[OpenSPIM] First SPIM image! and new acquisition problem: writing to disk

Aurelia Honerkamp-Smith aureliaomega at gmail.com
Wed Oct 9 12:55:37 CDT 2013 

Hello,

Thanks!  I'm glad you are enjoying my constant questions.

I have added the Volvox picture to the gallery on the wiki, and also added
my lab to the "who has an OpenSPIM" page.

There is in fact an exception, here is the debug console output:


LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.lang.R
unnable
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AcqOutputHandler
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.lang.T
hread$UncaughtExceptionHandler
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AcqOutputHandler
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AcqOutputHandler
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AcqOutputHandler
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AntiDrift$Callback
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.lang.R
unnable
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.lang.R
unnable
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.progac
q.AntiDrift$Callback
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.awt.ev
ent.KeyListener
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
javax.swing
.event.ChangeListener
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.awt.ev
ent.KeyListener
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.lang.I
terable
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.awt.ev
ent.ItemListener
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
java.util.E
ventListener
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found:
spim.setup.
Device$Factory
LOG(2013-10-09T18:35:30.794132, 7896, 60C856A8:): > Attempting to install
plugin
 spim.SPIMAcquisition
LOG(2013-10-09T18:35:31.725185, 7896, 633ED618:): All devices unloaded.
LOG(2013-10-09T18:35:31.725185, 7896, 633ED618:): > Notification for
Device: Cor
e Property: Initialize changed to value: 0
LOG(2013-10-09T18:35:31.780188, 7896, 633ED618:): Device COM3 loaded from
Serial
Manager and labeled as COM3
LOG(2013-10-09T18:35:31.817191, 7896, 633ED618:): Device Camera-1 loaded
from PV
CAM and labeled as CoolsnapMyo
LOG(2013-10-09T18:35:31.817191, 7896, 633ED618:): Device CoolsnapMyo set as
defa
ult camera.
Pinging motors...
Found 3 motors and 1 twisters.
LOG(2013-10-09T18:35:32.917254, 7896, 633ED618:): Device Picard Twister
loaded f
rom PicardStage and labeled as Picard Twister
LOG(2013-10-09T18:35:32.917254, 7896, 633ED618:): Device Picard Z Stage
loaded f
rom PicardStage and labeled as Picard Z Stage
LOG(2013-10-09T18:35:32.918254, 7896, 633ED618:): Device Picard XY Stage
loaded
from PicardStage and labeled as Picard XY Stage
LOG(2013-10-09T18:35:32.918254, 7896, 633ED618:): Device Picard XY Stage
set as
default xyStage.
LOG(2013-10-09T18:35:32.967256, 7896, 633ED618:): Device SC10 loaded from
Thorla
bsSC10 and labeled as SC10
LOG(2013-10-09T18:35:32.967256, 7896, 633ED618:): Device SC10 set as
default shu
tter.
LOG(2013-10-09T18:35:33.020259, 7896, 633ED618:): Starting initialization
sequen
ce for 6 devices...
LOG(2013-10-09T18:35:33.114265, 7896, 633ED618:): Device COM3 initialized.
LOG(2013-10-09T18:35:33.121265, 7896, 633ED618:): Device CoolsnapMyo
message: PV
CAM VERSION: 2.9.5. Number of cameras detected: 1
LOG(2013-10-09T18:35:33.174268, 7896, 633ED618:): Device CoolsnapMyo
message: Bu
ilding Speed Table
LOG(2013-10-09T18:35:33.291275, 7896, 633ED618:): Device CoolsnapMyo
message: In
itializing Static Camera Properties
LOG(2013-10-09T18:35:33.303276, 7896, 633ED618:): Device CoolsnapMyo
message: In
itializing Dynamic Camera Properties
LOG(2013-10-09T18:35:33.484286, 7896, 633ED618:): Device CoolsnapMyo
message: Th
is Camera does not have EM Gain
LOG(2013-10-09T18:35:33.484286, 7896, 633ED618:): Device CoolsnapMyo
message: Fr
ame Transfer mode not available
LOG(2013-10-09T18:35:33.528288, 7896, 633ED618:): Device CoolsnapMyo
message: Us
ing PVCAM callbacks for frame acquisition
LOG(2013-10-09T18:35:33.528288, 7896, 633ED618:): Device CoolsnapMyo
initialized
.
LOG(2013-10-09T18:35:33.536289, 7896, 633ED618:): Device Picard Twister
initiali
zed.
LOG(2013-10-09T18:35:33.540289, 7896, 633ED618:): Device Picard Z Stage
initiali
zed.
LOG(2013-10-09T18:35:33.564291, 7896, 633ED618:): Device Picard XY Stage
initial
ized.
LOG(2013-10-09T18:35:33.612293, 7896, 633ED618:): Device SC10 message:
THORLABS
SC10 VERSION 1.07
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Device SC10 initialized.
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for
Device: Cor
e Property: Initialize changed to value: 1
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Camera device set to
CoolsnapM
yo
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for
Device: Cor
e Property: Camera changed to value: CoolsnapMyo
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for
Device: Cor
e Property: Shutter changed to value: SC10
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Focus device set to
Picard Z S
tage
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for
Device: Cor
e Property: Focus changed to value: Picard Z Stage
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Auto shutter ON.
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for
Device: Cor
e Property: AutoShutter changed to value: 1
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard Z Stage defined as StepSize=1.5000
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard Z Stage defined as Velocity=10
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as TransposeMirrorX=0
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as TransposeMirrorY=0
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as X-StepSize=1.5000
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as X-Velocity=10
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as Y-StepSize=1.5000
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for
device
Picard XY Stage defined as Y-Velocity=10
LOG(2013-10-09T18:35:33.628294, 7896, 633ED618:): Pixel size 0.500000 um
set for
 resolution ID: 20X
LOG(2013-10-09T18:35:33.656296, 7896, 633ED618:): System state cache
updated.
LOG(2013-10-09T18:35:33.740301, 7896, 633ED618:): Device SC10 message: 1
LOG(2013-10-09T18:35:33.752301, 7896, 633ED618:): System state cache
updated.
LOG(2013-10-09T18:35:33.820305, 7896, 633ED618:): > Startup script file
(C:\User
s\ah659\Desktop\OpenSPIM-20130131\OpenSPIM.app/MMStartup.bsh) not present.
LOG(2013-10-09T18:40:18.799605, 7896, 633ED618:): > Plugin command: Acquire
SPIM
 image
LOG(2013-10-09T18:40:19.135624, 7896, 633ED618:): Device SC10 message: 1
LOG(2013-10-09T18:40:19.220629, 7896, 633ED618:): Device CoolsnapMyo
message: St
arted sequence on CoolsnapMyo, at 434659219 220629, with 2147483647 and 0 ms

LOG(2013-10-09T18:40:19.902668, 7896, 633ED618:): Device SC10 message: 1
LOG(2013-10-09T18:40:20.040676, 7896, 633ED618:): Device CoolsnapMyo
message: St
arted sequence on CoolsnapMyo, at 434659220 40676, with 2147483647 and 0 ms

java.lang.NoClassDefFoundError: loci/common/services/ServiceFactory
        at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:55)
        at spim.SPIMAcquisition.actionPerformed(SPIMAcquisition.java:1721)
        at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19
95)
        at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
a:2318)
        at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
.java:387)
        at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242
)
        at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
istener.java:236)
        at java.awt.Component.processMouseEvent(Component.java:6289)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6054)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4652)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577
)
        at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
        at java.awt.EventQueue.access$000(EventQueue.java:85)
        at java.awt.EventQueue$1.run(EventQueue.java:603)
        at java.awt.EventQueue$1.run(EventQueue.java:601)
        at java.security.AccessController.doPrivileged(Native Method)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:98)
        at java.awt.EventQueue$2.run(EventQueue.java:617)
        at java.awt.EventQueue$2.run(EventQueue.java:615)
        at java.security.AccessController.doPrivileged(Native Method)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
        at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:174)
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.ClassNotFoundException:
loci.common.services.ServiceFactory

        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        ... 38 more
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException:
java.
lang.NoClassDefFoundError: loci/common/services/ServiceFactory
        at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:110)
        at spim.SPIMAcquisition.actionPerformed(SPIMAcquisition.java:1721)
        at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19
95)
        at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
a:2318)
        at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
.java:387)
        at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242
)
        at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
istener.java:236)
        at java.awt.Component.processMouseEvent(Component.java:6289)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6054)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4652)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577
)
        at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
        at java.awt.EventQueue.access$000(EventQueue.java:85)
        at java.awt.EventQueue$1.run(EventQueue.java:603)
        at java.awt.EventQueue$1.run(EventQueue.java:601)
        at java.security.AccessController.doPrivileged(Native Method)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:98)
        at java.awt.EventQueue$2.run(EventQueue.java:617)
        at java.awt.EventQueue$2.run(EventQueue.java:615)
        at java.security.AccessController.doPrivileged(Native Method)
        at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
        at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:174)
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.NoClassDefFoundError:
loci/common/services/ServiceFactory
        at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:55)
        ... 37 more
Caused by: java.lang.ClassNotFoundException:
loci.common.services.ServiceFactory

        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        ... 38 more

Hopefully that is useful.

Thanks again,
Aurelia



On Wed, Oct 9, 2013 at 1:37 AM, Johannes Schindelin <
Johannes.Schindelin at gmx.de> wrote:

> Hi Aurelia,
>
> On Tue, 8 Oct 2013, Aurelia Honerkamp-Smith wrote:
>
> > Sorry, I have been asking a lot of questions lately,
>
> There is really no reason to be sorry about that. Scientists have a track
> record of lacking the desire to communicate effectively, so I enjoy very
> much that you are an exception!
>
> > but I have at least one more today.  I can now acquire a stack, but only
> > if I leave the Output directory field blank (I attach a projection of my
> > first SPIM image, which I'm very happy about).
>
> This is a really awesome picture! Would you mind uploading it to the wiki
> and adding it to the gallery? I can help you with that should there be any
> problems.
>
> > If I put in a directory, then when I push Snap nothing happens.  It
> > doesn't seem to matter which folder I use, and there's no entry in the
> > core log.
>
> Could you copy the ImageJ-win32.exe in OpenSPIM.app/ and rename the copied
> file to debug.exe and run that? This should give you a console output (I
> strongly suspect an exception to occur, which I would be really eager to
> see, maybe you could copy/paste it into a reply?).
>
> > If it's a non-empty directory, I do get a message warning me that any
> > OME-tiff files will be deleted, but after I dismiss the message nothing
> > happens once more.
>
> It is probably the same issue in that case.
>
> > Has anyone had a problem like this before?  Could it be Windows 7
> related?
>
> Quite possibly. But I can only guess without having a glimpse at the
> console output.
>
> Ciao,
> Johannes
>
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