[OpenSPIM] SPIM with no laser control
Aurelia Honerkamp-Smith
aureliaomega at gmail.com
Fri Oct 4 06:43:59 CDT 2013
> Could you just run the "msys.bat" again? It should have gotten the newest
> version in the previous run and use that from now on.
>
>
Yes, but how do I run it again, and where can I find it? I tried running
the installer again, and I tried building Micromanager again from the
git-bash file in the development environment folder, but I got the same
error both times.
Please look at the end of said core log. In the line above that
stacktrace, it suggests that "the user has the camera open already"? Is
it possible that another uManager instance is still running?
This is pretty strange. This morning I got the same message in the log
about the camera being open already, but I have made absolutely certain
that there was not another instance running. I then tried Live view and
Snap, which both work correctly. After this I tried to open the SPIM plugin
again, and there is still no response, but I don't get the message about
the camera being open anymore.
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LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): -------->>
LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): Core session started on 2013-10-04T12:28:58.327611 by ah659 on INVERT
LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): Debug logging disabled
LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): Debug logging disabled
LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): > MM Studio version: 1.4.x dev
LOG(2013-10-04T12:28:58.327611, 5552, 60C62E88:): > MMCore version 2.3.2
LOG(2013-10-04T12:28:58.328611, 5552, 60C62E88:): > Device API version 53, Module API version 7
LOG(2013-10-04T12:28:58.328611, 5552, 60C62E88:): > Operating System: Windows 7 6.1
LOG(2013-10-04T12:28:58.328611, 5552, 60C62E88:): > JVM: Java HotSpot(TM) Client VM, version 1.6.0_24; 32 bit
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > #uManager plugins: 118
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: org.apache.commons.math.analysis.MultivariateRealFunction
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.MouseListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ItemListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ItemListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.util.Comparator
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.io.FilenameFilter
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: spim.progacq.AntiDrift$Factory
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: spim.progacq.ProgrammaticAcquisitor$AcqProgressCallback
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: org.micromanager.api.MMPlugin
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ItemListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: spim.SPIMAutoCalibrator$RunnableWRet
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: spim.SPIMCalibrator
LOG(2013-10-04T12:29:00.009707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.MouseListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.MouseMotionListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.SPIMCalibrator
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.SPIMCalibrator
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.MouseListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.WindowListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.KeyListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.FocusListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.ActionListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: javax.swing.event.ChangeListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Thread$UncaughtExceptionHandler
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AcqOutputHandler
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AntiDrift$Callback
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Runnable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.progacq.AntiDrift$Callback
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.KeyListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: javax.swing.event.ChangeListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.awt.event.KeyListener
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: java.lang.Iterable
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.010707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: java.awt.event.ItemListener
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: java.util.EventListener
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > interface found: spim.setup.Device$Factory
LOG(2013-10-04T12:29:00.011707, 5552, 60C631D0:): > Attempting to install plugin spim.SPIMAcquisition
LOG(2013-10-04T12:30:49.579974, 5552, 60C62E88:): All devices unloaded.
LOG(2013-10-04T12:30:49.579974, 5552, 60C62E88:): > Notification for Device: Core Property: Initialize changed to value: 0
LOG(2013-10-04T12:30:49.637977, 5552, 60C62E88:): Device COM3 loaded from SerialManager and labeled as COM3
LOG(2013-10-04T12:30:49.710981, 5552, 60C62E88:): Device Camera-1 loaded from PVCAM and labeled as CoolsnapMyo
LOG(2013-10-04T12:30:49.710981, 5552, 60C62E88:): Device CoolsnapMyo set as default camera.
LOG(2013-10-04T12:30:50.800044, 5552, 60C62E88:): Device Picard Twister loaded from PicardStage and labeled as Picard Twister
LOG(2013-10-04T12:30:50.800044, 5552, 60C62E88:): Device Picard Z Stage loaded from PicardStage and labeled as Picard Z Stage
LOG(2013-10-04T12:30:50.801044, 5552, 60C62E88:): Device Picard XY Stage loaded from PicardStage and labeled as Picard XY Stage
LOG(2013-10-04T12:30:50.801044, 5552, 60C62E88:): Device Picard XY Stage set as default xyStage.
LOG(2013-10-04T12:30:50.933051, 5552, 60C62E88:): Device SC10 loaded from ThorlabsSC10 and labeled as SC10
LOG(2013-10-04T12:30:50.933051, 5552, 60C62E88:): Device SC10 set as default shutter.
LOG(2013-10-04T12:30:51.019056, 5552, 60C62E88:): Starting initialization sequence for 6 devices...
LOG(2013-10-04T12:30:51.113062, 5552, 60C62E88:): Device COM3 initialized.
LOG(2013-10-04T12:30:51.120062, 5552, 60C62E88:): Device CoolsnapMyo message: PVCAM VERSION: 2.9.5. Number of cameras detected: 1
LOG(2013-10-04T12:30:51.172065, 5552, 60C62E88:): Device CoolsnapMyo message: Building Speed Table
LOG(2013-10-04T12:30:51.289072, 5552, 60C62E88:): Device CoolsnapMyo message: Initializing Static Camera Properties
LOG(2013-10-04T12:30:51.301072, 5552, 60C62E88:): Device CoolsnapMyo message: Initializing Dynamic Camera Properties
LOG(2013-10-04T12:30:51.482083, 5552, 60C62E88:): Device CoolsnapMyo message: This Camera does not have EM Gain
LOG(2013-10-04T12:30:51.482083, 5552, 60C62E88:): Device CoolsnapMyo message: Frame Transfer mode not available
LOG(2013-10-04T12:30:51.526085, 5552, 60C62E88:): Device CoolsnapMyo message: Using PVCAM callbacks for frame acquisition
LOG(2013-10-04T12:30:51.526085, 5552, 60C62E88:): Device CoolsnapMyo initialized.
LOG(2013-10-04T12:30:51.535086, 5552, 60C62E88:): Device Picard Twister initialized.
LOG(2013-10-04T12:30:51.559087, 5552, 60C62E88:): Device Picard Z Stage initialized.
LOG(2013-10-04T12:30:51.595089, 5552, 60C62E88:): Device Picard XY Stage initialized.
LOG(2013-10-04T12:30:51.647092, 5552, 60C62E88:): Device SC10 message: THORLABS SC10 VERSION 1.07
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): Device SC10 initialized.
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): > Notification for Device: Core Property: Initialize changed to value: 1
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): Camera device set to CoolsnapMyo
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): > Notification for Device: Core Property: Camera changed to value: CoolsnapMyo
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): > Notification for Device: Core Property: Shutter changed to value: SC10
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): Focus device set to Picard Z Stage
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): > Notification for Device: Core Property: Focus changed to value: Picard Z Stage
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): Auto shutter ON.
LOG(2013-10-04T12:30:51.663093, 5552, 60C62E88:): > Notification for Device: Core Property: AutoShutter changed to value: 1
LOG(2013-10-04T12:30:51.691095, 5552, 60C62E88:): System state cache updated.
LOG(2013-10-04T12:30:51.743098, 5552, 60C62E88:): Device SC10 message: 1
LOG(2013-10-04T12:30:51.755098, 5552, 60C62E88:): System state cache updated.
LOG(2013-10-04T12:30:51.788100, 5552, 60C62E88:): > Startup script file (C:\Users\ah659\Desktop\OpenSPIM-20130131\OpenSPIM.app/MMStartup.bsh) not present.
LOG(2013-10-04T12:31:03.124749, 5552, 60C62E88:): > Plugin command: Acquire SPIM image
LOG(2013-10-04T12:31:03.154750, 5552, 60C62E88:): Resolution ID Uncalibrated: for device Core defined as Initialize=1
LOG(2013-10-04T12:31:03.154750, 5552, 60C62E88:): Pixel size 1.000000 um set for resolution ID: Uncalibrated
LOG(2013-10-04T12:31:03.154750, 5552, 60C62E88:): Starting initialization sequence for 6 devices...
LOG(2013-10-04T12:31:03.155750, 5552, 60C62E88:): Device COM3 initialized.
LOG(2013-10-04T12:31:03.155750, 5552, 60C62E88:): Device CoolsnapMyo message: PVCAM VERSION: 2.9.5. Number of cameras detected: 1
LOG(2013-10-04T12:31:03.155750, 5552, 60C62E88:): 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(2013-10-04T12:31:03.155750, 5552, 60C62E88:): 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(2013-10-04T12:31:03.155750, 5552, 60C62E88:): Error occurred. Device setPixelSizeConfig. Device error encountered.
LOG(2013-10-04T12:31:03.155750, 5552, 60C62E88:): > Couldn't define uncalibrated pixel size:
LOG(2013-10-04T12:31:03.156750, 5552, 60C62E88:): > 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(2013-10-04T12:36:48.648511, 5552, 60C63298:): Device SC10 message: 1
LOG(2013-10-04T12:36:48.731516, 5552, 60C63298:): Device CoolsnapMyo message: Started sequence on CoolsnapMyo, at 434205408 731516, with 2147483647 and 0 ms
LOG(2013-10-04T12:37:03.113339, 5552, 60C63298:): Device SC10 message: 1
LOG(2013-10-04T12:37:03.464359, 5552, 60C63298:): Device SC10 message: 1
LOG(2013-10-04T12:37:08.980674, 5552, 60C63298:): > Plugin command: Acquire SPIM image
LOG(2013-10-04T12:41:17.572893, 5552, 00828998:): > Plugin command: Acquire SPIM image
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