2016-11-17T15:21:35.608012 tid304 [IFO,LogManager] Enabled primary log file D:\mFiji\CoreLogs\CoreLog20161117T152135_pid2360.txt 2016-11-17T15:21:35.608012 tid304 [IFO,App] User: Admin 2016-11-17T15:21:35.608012 tid304 [IFO,App] Host: SPIM 2016-11-17T15:21:35.608012 tid304 [IFO,App] MM Studio version: 1.4.18 2016-11-17T15:21:35.608012 tid304 [IFO,App] MMCore version 5.0.3 2016-11-17T15:21:35.608012 tid304 [IFO,App] Device API version 60, Module API version 10 2016-11-17T15:21:35.608012 tid304 [IFO,App] Operating System: Windows 7 (amd64) 6.1 2016-11-17T15:21:35.608012 tid304 [IFO,App] JVM: Java HotSpot(TM) 64-Bit Server VM, version 1.6.0_31, 64-bit 2016-11-17T15:21:35.639212 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/ 2016-11-17T15:21:35.639212 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Big.jar!/ 2016-11-17T15:21:35.701612 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\DataBrowser.jar!/ 2016-11-17T15:21:36.169613 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Recall.jar!/ 2016-11-17T15:21:36.185213 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\SPIMacquisition.jar!/ 2016-11-17T15:21:36.325614 tid2644 [IFO,App] Installing plugin org.micromanager.browser.Data_Browser... 2016-11-17T15:21:36.325614 tid2644 [IFO,App] Error: Plugin [org.micromanager.browser.Data_Browser] has no menuName field 2016-11-17T15:21:36.325614 tid2644 [IFO,App] org.micromanager.browser.Data_Browser fails to implement static String tooltipDescription. 2016-11-17T15:21:36.325614 tid2644 [IFO,App] Installing plugin org.micromanager.recall.RecallPlugin... 2016-11-17T15:21:36.325614 tid2644 [IFO,App] Installing plugin spim.SPIMAcquisition... 2016-11-17T15:21:36.341214 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/Acquisition_Tools/ 2016-11-17T15:21:36.341214 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\AcquireMultipleRegions.jar!/ 2016-11-17T15:21:36.434814 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\Gaussian.jar!/ 2016-11-17T15:21:36.668814 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\HCS.jar!/ 2016-11-17T15:21:36.778014 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\IntelligentAcquisition.jar!/ 2016-11-17T15:21:36.871614 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\MMTracker.jar!/ 2016-11-17T15:21:36.918415 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Acquisition_Tools\SlideExplorer.jar!/ 2016-11-17T15:21:36.980815 tid2644 [IFO,App] Installing plugin org.micromanager.acquiremultipleregions.AcquireMultipleRegions... 2016-11-17T15:21:36.980815 tid2644 [IFO,App] Installing plugin GaussianTrack_... 2016-11-17T15:21:36.980815 tid2644 [IFO,App] Installing plugin org.micromanager.hcs.SiteGenerator... 2016-11-17T15:21:36.980815 tid2644 [IFO,App] Installing plugin org.micromanager.intelligentacquisition.IntelligentAcquisition... 2016-11-17T15:21:36.980815 tid2644 [IFO,App] Installing plugin com.imaging100x.tracker.TrackerControl... 2016-11-17T15:21:36.996415 tid2644 [IFO,App] Installing plugin org.micromanager.slideexplorer.SlideExplorerPlugin... 2016-11-17T15:21:36.996415 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/Beta/ 2016-11-17T15:21:36.996415 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Beta\PixelCalibrator.jar!/ 2016-11-17T15:21:37.043215 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Beta\SlideExplorer2.jar!/ 2016-11-17T15:21:38.774818 tid304 [IFO,App] Waiting for plugins to finish loading... 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Installing plugin org.micromanager.pixelcalibrator.PixelCalibratorPlugin... 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Installing plugin org.micromanager.SlideExplorer2... 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Error: Plugin [org.micromanager.SlideExplorer2] has no menuName field 2016-11-17T15:21:40.085220 tid2644 [IFO,App] org.micromanager.SlideExplorer2 fails to implement static String tooltipDescription. 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/Developer_Tools/ 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Developer_Tools\ClojureEditor.jar!/ 2016-11-17T15:21:40.085220 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Developer_Tools\DLLAutoReloader.jar!/ 2016-11-17T15:21:40.194420 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Developer_Tools\SequenceBufferMonitor.jar!/ 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Installing plugin org.micromanager.clojureeditor.ClojureEditorPlugin... 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Installing plugin org.micromanager.DLLAutoReloader... 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Error: Plugin [org.micromanager.DLLAutoReloader] has no menuName field 2016-11-17T15:21:40.210020 tid2644 [IFO,App] org.micromanager.DLLAutoReloader fails to implement static String tooltipDescription. 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Installing plugin org.micromanager.plugins.sequencebuffermonitor.SequenceBufferMonitor... 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/Device_Control/ 2016-11-17T15:21:40.210020 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\ASIdiSPIM.jar!/ 2016-11-17T15:21:40.334821 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\AutoLase.jar!/ 2016-11-17T15:21:40.475221 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\CRISP.jar!/ 2016-11-17T15:21:40.537621 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\MultiCamera.jar!/ 2016-11-17T15:21:40.584421 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\pgFocus.jar!/ 2016-11-17T15:21:40.709221 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\Projector.jar!/ 2016-11-17T15:21:40.787221 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Device_Control\StageControl.jar!/ 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin org.micromanager.asidispim.ASIdiSPIM... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin ch.epfl.leb.autolase.AutoLasePlugin... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin org.micromanager.CRISP.CRISP... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin org.micromanager.multicamera.MultiCamera... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin edu.umassmed.pgfocus.pgFocus... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin org.micromanager.projector.ProjectorPlugin... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Installing plugin org.micromanager.stagecontrol.StageControl... 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmplugins/Image_Processing/ 2016-11-17T15:21:40.834021 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Image_Processing\ImageFlipper.jar!/ 2016-11-17T15:21:40.865221 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Image_Processing\MultiChannelShading.jar!/ 2016-11-17T15:21:40.990022 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmplugins\Image_Processing\SplitView.jar!/ 2016-11-17T15:21:41.036822 tid2644 [IFO,App] Installing plugin org.micromanager.newimageflipper.NewTaggedImageFlipper... 2016-11-17T15:21:41.036822 tid2644 [IFO,App] Installing plugin org.micromanager.multichannelshading.MultiChannelShading... 2016-11-17T15:21:41.036822 tid2644 [IFO,App] Installing plugin org.micromanager.splitview.SplitView... 2016-11-17T15:21:41.083622 tid2644 [IFO,App] Added URL to system class loader: file:/D:/mFiji/mmautofocus/ 2016-11-17T15:21:41.083622 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmautofocus\MMAutofocus.jar!/ 2016-11-17T15:21:41.114822 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmautofocus\MMAutofocusDuo.jar!/ 2016-11-17T15:21:41.114822 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmautofocus\MMAutofocusTB.jar!/ 2016-11-17T15:21:41.130422 tid2644 [IFO,App] Added URL to system class loader: jar:file:D:\mFiji\mmautofocus\MMOughtaFocus.jar!/ 2016-11-17T15:21:41.177222 tid2644 [IFO,App] Installing autofocus plugin Autofocus... 2016-11-17T15:21:41.177222 tid2644 [IFO,App] Installing autofocus plugin AutofocusDuo... 2016-11-17T15:21:41.177222 tid2644 [IFO,App] Installing autofocus plugin AutofocusTB... 2016-11-17T15:21:41.177222 tid2644 [IFO,App] Installing autofocus plugin OughtaFocus... 2016-11-17T15:21:41.177222 tid304 [IFO,App] Finished waiting for plugins to load 2016-11-17T15:21:41.239622 tid304 [IFO,Core] Did unload all devices 2016-11-17T15:21:41.286422 tid304 [IFO,Core] Did load device COM3 from SerialManager; label = COM3 2016-11-17T15:21:41.380022 tid304 [IFO,Core] Did load device Picard Twister from PicardStage; label = Picard Twister 2016-11-17T15:21:41.380022 tid304 [IFO,Core] Did load device Picard Z Stage from PicardStage; label = Picard Z Stage 2016-11-17T15:21:41.380022 tid304 [IFO,Core] Did load device Picard XY Stage from PicardStage; label = Picard XY Stage 2016-11-17T15:21:42.284824 tid304 [IFO,Core] Did load device HamamatsuHam_DCAM from HamamatsuHam; label = OrcaFlash 2016-11-17T15:21:42.300424 tid304 [IFO,Core] Did load device Cobolt from Cobolt; label = Cobolt 2016-11-17T15:21:42.409624 tid304 [IFO,Core] Will initialize 6 devices 2016-11-17T15:21:42.409624 tid304 [IFO,Core] Will initialize device COM3 2016-11-17T15:21:42.425224 tid304 [IFO,Core] Did initialize device COM3 2016-11-17T15:21:42.425224 tid304 [IFO,Core] Will initialize device Picard Twister 2016-11-17T15:21:42.456424 tid304 [IFO,Core] Did initialize device Picard Twister 2016-11-17T15:21:42.456424 tid304 [IFO,Core] Will initialize device Picard Z Stage 2016-11-17T15:21:42.456424 tid304 [IFO,Core] Did initialize device Picard Z Stage 2016-11-17T15:21:42.456424 tid304 [IFO,Core] Will initialize device Picard XY Stage 2016-11-17T15:21:42.503224 tid304 [IFO,Core] Did initialize device Picard XY Stage 2016-11-17T15:21:42.503224 tid304 [IFO,Core] Default xy stage set to Picard XY Stage 2016-11-17T15:21:42.503224 tid304 [IFO,Core] Will initialize device OrcaFlash 2016-11-17T15:21:46.012188 tid304 [IFO,Core] Did initialize device OrcaFlash 2016-11-17T15:21:46.012188 tid304 [IFO,Core] Default camera set to OrcaFlash 2016-11-17T15:21:46.012188 tid304 [IFO,Core] Will initialize device Cobolt 2016-11-17T15:21:46.121194 tid304 [IFO,Core] Did initialize device Cobolt 2016-11-17T15:21:46.121194 tid304 [IFO,Core] Default shutter set to Cobolt 2016-11-17T15:21:46.121194 tid304 [IFO,Core] Finished initializing 6 devices 2016-11-17T15:21:46.121194 tid304 [IFO,Core] Default camera set to OrcaFlash 2016-11-17T15:21:46.121194 tid304 [IFO,Core] Default stage set to Picard Z Stage 2016-11-17T15:21:46.240201 tid304 [IFO,Core] Did update system state cache 2016-11-17T15:21:46.281203 tid304 [ERR,Core] Error occurred in device CMMCore::getShutterOpen(): Error in device "Cobolt": Invalid state (position) requested (12) 2016-11-17T15:21:46.288204 tid304 [IFO,App] [ ] java.lang.Exception: Error in device "Cobolt": Invalid state (position) requested (12) in Thread[AWT-EventQueue-0,6,main] [ ] at mmcorej.MMCoreJJNI.CMMCore_getShutterOpen__SWIG_0(Native Method) [ ] at mmcorej.CMMCore.getShutterOpen(CMMCore.java:881) [ ] at org.micromanager.MMStudioMainFrame.updateGUI(MMStudioMainFrame.java:2555) [ ] at org.micromanager.MMStudioMainFrame.updateGUI(MMStudioMainFrame.java:2526) [ ] at org.micromanager.MMStudioMainFrame.initializeGUI(MMStudioMainFrame.java:2414) [ ] at org.micromanager.MMStudioMainFrame.loadSystemConfiguration(MMStudioMainFrame.java:2877) [ ] at org.micromanager.MMStudioMainFrame.initializationSequence(MMStudioMainFrame.java:589) [ ] at org.micromanager.MMStudioMainFrame.access$100(MMStudioMainFrame.java:176) [ ] at org.micromanager.MMStudioMainFrame$1.windowOpened(MMStudioMainFrame.java:477) [ ] at java.awt.AWTEventMulticaster.windowOpened(Unknown Source) [ ] at java.awt.Window.processWindowEvent(Unknown Source) [ ] at javax.swing.JFrame.processWindowEvent(Unknown Source) [ ] at java.awt.Window.processEvent(Unknown Source) [ ] at java.awt.Component.dispatchEventImpl(Unknown Source) [ ] at java.awt.Container.dispatchEventImpl(Unknown Source) [ ] at java.awt.Window.dispatchEventImpl(Unknown Source) [ ] at java.awt.Component.dispatchEvent(Unknown Source) [ ] at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [ ] at java.awt.EventQueue.access$000(Unknown Source) [ ] at java.awt.EventQueue$1.run(Unknown Source) [ ] at java.awt.EventQueue$1.run(Unknown Source) [ ] at java.security.AccessController.doPrivileged(Native Method) [ ] at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) [ ] at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) [ ] at java.awt.EventQueue$2.run(Unknown Source) [ ] at java.awt.EventQueue$2.run(Unknown Source) [ ] at java.security.AccessController.doPrivileged(Native Method) [ ] at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) [ ] at java.awt.EventQueue.dispatchEvent(Unknown Source) [ ] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [ ] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [ ] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [ ] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [ ] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [ ] at java.awt.EventDispatchThread.run(Unknown Source) 2016-11-17T15:21:46.338207 tid304 [IFO,App] Startup script file (D:\mFiji\MMStartup.bsh) not present. 2016-11-17T15:44:45.949116 tid304 [IFO,App] Stop called in LivemodeTimer, true 2016-11-17T15:44:55.108640 tid4064 [ERR,Core] Error occurred in device CMMCore::getShutterOpen(): Error in device "Cobolt": Invalid state (position) requested (12) 2016-11-17T15:44:55.110640 tid3088 [IFO,App] Acquisition failed. [ ] java.lang.RuntimeException: java.lang.Exception: Error in device "Cobolt": Invalid state (position) requested (12) in Thread[clojure-agent-send-off-pool-0,6,main] [ ] at clojure.lang.Util.runtimeException(Util.java:165) [ ] at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:97) [ ] at clojure.lang.Reflector.invokeNoArgInstanceMember(Reflector.java:316) [ ] at org.micromanager.acq_engine$prepare_state.invoke(acq_engine.clj:643) [ ] at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:740) [ ] at org.micromanager.acq_engine$run$fn__1408.invoke(acq_engine.clj:896) [ ] at clojure.lang.AFn.run(AFn.java:24) [ ] at java.lang.Thread.run(Unknown Source) [ ] Caused by: java.lang.Exception: Error in device "Cobolt": Invalid state (position) requested (12) [ ] at mmcorej.MMCoreJJNI.CMMCore_getShutterOpen__SWIG_0(Native Method) [ ] at mmcorej.CMMCore.getShutterOpen(CMMCore.java:881) [ ] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [ ] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) [ ] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) [ ] at java.lang.reflect.Method.invoke(Unknown Source) [ ] at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92) [ ] at clojure.lang.Reflector.invokeNoArgInstanceMember(Reflector.java:316) [ ] at org.micromanager.acq_engine$prepare_state.invoke(acq_engine.clj:643) [ ] at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:740) [ ] at org.micromanager.acq_engine$run$fn__1408.invoke(acq_engine.clj:896) [ ] at clojure.lang.AFn.run(AFn.java:24) [ ] at java.lang.Thread.run(Unknown Source) 2016-11-17T15:44:55.161643 tid4064 [IFO,App] Acquisition cleanup failed. [ ] java.lang.IllegalArgumentException in Thread[AcquisitionEngine2010 Thread (Clojure),6,main] [ ] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [ ] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) [ ] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) [ ] at java.lang.reflect.Method.invoke(Unknown Source) [ ] at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92) [ ] at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:30) [ ] at org.micromanager.acq_engine$cleanup$fn__1200.invoke(acq_engine.clj:672) [ ] at org.micromanager.acq_engine$cleanup.invoke(acq_engine.clj:663) [ ] at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:750) [ ] at org.micromanager.acq_engine$run$fn__1408.invoke(acq_engine.clj:896) [ ] at clojure.lang.AFn.run(AFn.java:24) [ ] at java.lang.Thread.run(Unknown Source) 2016-11-17T15:44:59.640899 tid1428 [IFO,App] 0 images stored in 4657 ms. 2016-11-17T15:45:05.502234 tid304 [IFO,App] Stop called in LivemodeTimer, true 2016-11-17T15:45:05.945647 tid304 [IFO,Core] Did unload all devices 2016-11-17T15:45:05.945647 tid304 [IFO,Core] System reset 2016-11-17T15:45:05.945647 tid304 [IFO,Core] Core session ended