[OpenSPIM] SPIM with no laser control
Aurelia Honerkamp-Smith
aureliaomega at gmail.com
Thu Oct 3 09:26:44 CDT 2013
Hi Luke,
Now that I have added the Thorlabs shutter to the configuration as the
default shutter, I don't get the error message about the configuration
being invalid, and the OpenSPIM window never opens at all. A corelog is
attached in case it's helpful.
I had a problem with the development environment self-installer - it seems
upset that I don't have Visual Studio 2008 (I have 2010; a screen grab of
the error message is attached) but it looks as though all the source files
ended up where they should be anyway, so I'll start having a look.
Thank you again!
Aurelia
On Wed, Oct 2, 2013 at 10:48 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>wrote:
> Aurelia,
>
> Is the ThorLabs shutter set as the default shutter for your setup? (i.e.
> does it respond to Micro-Manager's auto-shutter functionality?) This is
> specified during hardware configuration. If so, please attach a core log
> (any should do, as long as you got the 'setup is invalid' warning) -- the
> SPIM device manager should be trying to use it as a laser; if this isn't
> happening, an exception may be appearing in the core log. If the issue is
> as simple as this, I may be able to fix it with minimal work, which is
> arguably preferable to the alternative.
>
>
> The alternative: Although the ThorLabs shutter *should* be supported as a
> 'generic laser', it is possible to specifically add support for the device,
> though it requires some Java programming. If you're already familiar with
> our development environment (see
> http://openspim.org/How_to_build_the_software -- fair warning: setting up
> the development environment can take some time), the place to start is
> plugins/SPIMAcquisition/src/main/java/; in here are various files like
> PicardStage.java and CoherentCube.java. I recommend reading the top of
> PicardStage.java for an explanation of the block at the top of the class,
> then copying and renaming CoherentCube.java to i.e. ThorLabsShutter.java.
> Rename the contained class and change the string "CoherentCube" to the
> appropriate device name -- according to the device adapter source code in
> DeviceAdapters/ThorlabsSC10/, the right string is "SC10" -- and change the
> rest of the functions however you see fit.
>
>
> Thanks,
> Luke
>
> On 10/01/13, Aurelia Honerkamp-Smith wrote:
> > Hi everyone,
> >
> >
> > I guess now is a good time to mention that I built my SPIM using a laser
> line we already had instead of purchasing the Coherent Cube, by diverting
> the existing line to the SPIM with a flip mirror and a periscope. Laser
> power control is manual. The fact that I have no laser connected is causing
> a problem for SPIM acquisition, though. I get an error message that my
> setup is invalid when I first start the plugin; then, although acquisition
> through the Video tab works OK, I can't acquire a regular stack or
> timelapse: I get "Error acquiring: null" when I push the Oh Snap button. I
> need to change the plugin so that it ignores the laser power control, and
> uses a Thorlabs shutter for blinking instead of the laser. I realize this
> might be a tall order, so I'm ready to start working on it myself, but
> I would appreciate being pointed in the right direction for how to do this
> most efficiently.
> >
> >
> > Thanks again,
> > Aurelia
> >
> >
>
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LOG(2013-10-03T12:33:57.752837, 2004, 00791590:): -------->>
LOG(2013-10-03T12:33:57.752837, 2004, 00791590:): Core session started on 2013-10-03T12:33:57.752837 by ah659 on INVERT
LOG(2013-10-03T12:33:57.752837, 2004, 00791590:): Debug logging disabled
LOG(2013-10-03T12:33:57.752837, 2004, 00791590:): Debug logging disabled
LOG(2013-10-03T12:33:57.752837, 2004, 00791590:): > MM Studio version: 1.4.x dev
LOG(2013-10-03T12:33:57.753837, 2004, 00791590:): > MMCore version 2.3.2
LOG(2013-10-03T12:33:57.753837, 2004, 00791590:): > Device API version 53, Module API version 7
LOG(2013-10-03T12:33:57.753837, 2004, 00791590:): > Operating System: Windows 7 6.1
LOG(2013-10-03T12:33:57.753837, 2004, 00791590:): > JVM: Java HotSpot(TM) Client VM, version 1.6.0_24; 32 bit
LOG(2013-10-03T12:33:57.936848, 2004, 00791A40:): > #uManager plugins: 118
LOG(2013-10-03T12:33:57.936848, 2004, 00791A40:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-03T12:33:57.936848, 2004, 00791A40:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-03T12:33:57.936848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.MouseListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ItemListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ItemListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.util.Comparator
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.io.FilenameFilter
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.progacq.AntiDrift$Factory
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.progacq.ProgrammaticAcquisitor$AcqProgressCallback
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: org.micromanager.api.MMPlugin
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ItemListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.SPIMAutoCalibrator$RunnableWRet
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.SPIMCalibrator
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.MouseListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.MouseMotionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.SPIMCalibrator
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: spim.SPIMCalibrator
LOG(2013-10-03T12:33:57.937848, 2004, 00791A40:): > interface found: java.awt.event.MouseListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.WindowListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.KeyListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.FocusListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.ActionListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: javax.swing.event.ChangeListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Thread$UncaughtExceptionHandler
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AntiDrift$Callback
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Runnable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.progacq.AntiDrift$Callback
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.KeyListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: javax.swing.event.ChangeListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.KeyListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.lang.Iterable
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.awt.event.ItemListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: java.util.EventListener
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.938848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.939848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.939848, 2004, 00791A40:): > interface found: spim.setup.Device$Factory
LOG(2013-10-03T12:33:57.939848, 2004, 00791A40:): > Attempting to install plugin spim.SPIMAcquisition
LOG(2013-10-03T12:34:02.951135, 2004, 00791590:): All devices unloaded.
LOG(2013-10-03T12:34:02.951135, 2004, 00791590:): > Notification for Device: Core Property: Initialize changed to value: 0
LOG(2013-10-03T12:34:02.999137, 2004, 00791590:): Device COM3 loaded from SerialManager and labeled as COM3
LOG(2013-10-03T12:34:03.072142, 2004, 00791590:): Device Camera-1 loaded from PVCAM and labeled as CoolsnapMyo
LOG(2013-10-03T12:34:03.072142, 2004, 00791590:): Device CoolsnapMyo set as default camera.
LOG(2013-10-03T12:34:04.191206, 2004, 00791590:): Device Picard Twister loaded from PicardStage and labeled as Picard Twister
LOG(2013-10-03T12:34:04.191206, 2004, 00791590:): Device Picard Z Stage loaded from PicardStage and labeled as Picard Z Stage
LOG(2013-10-03T12:34:04.192206, 2004, 00791590:): Device Picard XY Stage loaded from PicardStage and labeled as Picard XY Stage
LOG(2013-10-03T12:34:04.192206, 2004, 00791590:): Device Picard XY Stage set as default xyStage.
LOG(2013-10-03T12:34:04.249209, 2004, 00791590:): Device SC10 loaded from ThorlabsSC10 and labeled as SC10
LOG(2013-10-03T12:34:04.249209, 2004, 00791590:): Device SC10 set as default shutter.
LOG(2013-10-03T12:34:04.314213, 2004, 00791590:): Starting initialization sequence for 6 devices...
LOG(2013-10-03T12:34:04.412218, 2004, 00791590:): Device COM3 initialized.
LOG(2013-10-03T12:34:04.419219, 2004, 00791590:): Device CoolsnapMyo message: PVCAM VERSION: 2.9.5. Number of cameras detected: 1
LOG(2013-10-03T12:34:04.471222, 2004, 00791590:): Device CoolsnapMyo message: Building Speed Table
LOG(2013-10-03T12:34:04.588228, 2004, 00791590:): Device CoolsnapMyo message: Initializing Static Camera Properties
LOG(2013-10-03T12:34:04.600229, 2004, 00791590:): Device CoolsnapMyo message: Initializing Dynamic Camera Properties
LOG(2013-10-03T12:34:04.781239, 2004, 00791590:): Device CoolsnapMyo message: This Camera does not have EM Gain
LOG(2013-10-03T12:34:04.781239, 2004, 00791590:): Device CoolsnapMyo message: Frame Transfer mode not available
LOG(2013-10-03T12:34:04.825242, 2004, 00791590:): Device CoolsnapMyo message: Using PVCAM callbacks for frame acquisition
LOG(2013-10-03T12:34:04.825242, 2004, 00791590:): Device CoolsnapMyo initialized.
LOG(2013-10-03T12:34:04.830242, 2004, 00791590:): Device Picard Twister initialized.
LOG(2013-10-03T12:34:04.854244, 2004, 00791590:): Device Picard Z Stage initialized.
LOG(2013-10-03T12:34:04.890246, 2004, 00791590:): Device Picard XY Stage initialized.
LOG(2013-10-03T12:34:04.945249, 2004, 00791590:): Device SC10 message: THORLABS SC10 VERSION 1.07
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): Device SC10 initialized.
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): > Notification for Device: Core Property: Initialize changed to value: 1
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): Camera device set to CoolsnapMyo
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): > Notification for Device: Core Property: Camera changed to value: CoolsnapMyo
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): > Notification for Device: Core Property: Shutter changed to value: SC10
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): Focus device set to Picard Z Stage
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): > Notification for Device: Core Property: Focus changed to value: Picard Z Stage
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): Auto shutter ON.
LOG(2013-10-03T12:34:04.961250, 2004, 00791590:): > Notification for Device: Core Property: AutoShutter changed to value: 1
LOG(2013-10-03T12:34:04.986251, 2004, 00791590:): System state cache updated.
LOG(2013-10-03T12:34:05.041254, 2004, 00791590:): Device SC10 message: 1
LOG(2013-10-03T12:34:05.050255, 2004, 00791590:): System state cache updated.
LOG(2013-10-03T12:34:05.085257, 2004, 00791590:): > Startup script file (C:\Users\ah659\Desktop\OpenSPIM-20130131\OpenSPIM.app/MMStartup.bsh) not present.
LOG(2013-10-03T12:34:12.678691, 2004, 00791590:): > Plugin command: Acquire SPIM image
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Resolution ID Uncalibrated: for device Core defined as Initialize=1
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Pixel size 1.000000 um set for resolution ID: Uncalibrated
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Starting initialization sequence for 6 devices...
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Device COM3 initialized.
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Device CoolsnapMyo message: PVCAM VERSION: 2.9.5. Number of cameras detected: 1
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Device CoolsnapMyo message: PVCAM API error: "C0_CAM_ALREADY_OPEN This user has already opened this camera", code: 117
In file: .\PVCAMUniversal.cpp, line: 308, pl_cam_open
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Error occurred. Device CoolsnapMyo. Error in device CoolsnapMyo: C0_CAM_ALREADY_OPEN This user has already opened this camera.
, file MMCore.cpp, line 873
LOG(2013-10-03T12:34:12.706693, 2004, 00791590:): Error occurred. Device setPixelSizeConfig. Device error encountered.
LOG(2013-10-03T12:34:12.707693, 2004, 00791590:): > Couldn't define uncalibrated pixel size:
LOG(2013-10-03T12:34:12.707693, 2004, 00791590:): > java.lang.Exception: Error in device CoolsnapMyo: C0_CAM_ALREADY_OPEN This user has already opened this camera.
Device error encountered.
at mmcorej.MMCoreJJNI.CMMCore_setPixelSizeConfig(Native Method)
at mmcorej.CMMCore.setPixelSizeConfig(CMMCore.java:707)
at spim.SPIMAcquisition.ensurePixelResolution(SPIMAcquisition.java:261)
at spim.SPIMAcquisition.show(SPIMAcquisition.java:218)
at org.micromanager.MMStudioMainFrame$50.actionPerformed(MMStudioMainFrame.java:3316)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
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(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.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(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.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)
LOG(2013-10-03T12:38:11.381344, 2004, 00775600:): > Plugin command: Acquire SPIM image
LOG(2013-10-03T12:38:19.855829, 2004, 00775600:): Device SC10 message: 1
LOG(2013-10-03T12:38:19.930833, 2004, 00775600:): Device CoolsnapMyo message: Started sequence on CoolsnapMyo, at 434119099 930833, with 2147483647 and 0 ms
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