the list about a bug where the contents of
> ImageJ windows are not rendered when ImageJ is running on Ubuntu with
> 3D desktop effects enabled.  I had a couple of useful replies from the
> list and submitted an issue to Sun, which has received a bit of
> attention over the last couple of days.
>
> At the moment, it appears that the empty window bug is fixed in JRE7,
> which you can download and test:
> https://jdk7.dev.java.net/
> (it is buggy at the moment - I keep on getting windows that are locked
> so I can't close them)
>
> But the second part of the bug is not fixed:  ImageJ windows are
> missing from the panel / Awn list.
>
> I'm hopeful that this will be resolved, so will keep you informed of
> progress.
>
> Cheers
>
> Mike
>

... [show rest of quote]

[Gabriel Landini]

On Monday 22 September 2008 17:34:09 Gabriel Lapointe wrote:
> This trick worked for me in 7.04
>
> http://ubuntuforums.org/showthread.php?t=506686

Or you can run IJ with this option (mentioned by Wayne some time ago):

-Dawt.toolkit=sun.awt.motif.MToolkit

In the run file:

cd ~/ImageJ
/usr/lib/jvm/java-1.6.0/bin/java -Dawt.toolkit=sun.awt.motif.MToolkit -mx256m -cp
ij.jar:jimi.jar:/usr/lib/jvm/java-1.6.0/lib/tools.jar ij.ImageJ $*

(the line break after -cp was inserted by the mailer).
With this option, IJ shows large fonts (and menues become too long) in my suse
linux install.

Regards,
G.

[Michael Doube]

Thanks Gabriel and Gabriel,

unfortunately both those suggestions give me a nasty error:

#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fedd40e0755, pid=7421, tid=1102747984
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (10.0-b23 mixed mode
linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x30755]  catgets+0x15
#
# An error report file with more information is saved as:
# /home/mdoube/ImageJ/hs_err_pid7421.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
./run: line 1:  7421 Aborted
/usr/lib/jvm/java-6-sun/bin/java -Dawt.toolkit=sun.awt.motif.MToolkit
-Xmx3g -cp ~/ImageJ/ij.jar:/usr/lib/jvm/java-6-sun/lib/tools.jar
ij.ImageJ -ijpath ~/ImageJ
mdoube@doris:~/ImageJ$

Gabriel Landini wrote:

> On Monday 22 September 2008 17:34:09 Gabriel Lapointe wrote:
>> This trick worked for me in 7.04
>>
>> http://ubuntuforums.org/showthread.php?t=506686
>
> Or you can run IJ with this option (mentioned by Wayne some time ago):
>
> -Dawt.toolkit=sun.awt.motif.MToolkit
>
> In the run file:
>
> cd ~/ImageJ
> /usr/lib/jvm/java-1.6.0/bin/java -Dawt.toolkit=sun.awt.motif.MToolkit -mx256m -cp
> ij.jar:jimi.jar:/usr/lib/jvm/java-1.6.0/lib/tools.jar ij.ImageJ $*
>
> (the line break after -cp was inserted by the mailer).
> With this option, IJ shows large fonts (and menues become too long) in my suse
> linux install.
>
> Regards,
> G

... [show rest of quote]

... [show rest of quote]

#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fedd40e0755, pid=7421, tid=1102747984
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (10.0-b23 mixed mode linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x30755]  catgets+0x15
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

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

Current thread (0x0000000040112800):  JavaThread "main" [_thread_in_native, id=7422, stack(0x0000000041aa9000,0x0000000041baa000)]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x0000000000000008

Registers:
RAX=0x00007fed09343950, RBX=0x00007fed041ea150, RCX=0x00007fed0921582d, RDX=0x0000000000000001
RSP=0x0000000041ba8230, RBP=0x0000000041ba8260, RSI=0x0000000000000013, RDI=0x0000000000000000
R8 =0x0000000040193a58, R9 =0x0000000000000000, R10=0x0000000000000001, R11=0x00007fedd40e0740
R12=0x000000000000011a, R13=0x0000000040193a58, R14=0x000000000000000f, R15=0x0000000041ba8738
RIP=0x00007fedd40e0755, EFL=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x0000000041ba8230)
0x0000000041ba8230:   00007fed041ea150 00007fed09173396
0x0000000041ba8240:   0000000040193a58 00007fed040bff20
0x0000000041ba8250:   00007fed040bff20 00007fed043b6aa0
0x0000000041ba8260:   0000000041ba82b0 00007fed09173fb5
0x0000000041ba8270:   0000000000cd8d01 000000000000011c
0x0000000041ba8280:   0000000000000dfc 0000000040193a58
0x0000000041ba8290:   00007fed09030280 000000000000011a
0x0000000041ba82a0:   000000000000011c 00007fed043b6aa0
0x0000000041ba82b0:   0000000040112998 00007fed0903038e
0x0000000041ba82c0:   00007fed093316d0 0000000041ba8350
0x0000000041ba82d0:   00007fed041ea150 00007fed09031053
0x0000000041ba82e0:   0000000000000000 00007fedd3a74ce3
0x0000000041ba82f0:   0000000000000000 00007fed040afef0
0x0000000041ba8300:   00007fed040afef0 02fb0031d390bb81
0x0000000041ba8310:   0000000040193a58 01017fed00000000
0x0000000041ba8320:   0000000040196f70 00007fed04156cd0
0x0000000041ba8330:   00007fed08995120 0000000000000000
0x0000000041ba8340:   0000000041ba8728 0000000000000000
0x0000000041ba8350:   00007fed08788192 0000000000000000
0x0000000041ba8360:   00007fed08788218 0000000000000001
0x0000000041ba8370:   00007fed08788168 00007fed040c1650
0x0000000041ba8380:   00007fed0878773a 0000000000000020
0x0000000041ba8390:   00007fed08787743 0000000000000018
0x0000000041ba83a0:   00007fed08787865 0000000000000000
0x0000000041ba83b0:   00007fed08787a15 00000000000002fb
0x0000000041ba83c0:   00007fed08787a17 0000000000000031
0x0000000041ba83d0:   00007fed08787a08 00000000000001f8
0x0000000041ba83e0:   00007fed0878778a 0000000000000046
0x0000000041ba83f0:   00007fed0920226b 00007fed043b68c0
0x0000000041ba8400:   00007fed09202287 00007fed043b6990
0x0000000041ba8410:   00007fed09202295 00007fed043b6a60
0x0000000041ba8420:   00007fed0920395f 0000000000000001

Instructions: (pc=0x00007fedd40e0755)
0x00007fedd40e0745:   41 89 d2 74 7a 83 c6 01 85 f6 7e 73 85 d2 78 6f
0x00007fedd40e0755:   48 8b 57 08 4c 8b 5f 18 48 8d 04 52 48 89 d3 31

Stack: [0x0000000041aa9000,0x0000000041baa000],  sp=0x0000000041ba8230,  free space=1020k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libc.so.6+0x30755]  catgets+0x15
C  [libmawt.so+0x1a6fb5]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::Interpreter
v  ~BufferBlob::StubRoutines (1)

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

Java Threads: ( => current thread )
  0x00007fed041e9000 JavaThread "AWT-Motif" daemon [_thread_blocked, id=7435, stack(0x0000000041cab000,0x0000000041dac000)]
  0x00007fed041e7400 JavaThread "AWT-Shutdown" [_thread_blocked, id=7434, stack(0x0000000041baa000,0x0000000041cab000)]
  0x00007fed040b3800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7433, stack(0x00000000415bb000,0x00000000416bc000)]
  0x00000000401cc400 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=7431, stack(0x0000000040da4000,0x0000000040ea5000)]
  0x00000000401c9c00 JavaThread "CompilerThread1" daemon [_thread_blocked, id=7430, stack(0x0000000040ca3000,0x0000000040da4000)]
  0x00000000401c6400 JavaThread "CompilerThread0" daemon [_thread_blocked, id=7429, stack(0x0000000040ba2000,0x0000000040ca3000)]
  0x00000000401c4c00 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=7428, stack(0x0000000040aa1000,0x0000000040ba2000)]
  0x0000000040198c00 JavaThread "Finalizer" daemon [_thread_blocked, id=7427, stack(0x000000004057d000,0x000000004067e000)]
  0x0000000040197400 JavaThread "Reference Handler" daemon [_thread_blocked, id=7426, stack(0x000000004047c000,0x000000004057d000)]
=>0x0000000040112800 JavaThread "main" [_thread_in_native, id=7422, stack(0x0000000041aa9000,0x0000000041baa000)]

Other Threads:
  0x0000000040192000 VMThread [stack: 0x0000000040ecf000,0x0000000040fd0000] [id=7425]
  0x00000000401ce000 WatcherThread [stack: 0x0000000040fd0000,0x00000000410d1000] [id=7432]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
 PSYoungGen      total 6656K, used 1072K [0x00007fed8f610000, 0x00007fed8fd10000, 0x00007fedcf610000)
  eden space 6144K, 9% used [0x00007fed8f610000,0x00007fed8f69c2e8,0x00007fed8fc10000)
  from space 512K, 100% used [0x00007fed8fc90000,0x00007fed8fd10000,0x00007fed8fd10000)
  to   space 512K, 0% used [0x00007fed8fc10000,0x00007fed8fc10000,0x00007fed8fc90000)
 PSOldGen        total 5312K, used 872K [0x00007fed0f610000, 0x00007fed0fb40000, 0x00007fed8f610000)
  object space 5312K, 16% used [0x00007fed0f610000,0x00007fed0f6ea0f0,0x00007fed0fb40000)
 PSPermGen       total 21248K, used 7124K [0x00007fed0a210000, 0x00007fed0b6d0000, 0x00007fed0f610000)
  object space 21248K, 33% used [0x00007fed0a210000,0x00007fed0a905388,0x00007fed0b6d0000)

Dynamic libraries:
40000000-40009000 r-xp 00000000 08:05 442480                             /usr/lib/jvm/java-6-sun-1.6.0.07/jre/bin/java
40108000-4010a000 rwxp 00008000 08:05 442480                             /usr/lib/jvm/java-6-sun-1.6.0.07/jre/bin/java
4010a000-40459000 rwxp 4010a000 00:00 0                                  [heap]
4047c000-4047f000 ---p 4047c000 00:00 0
4047f000-4057d000 rwxp 4047f000 00:00 0
4057d000-40580000 ---p 4057d000 00:00 0
40580000-4067e000 rwxp 40580000 00:00 0
40738000-40739000 ---p 40738000 00:00 0
40739000-40839000 rwxp 40739000 00:00 0
40839000-4083a000 ---p 40839000 00:00 0
4083a000-4093a000 rwxp 4083a000 00:00 0
40aa1000-40aa4000 ---p 40aa1000 00:00 0
40aa4000-40ba2000 rwxp 40aa4000 00:00 0
40ba2000-40ba5000 ---p 40ba2000 00:00 0
40ba5000-40ca3000 rwxp 40ba5000 00:00 0
40ca3000-40ca6000 ---p 40ca3000 00:00 0
40ca6000-40da4000 rwxp 40ca6000 00:00 0
40da4000-40da7000 ---p 40da4000 00:00 0
40da7000-40ea5000 rwxp 40da7000 00:00 0
40ecf000-40ed0000 ---p 40ecf000 00:00 0
40ed0000-40fd0000 rwxp 40ed0000 00:00 0
40fd0000-40fd1000 ---p 40fd0000 00:00 0
40fd1000-410d1000 rwxp 40fd1000 00:00 0
415bb000-415be000 ---p 415bb000 00:00 0
415be000-416bc000 rwxp 415be000 00:00 0
41aa9000-41aac000 ---p 41aa9000 00:00 0
41aac000-41baa000 rwxp 41aac000 00:00 0
41baa000-41bad000 ---p 41baa000 00:00 0
41bad000-41cab000 rwxp 41bad000 00:00 0
41cab000-41cae000 ---p 41cab000 00:00 0
41cae000-41dac000 rwxp 41cae000 00:00 0
7fed02994000-7fed0299d000 r-xs 00000000 08:05 248893                     /var/cache/fontconfig/945677eb7aeaf62f1d50efc3fb3ec7d8-x86-64.cache-2
7fed0299d000-7fed029a2000 r-xs 00000000 08:05 508138                     /var/cache/fontconfig/926e794c3d5e5dffcaf2fa83ef8d36c2-x86-64.cache-2
7fed029a2000-7fed029d0000 r-xs 00000000 08:05 508137                     /var/cache/fontconfig/365b55f210c0a22e9a19e35191240f32-x86-64.cache-2
7fed02b8d000-7fed02b92000 r-xp 00000000 08:05 295939                     /usr/lib/libXfixes.so.3.1.0
7fed02b92000-7fed02d91000 ---p 00005000 08:05 295939                     /usr/lib/libXfixes.so.3.1.0
7fed02d91000-7fed02d92000 rwxp 00004000 08:05 295939                     /usr/lib/libXfixes.so.3.1.0
7fed02d92000-7fed02d9b000 r-xp 00000000 08:05 295959                     /usr/lib/libXrender.so.1.3.0
7fed02d9b000-7fed02f9a000 ---p 00009000 08:05 295959                     /usr/lib/libXrender.so.1.3.0
7fed02f9a000-7fed02f9b000 rwxp 00008000 08:05 295959                     /usr/lib/libXrender.so.1.3.0
7fed02f9b000-7fed02fa4000 r-xp 00000000 08:05 295929                     /usr/lib/libXcursor.so.1.0.2
7fed02fa4000-7fed031a4000 ---p 00009000 08:05 295929                     /usr/lib/libXcursor.so.1.0.2
7fed031a4000-7fed031a5000 rwxp 00009000 08:05 295929                     /usr/lib/libXcursor.so.1.0.2
7fed031b4000-7fed031b5000 r-xs 00005000 08:03 3015381                    /home/mdoube/ImageJ/plugins/Analyze/Color_Histogram.jar
7fed031b5000-7fed031b7000 r-xs 00007000 08:03 3015380                    /home/mdoube/ImageJ/plugins/Analyze/Cell_Counter.jar
7fed031b7000-7fed031b8000 r-xs 00009000 08:03 3015408                    /home/mdoube/ImageJ/plugins/Input-Output/Animated_Gif.jar
7fed031b8000-7fed031b9000 r-xs 00002000 08:03 3015413                    /home/mdoube/ImageJ/plugins/Input-Output/Deltavision_Opener.jar
7fed031b9000-7fed033b9000 rwxp 7fed031b9000 00:00 0
7fed033b9000-7fed03437000 r-xp 00000000 08:05 442508                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libfontmanager.so
7fed03437000-7fed03536000 ---p 0007e000 08:05 442508                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libfontmanager.so
7fed03536000-7fed0354c000 rwxp 0007d000 08:05 442508                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libfontmanager.so
7fed0354c000-7fed0355d000 rwxp 7fed0354c000 00:00 0
7fed0355d000-7fed035bc000 r-xs 00b89000 08:05 442449                     /usr/lib/jvm/java-6-sun-1.6.0.07/lib/tools.jar
7fed035bc000-7fed035c1000 r-xp 00000000 08:05 295933                     /usr/lib/libXdmcp.so.6.0.0
7fed035c1000-7fed037c0000 ---p 00005000 08:05 295933                     /usr/lib/libXdmcp.so.6.0.0
7fed037c0000-7fed037c1000 rwxp 00004000 08:05 295933                     /usr/lib/libXdmcp.so.6.0.0
7fed037c1000-7fed037dc000 r-xp 00000000 08:05 296768                     /usr/lib/libxcb.so.1.0.0
7fed037dc000-7fed039db000 ---p 0001b000 08:05 296768                     /usr/lib/libxcb.so.1.0.0
7fed039db000-7fed039dc000 rwxp 0001a000 08:05 296768                     /usr/lib/libxcb.so.1.0.0
7fed039dc000-7fed039dd000 r-xp 00000000 08:05 296766                     /usr/lib/libxcb-xlib.so.0.0.0
7fed039dd000-7fed03bdc000 ---p 00001000 08:05 296766                     /usr/lib/libxcb-xlib.so.0.0.0
7fed03bdc000-7fed03bdd000 rwxp 00000000 08:05 296766                     /usr/lib/libxcb-xlib.so.0.0.0
7fed03bdd000-7fed03bf4000 r-xp 00000000 08:05 295886                     /usr/lib/libICE.so.6.3.0
7fed03bf4000-7fed03df3000 ---p 00017000 08:05 295886                     /usr/lib/libICE.so.6.3.0
7fed03df3000-7fed03df5000 rwxp 00016000 08:05 295886                     /usr/lib/libICE.so.6.3.0
7fed03df5000-7fed03df8000 rwxp 7fed03df5000 00:00 0
7fed03df8000-7fed03e00000 r-xp 00000000 08:05 295910                     /usr/lib/libSM.so.6.0.0
7fed03e00000-7fed03fff000 ---p 00008000 08:05 295910                     /usr/lib/libSM.so.6.0.0
7fed03fff000-7fed04000000 rwxp 00007000 08:05 295910                     /usr/lib/libSM.so.6.0.0
7fed04000000-7fed0444c000 rwxp 7fed04000000 00:00 0
7fed0444c000-7fed08000000 ---p 7fed0444c000 00:00 0
7fed08000000-7fed08003000 r-xs 00000000 08:05 248891                     /var/cache/fontconfig/e383d7ea5fbe662a33d9b44caf393297-x86-64.cache-2
7fed08003000-7fed08004000 r-xs 00000000 08:05 248888                     /var/cache/fontconfig/4c73fe0c47614734b17d736dbde7580a-x86-64.cache-2
7fed08004000-7fed08008000 r-xs 00000000 08:05 248887                     /var/cache/fontconfig/a755afe4a08bf5b97852ceb7400b47bc-x86-64.cache-2
7fed08008000-7fed08011000 r-xs 00000000 08:05 248886                     /var/cache/fontconfig/6d41288fd70b0be22e8c3a91e032eec0-x86-64.cache-2
7fed08011000-7fed0801c000 r-xs 00000000 08:05 248884                     /var/cache/fontconfig/e3de0de479f42330eadf588a55fb5bf4-x86-64.cache-2
7fed0801c000-7fed08027000 r-xs 00000000 08:05 248883                     /var/cache/fontconfig/0f34bcd4b6ee430af32735b75db7f02b-x86-64.cache-2
7fed08027000-7fed08029000 r-xp 00000000 08:05 295922                     /usr/lib/libXau.so.6.0.0
7fed08029000-7fed08228000 ---p 00002000 08:05 295922                     /usr/lib/libXau.so.6.0.0
7fed08228000-7fed08229000 rwxp 00001000 08:05 295922                     /usr/lib/libXau.so.6.0.0
7fed08229000-7fed08232000 r-xp 00000000 08:05 295945                     /usr/lib/libXi.so.6.0.0
7fed08232000-7fed08431000 ---p 00009000 08:05 295945                     /usr/lib/libXi.so.6.0.0
7fed08431000-7fed08432000 rwxp 00008000 08:05 295945                     /usr/lib/libXi.so.6.0.0
7fed08432000-7fed08531000 r-xp 00000000 08:05 295916                     /usr/lib/libX11.so.6.2.0
7fed08531000-7fed08730000 ---p 000ff000 08:05 295916                     /usr/lib/libX11.so.6.2.0
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7fed08735000-7fed08792000 r-xp 00000000 08:05 295963                     /usr/lib/libXt.so.6.0.0
7fed08792000-7fed08992000 ---p 0005d000 08:05 295963                     /usr/lib/libXt.so.6.0.0
7fed08992000-7fed08998000 rwxp 0005d000 08:05 295963                     /usr/lib/libXt.so.6.0.0
7fed08998000-7fed08999000 rwxp 7fed08998000 00:00 0
7fed08999000-7fed089aa000 r-xp 00000000 08:05 295937                     /usr/lib/libXext.so.6.4.0
7fed089aa000-7fed08ba9000 ---p 00011000 08:05 295937                     /usr/lib/libXext.so.6.4.0
7fed08ba9000-7fed08baa000 rwxp 00010000 08:05 295937                     /usr/lib/libXext.so.6.4.0
7fed08baa000-7fed08baf000 r-xp 00000000 08:05 295965                     /usr/lib/libXtst.so.6.1.0
7fed08baf000-7fed08daf000 ---p 00005000 08:05 295965                     /usr/lib/libXtst.so.6.1.0
7fed08daf000-7fed08db0000 rwxp 00005000 08:05 295965                     /usr/lib/libXtst.so.6.1.0
7fed08db0000-7fed08db8000 r-xp 00000000 08:05 295953                     /usr/lib/libXp.so.6.2.0
7fed08db8000-7fed08fb8000 ---p 00008000 08:05 295953                     /usr/lib/libXp.so.6.2.0
7fed08fb8000-7fed08fb9000 rwxp 00008000 08:05 295953                     /usr/lib/libXp.so.6.2.0
7fed08fb9000-7fed08fba000 r-xs 00004000 08:03 3015420                    /home/mdoube/ImageJ/plugins/Input-Output/LSM_Reader.jar
7fed08fba000-7fed08fbd000 r-xs 00000000 08:05 248881                     /var/cache/fontconfig/de9486f0b47a4d768a594cb4198cb1c6-x86-64.cache-2
7fed08fbd000-7fed08fc6000 r-xs 00000000 08:05 248880                     /var/cache/fontconfig/d52a8644073d54c13679302ca1180695-x86-64.cache-2
7fed08fc6000-7fed08fcd000 r-xs 00000000 08:05 248879                     /var/cache/fontconfig/089dead882dea3570ffc31a9898cfb69-x86-64.cache-2
7fed08fcd000-7fed09232000 r-xp 00000000 08:05 442519                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/motif21/libmawt.so
7fed09232000-7fed09331000 ---p 00265000 08:05 442519                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/motif21/libmawt.so
7fed09331000-7fed09385000 rwxp 00264000 08:05 442519                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/motif21/libmawt.so
7fed09385000-7fed09388000 rwxp 7fed09385000 00:00 0
7fed09388000-7fed09412000 r-xp 00000000 08:05 442540                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libawt.so
7fed09412000-7fed09511000 ---p 0008a000 08:05 442540                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libawt.so
7fed09511000-7fed0952a000 rwxp 00089000 08:05 442540                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libawt.so
7fed0952a000-7fed0954e000 rwxp 7fed0952a000 00:00 0
7fed0954e000-7fed09555000 r-xs 00000000 08:05 301020                     /usr/lib/gconv/gconv-modules.cache
7fed09555000-7fed09594000 r-xp 00000000 08:05 360481                     /usr/lib/locale/en_GB.utf8/LC_CTYPE
7fed09594000-7fed09608000 rwxp 7fed09594000 00:00 0
7fed09608000-7fed09793000 r-xs 02def000 08:05 442573                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/rt.jar
7fed09793000-7fed097c6000 rwxp 7fed09793000 00:00 0
7fed097c6000-7fed097e5000 rwxp 7fed097c6000 00:00 0
7fed097e5000-7fed097e8000 rwxp 7fed097e5000 00:00 0
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7fed09be5000-7fed09bf0000 rwxp 7fed09be5000 00:00 0
7fed09bf0000-7fed09c0f000 rwxp 7fed09bf0000 00:00 0
7fed09c0f000-7fed09c12000 rwxp 7fed09c0f000 00:00 0
7fed09c12000-7fed0a00f000 rwxp 7fed09c12000 00:00 0
7fed0a00f000-7fed0a013000 rwxp 7fed0a00f000 00:00 0
7fed0a013000-7fed0a20f000 rwxp 7fed0a013000 00:00 0
7fed0a20f000-7fed0b6d0000 rwxp 7fed0a20f000 00:00 0
7fed0b6d0000-7fed0f610000 rwxp 7fed0b6d0000 00:00 0
7fed0f610000-7fed0fb40000 rwxp 7fed0f610000 00:00 0
7fed0fb40000-7fed8f610000 rwxp 7fed0fb40000 00:00 0
7fed8f610000-7fed8fd10000 rwxp 7fed8f610000 00:00 0
7fed8fd10000-7fedcf610000 rwxp 7fed8fd10000 00:00 0
7fedcf610000-7fedcf611000 r-xs 00002000 08:03 3015407                    /home/mdoube/ImageJ/plugins/Input-Output/Analyze_Reader_Writer.jar
7fedcf611000-7fedcf612000 r-xs 00000000 08:03 3014734                    /home/mdoube/ImageJ/plugins/Topo_.jar
7fedcf612000-7fedcf615000 r-xs 00000000 08:05 248885                     /var/cache/fontconfig/de156ccd2eddbdc19d37a45b8b2aac9c-x86-64.cache-2
7fedcf615000-7fedcf885000 rwxp 7fedcf615000 00:00 0
7fedcf885000-7fedd2615000 rwxp 7fedcf885000 00:00 0
7fedd2615000-7fedd2623000 r-xp 00000000 08:05 442510                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libzip.so
7fedd2623000-7fedd2725000 ---p 0000e000 08:05 442510                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libzip.so
7fedd2725000-7fedd2728000 rwxp 00010000 08:05 442510                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libzip.so
7fedd2728000-7fedd2729000 rwxp 7fedd2728000 00:00 0
7fedd2729000-7fedd2752000 r-xp 00000000 08:05 442523                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libjava.so
7fedd2752000-7fedd2851000 ---p 00029000 08:05 442523                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libjava.so
7fedd2851000-7fedd2858000 rwxp 00028000 08:05 442523                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libjava.so
7fedd2858000-7fedd2865000 r-xp 00000000 08:05 442505                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libverify.so
7fedd2865000-7fedd2964000 ---p 0000d000 08:05 442505                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libverify.so
7fedd2964000-7fedd2967000 rwxp 0000c000 08:05 442505                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/libverify.so
7fedd2967000-7fedd2971000 r-xp 00000000 08:05 513885                     /lib/libnss_files-2.7.so
7fedd2971000-7fedd2b71000 ---p 0000a000 08:05 513885                     /lib/libnss_files-2.7.so
7fedd2b71000-7fedd2b73000 rwxp 0000a000 08:05 513885                     /lib/libnss_files-2.7.so
7fedd2b73000-7fedd2b7d000 r-xp 00000000 08:05 513887                     /lib/libnss_nis-2.7.so
7fedd2b7d000-7fedd2d7c000 ---p 0000a000 08:05 513887                     /lib/libnss_nis-2.7.so
7fedd2d7c000-7fedd2d7e000 rwxp 00009000 08:05 513887                     /lib/libnss_nis-2.7.so
7fedd2d7e000-7fedd2d86000 r-xp 00000000 08:05 513883                     /lib/libnss_compat-2.7.so
7fedd2d86000-7fedd2f85000 ---p 00008000 08:05 513883                     /lib/libnss_compat-2.7.so
7fedd2f85000-7fedd2f87000 rwxp 00007000 08:05 513883                     /lib/libnss_compat-2.7.so
7fedd2f87000-7fedd2f9d000 r-xp 00000000 08:05 513882                     /lib/libnsl-2.7.so
7fedd2f9d000-7fedd319c000 ---p 00016000 08:05 513882                     /lib/libnsl-2.7.so
7fedd319c000-7fedd319e000 rwxp 00015000 08:05 513882                     /lib/libnsl-2.7.so
7fedd319e000-7fedd31a0000 rwxp 7fedd319e000 00:00 0
7fedd31a0000-7fedd31a7000 r-xp 00000000 08:05 442512                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/native_threads/libhpi.so
7fedd31a7000-7fedd32a8000 ---p 00007000 08:05 442512                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/native_threads/libhpi.so
7fedd32a8000-7fedd32aa000 rwxp 00008000 08:05 442512                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/native_threads/libhpi.so
7fedd32aa000-7fedd32ab000 rwxp 7fedd32aa000 00:00 0
7fedd32ab000-7fedd32b3000 r-xp 00000000 08:05 513892                     /lib/librt-2.7.so
7fedd32b3000-7fedd34b2000 ---p 00008000 08:05 513892                     /lib/librt-2.7.so
7fedd34b2000-7fedd34b4000 rwxp 00007000 08:05 513892                     /lib/librt-2.7.so
7fedd34b4000-7fedd3534000 r-xp 00000000 08:05 513880                     /lib/libm-2.7.so
7fedd3534000-7fedd3733000 ---p 00080000 08:05 513880                     /lib/libm-2.7.so
7fedd3733000-7fedd3735000 rwxp 0007f000 08:05 513880                     /lib/libm-2.7.so
7fedd3735000-7fedd3e2a000 r-xp 00000000 08:05 442529                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server/libjvm.so
7fedd3e2a000-7fedd3f29000 ---p 006f5000 08:05 442529                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server/libjvm.so
7fedd3f29000-7fedd4073000 rwxp 006f4000 08:05 442529                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server/libjvm.so
7fedd4073000-7fedd40b0000 rwxp 7fedd4073000 00:00 0
7fedd40b0000-7fedd4208000 r-xp 00000000 08:05 513876                     /lib/libc-2.7.so
7fedd4208000-7fedd4408000 ---p 00158000 08:05 513876                     /lib/libc-2.7.so
7fedd4408000-7fedd440b000 r-xp 00158000 08:05 513876                     /lib/libc-2.7.so
7fedd440b000-7fedd440d000 rwxp 0015b000 08:05 513876                     /lib/libc-2.7.so
7fedd440d000-7fedd4412000 rwxp 7fedd440d000 00:00 0
7fedd4412000-7fedd4414000 r-xp 00000000 08:05 513879                     /lib/libdl-2.7.so
7fedd4414000-7fedd4614000 ---p 00002000 08:05 513879                     /lib/libdl-2.7.so
7fedd4614000-7fedd4616000 rwxp 00002000 08:05 513879                     /lib/libdl-2.7.so
7fedd4616000-7fedd462c000 r-xp 00000000 08:05 513890                     /lib/libpthread-2.7.so
7fedd462c000-7fedd482c000 ---p 00016000 08:05 513890                     /lib/libpthread-2.7.so
7fedd482c000-7fedd482e000 rwxp 00016000 08:05 513890                     /lib/libpthread-2.7.so
7fedd482e000-7fedd4832000 rwxp 7fedd482e000 00:00 0
7fedd4832000-7fedd484f000 r-xp 00000000 08:05 513370                     /lib/ld-2.7.so
7fedd484f000-7fedd4850000 r-xs 00000000 08:05 248890                     /var/cache/fontconfig/c69f04ab05004e31a6d5e715764f16d8-x86-64.cache-2
7fedd4850000-7fedd4851000 r-xs 00000000 08:05 248882                     /var/cache/fontconfig/4794a0821666d79190d59a36cb4f44b5-x86-64.cache-2
7fedd4851000-7fedd485d000 r-xs 002c7000 08:05 441587                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/ext/j3dcore.jar
7fedd485d000-7fedd486b000 r-xs 00193000 08:05 441591                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/ext/j3dutils.jar
7fedd486b000-7fedd4875000 rwxp 7fedd486b000 00:00 0
7fedd4875000-7fedd492b000 rwxp 7fedd4875000 00:00 0
7fedd492b000-7fedd492d000 rwxp 7fedd492b000 00:00 0
7fedd492d000-7fedd4934000 r-xp 00000000 08:05 442496                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/jli/libjli.so
7fedd4934000-7fedd4a35000 ---p 00007000 08:05 442496                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/jli/libjli.so
7fedd4a35000-7fedd4a37000 rwxp 00008000 08:05 442496                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/jli/libjli.so
7fedd4a37000-7fedd4a38000 rwxp 7fedd4a37000 00:00 0
7fedd4a38000-7fedd4a3a000 r-xs 00000000 08:05 248873                     /var/cache/fontconfig/e13b20fdb08344e0e664864cc2ede53d-x86-64.cache-2
7fedd4a3a000-7fedd4a40000 r-xs 00139000 08:03 2981917                    /home/mdoube/ImageJ/ij.jar
7fedd4a40000-7fedd4a42000 r-xs 0004c000 08:05 441639                     /usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/ext/vecmath.jar
7fedd4a42000-7fedd4a4a000 rwxs 00000000 08:05 687017                     /tmp/hsperfdata_mdoube/7421
7fedd4a4a000-7fedd4a4b000 rwxp 7fedd4a4a000 00:00 0
7fedd4a4b000-7fedd4a4c000 r-xp 7fedd4a4b000 00:00 0
7fedd4a4c000-7fedd4a4f000 rwxp 7fedd4a4c000 00:00 0
7fedd4a4f000-7fedd4a51000 rwxp 0001d000 08:05 513370                     /lib/ld-2.7.so
7fffdca3b000-7fffdca50000 rwxp 7ffffffea000 00:00 0                      [stack]
7fffdcbfe000-7fffdcc00000 r-xp 7fffdcbfe000 00:00 0                      [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Dawt.toolkit=sun.awt.motif.MToolkit -Xmx3g
java_command: ij.ImageJ -ijpath /home/mdoube/ImageJ
Launcher Type: SUN_STANDARD

Environment Variables:
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
USERNAME=mdoube
LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.07/jre/../lib/amd64
SHELL=/bin/bash
DISPLAY=:0.0

Signal Handlers:
SIGSEGV: [libjvm.so+0x661750], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x661750], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x504550], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x504550], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x504550], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x504550], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x5067c0], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x506520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x506520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x506520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x506520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004


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

OS:lenny/sid

uname:Linux 2.6.24-20-generic #1 SMP Mon Jul 28 13:06:07 UTC 2008 x86_64
libc:glibc 2.7 NPTL 2.7
rlimit: STACK 8192k, CORE 0k, NPROC 40960, NOFILE 1024, AS infinity
load average:0.61 0.83 0.40

CPU:total 2 (2 cores per cpu, 1 threads per core) family 6 model 15 stepping 11, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3

Memory: 4k page, physical 4041908k(2859572k free), swap 2096440k(2096440k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (10.0-b23) for linux-amd64 JRE (1.6.0_07-b06), built on Jun 10 2008 01:53:27 by "java_re" with gcc 3.2.2 (SuSE Linux)

time: Mon Sep 22 18:06:39 2008
elapsed time: 0 seconds

[Liang Ding]

I try to get the information about particle size distribution. However,
the particles aggregate on TEM micrographs. I tend to avoid the aggregated
particles and include only discrete ones for size histograpm. But I am not
sure if this is acceptable. What is usually done in this situation?

Any suggestions and thoughts are greatly appreciated.

Best,

Liang

[Stephan Saalfeld]

Hi Liang,

if you are sure in prior that the aggregated particles did not aggregate
due to some size-related properties and given that you have enough
discrete particles that you can really distinguish from e.g. aggregates
of two or three single particles, I do not see an argument against
avoiding the aggregated.

Best regards,
Stephan


On Mon, 2008-09-22 at 16:33 -0400, Liang Ding wrote:

> I try to get the information about particle size distribution.
> However,
> the particles aggregate on TEM micrographs. I tend to avoid the
> aggregated
> particles and include only discrete ones for size histograpm. But I am
> not
> sure if this is acceptable. What is usually done in this situation?
>
> Any suggestions and thoughts are greatly appreciated.
>
> Best,
>
> Liang

[Michael Doube]

Sun have assigned a bug report to this issue:
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6752009

Michael Doube wrote:

> Hi all
>
> Some time ago I asked the list about a bug where the contents of
> ImageJ windows are not rendered when ImageJ is running on Ubuntu with
> 3D desktop effects enabled.  I had a couple of useful replies from the
> list and submitted an issue to Sun, which has received a bit of
> attention over the last couple of days.
>
> At the moment, it appears that the empty window bug is fixed in JRE7,
> which you can download and test:
> https://jdk7.dev.java.net/
> (it is buggy at the moment - I keep on getting windows that are locked
> so I can't close them)
>
> But the second part of the bug is not fixed:  ImageJ windows are
> missing from the panel / Awn list.
>
> I'm hopeful that this will be resolved, so will keep you informed of
> progress.
>
> Cheers
>
> Mike

... [show rest of quote]

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom

Phone: [phone]
Fax: [phone]