[OpenSPIM] OpenSPIM plugin not opening
Robert Konstandelos
rk685 at york.ac.uk
Mon Mar 16 17:10:30 CDT 2015
Hi all,
As you maybe aware from the OpenSPIM digest vol23, issue 2 I have been
trying to get my Coherent OBIS to work with your plugin on Micro-Manager.
I have had a lot of assistance already from Graham Marquart- which I
greatly appreciate- taking the download of the SPIM acquisition plugin to
constructing the required plugin using Maven. I alter your CoherentCube
java file to that which has Coherent Obis instead. Then Create the
executable files using maven with each install resulting in a build
success.
I copy the resulting plugin from the new target folder to the mmplugins
folder and subsequently run Fiji with MM- the developmental version which
installed with the latest version of Fiji. I tried to run the app but the
app does not open. It fails.
I have attached the error report generated by Micro-Manager to see where my
error might be? I have also attached the compile Graham had wrote for me
which has done an excellent job.
I apologise for having to bring this issue up again but I am not the
greatest when it comes to coding.
Thanks
Rob
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#Report Format Version: 2.1
#User Name: null
#Organization: null
#User e-mail: null
#User Description:
#MAC: f8-b1-56-c2-20-e7
#Host: biolpc2829
#User: biolpc2829
#Pid: 2960
#Starting Config File: C:\Users\biolpc2829\Desktop\Fiji.app\OpenSPIM.cfg
#Config Changed: no
***** BEGIN Starting Config (C:\Users\biolpc2829\Desktop\Fiji.app\OpenSPIM.cfg) *****
# Generated by Configurator on Fri Mar 13 10:50:10 GMT 2015
# Reset
Property,Core,Initialize,0
# Devices
Device,COM3,SerialManager,COM3
Device,CoherentObis,CoherentOBIS,CoherentObis
Device,HamamatsuHam_DCAM,HamamatsuHam,HamamatsuHam_DCAM
Device,Picard Twister,PicardStage,Picard Twister
Device,Picard Z Stage,PicardStage,Picard Z Stage
Device,Picard XY Stage,PicardStage,Picard XY Stage
# Pre-init settings for devices
Property,CoherentObis,Port,COM3
Property,Picard Twister,Max,32767
Property,Picard Twister,Min,-32767
Property,Picard Twister,Serial Number,100
Property,Picard Twister,StepSize,1.0000
Property,Picard Z Stage,Max,7800
Property,Picard Z Stage,Min,0
Property,Picard Z Stage,Serial Number,296
Property,Picard Z Stage,StepSize,1.5000
Property,Picard XY Stage,Serial Number (X),294
Property,Picard XY Stage,Serial Number (Y),295
Property,Picard XY Stage,X-Max,7800
Property,Picard XY Stage,X-Min,0
Property,Picard XY Stage,X-StepSize,1.5000
Property,Picard XY Stage,Y-Max,7800
Property,Picard XY Stage,Y-Min,0
Property,Picard XY Stage,Y-StepSize,1.5000
# Pre-init settings for COM ports
Property,COM3,AnswerTimeout,500.0000
Property,COM3,BaudRate,115200
Property,COM3,DelayBetweenCharsMs,0.0000
Property,COM3,Handshaking,Off
Property,COM3,Parity,None
Property,COM3,StopBits,1
Property,COM3,Verbose,1
# Hub (parent) references
# Initialize
Property,Core,Initialize,1
# Delays
# Roles
Property,Core,Camera,HamamatsuHam_DCAM
Property,Core,Shutter,CoherentObis
Property,Core,Focus,Picard Z Stage
Property,Core,AutoShutter,1
# Camera-synchronized devices
# Labels
# Configuration presets
# Group: Channel
# Group: System
# Preset: Startup
# PixelSize settings
***** END Starting Config (C:\Users\biolpc2829\Desktop\Fiji.app\OpenSPIM.cfg) *****
***** BEGIN Captured Log *****
2015-03-13T11:28:01.658236 tid3832 [IFO,LogManager] Added secondary log file C:\Users\biolpc2829\MMProblemReport\CoreLogCapture.txt with log level trace
2015-03-13T11:28:01.658236 tid3832 [IFO,App] Problem Report: Start of log capture
2015-03-13T11:28:01.788243 tid4308 [IFO,App] ***** BEGIN Problem Report System Info *****
2015-03-13T11:28:01.805244 tid4308 [IFO,App] MMStudio version: 1.4.21 20150312
[ ] Core version: MMCore version 7.0.2
[ ] Core device API version: Device API version 61, Module API version 10
2015-03-13T11:28:01.805244 tid4308 [IFO,App] Operating system: Windows 7 (amd64) 6.1
2015-03-13T11:28:01.806244 tid4308 [IFO,App] Java version: 1.6.0_24
[ ] Java runtime: Java(TM) SE Runtime Environment 1.6.0_24-b07
[ ] JVM: Java HotSpot(TM) 64-Bit Server VM; mixed mode
[ ] JVM architecture: 64-bit
2015-03-13T11:28:01.806244 tid4308 [IFO,App] JVM arguments:
[ ] -Dpython.cachedir.skip=true
[ ] -Dplugins.dir=C:\Users\BIOLPC~1\Desktop\Fiji.app
[ ] -Xmx12246m
[ ] -Xincgc
[ ] -XX:PermSize=128m
[ ] (End JVM args)
2015-03-13T11:28:01.806244 tid4308 [IFO,App] Java system properties:
[ ] awt.toolkit = sun.awt.windows.WToolkit
[ ] fiji.defaultLibPath = bin/server/jvm.dll
[ ] fiji.dir = C:\Users\BIOLPC~1\Desktop\Fiji.app
[ ] fiji.executable = C:\Users\biolpc2829\Desktop\Fiji.app\ImageJ-win64.exe
[ ] file.encoding = Cp1252
[ ] file.encoding.pkg = sun.io
[ ] file.separator = \
[ ] ij.dir = C:\Users\BIOLPC~1\Desktop\Fiji.app
[ ] ij.executable = C:\Users\biolpc2829\Desktop\Fiji.app\ImageJ-win64.exe
[ ] imagej.dir = C:\Users\BIOLPC~1\Desktop\Fiji.app
[ ] java.awt.graphicsenv = sun.awt.Win32GraphicsEnvironment
[ ] java.awt.printerjob = sun.awt.windows.WPrinterJob
[ ] java.class.path (split at ';') =
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app/jars/imagej-launcher-3.1.6.jar
[ ] java.class.version = 50.0
[ ] java.endorsed.dirs = C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\endorsed
[ ] java.ext.dirs = C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\ext;C:\Windows\Sun\Java\lib\ext
[ ] java.home = C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre
[ ] java.io.tmpdir = C:\Users\BIOLPC~1\AppData\Local\Temp\
[ ] java.library.path (split at ';') =
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app/lib/win64
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app/mm/win64
[ ] java.runtime.name = Java(TM) SE Runtime Environment
[ ] java.runtime.version = 1.6.0_24-b07
[ ] java.specification.name = Java Platform API Specification
[ ] java.specification.vendor = Sun Microsystems Inc.
[ ] java.specification.version = 1.6
[ ] java.vendor = Sun Microsystems Inc.
[ ] java.vendor.url = http://java.sun.com/
[ ] java.vendor.url.bug = http://java.sun.com/cgi-bin/bugreport.cgi
[ ] java.version = 1.6.0_24
[ ] java.vm.info = mixed mode
[ ] java.vm.name = Java HotSpot(TM) 64-Bit Server VM
[ ] java.vm.specification.name = Java Virtual Machine Specification
[ ] java.vm.specification.vendor = Sun Microsystems Inc.
[ ] java.vm.specification.version = 1.0
[ ] java.vm.vendor = Sun Microsystems Inc.
[ ] java.vm.version = 19.1-b02
[ ] line.separator =
[ ]
[ ] os.arch = amd64
[ ] os.name = Windows 7
[ ] os.version = 6.1
[ ] path.separator = ;
[ ] plugins.dir = C:\Users\BIOLPC~1\Desktop\Fiji.app
[ ] python.cachedir.skip = true
[ ] sun.arch.data.model = 64
[ ] sun.awt.exception.handler = org.micromanager.diagnostics.ThreadExceptionLogger
[ ] sun.boot.class.path (split at ';') =
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\resources.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\rt.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\sunrsasign.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\jsse.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\jce.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\charsets.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\lib\modules\jdk.boot.jar
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\classes
[ ] sun.boot.library.path (split at ';') =
[ ] C:\Users\BIOLPC~1\Desktop\Fiji.app\java\win64\jdk1.6.0_24\jre\bin
[ ] sun.cpu.endian = little
[ ] sun.cpu.isalist = amd64
[ ] sun.desktop = windows
[ ] sun.io.unicode.encoding = UnicodeLittle
[ ] sun.java2d.noddraw = true
[ ] sun.jnu.encoding = Cp1252
[ ] sun.management.compiler = HotSpot 64-Bit Server Compiler
[ ] sun.os.patch.level = Service Pack 1
[ ] user.country = GB
[ ] user.dir = C:\Users\biolpc2829\Desktop\Fiji.app
[ ] user.home = C:\Users\biolpc2829
[ ] user.language = en
[ ] user.name = biolpc2829
[ ] user.timezone = Europe/London
[ ] user.variant =
[ ] (End Java system properties)
2015-03-13T11:28:01.807244 tid4308 [IFO,App] Processors available to JVM: 4
2015-03-13T11:28:01.821245 tid4308 [IFO,App] Total physical memory (caveats apply if JVM is 32-bit): 17121382400 (15.9 GiB)
[ ] Committed virtual memory size: 710508544 (677.6 MiB)
[ ] Free physical memory (may be meaningless if JVM is 32-bit): 14180651008 (13.2 GiB)
2015-03-13T11:28:01.955253 tid4308 [IFO,App] JVM heap memory usage: used = 28623888 (27.3 MiB); committed = 85000192 (81.1 MiB); max = 12832145408 (12.0 GiB)
[ ] JVM non-heap memory usage: used = 77506824 (73.9 MiB); committed = 137756672 (131.4 MiB); max = 184549376 (176.0 MiB)
2015-03-13T11:28:01.959253 tid4308 [IFO,App] All Java threads:
[ ] id 2 ("Reference Handler"): WAITING
[ ] id 3 ("Finalizer"): WAITING
[ ] id 5 ("Signal Dispatcher"): RUNNABLE
[ ] id 6 ("Attach Listener"): RUNNABLE
[ ] id 11 ("Java2D Disposer"): WAITING
[ ] id 12 ("AWT-Shutdown"): WAITING
[ ] id 13 ("AWT-Windows"): RUNNABLE
[ ] id 15 ("AWT-EventQueue-0"): WAITING
[ ] id 17 ("SciJava-54cee271-Thread-0"): TIMED_WAITING
[ ] id 18 ("SciJava-54cee271-Thread-1"): TIMED_WAITING
[ ] id 21 ("DestroyJavaVM"): RUNNABLE
[ ] id 25 ("TimerQueue"): TIMED_WAITING
[ ] id 27 ("Thread-4"): TIMED_WAITING
[ ] id 28 ("BeanShell interpreter"): TIMED_WAITING
[ ] id 33 ("SwingWorker-pool-4-thread-1"): RUNNABLE
[ ] (End all Java threads)
2015-03-13T11:28:01.959253 tid4308 [IFO,App] Deadlocked Java threads: none detected
2015-03-13T11:28:01.959253 tid4308 [IFO,App] MMCore version: MMCore version 7.0.2
[ ] Circular buffer size (MB): 250
2015-03-13T11:28:01.982254 tid4308 [IFO,App] Core property cache ("system state cache") contents:
[ ] COM3/AnswerTimeout = 500.0000
[ ] COM3/BaudRate = 115200
[ ] COM3/DataBits [RO] = 8
[ ] COM3/DelayBetweenCharsMs = 0.0000
[ ] COM3/Description [RO] = Serial port driver (boost:asio)
[ ] COM3/Handshaking = Off
[ ] COM3/Name [RO] = COM3
[ ] COM3/Parity = None
[ ] COM3/StopBits = 1
[ ] COM3/Verbose = 1
[ ] CoherentObis/Description [RO] = CoherentObis Laser
[ ] CoherentObis/Head Usage Hours [RO] = 44
[ ] CoherentObis/HeadID [RO] = M140606003
[ ] CoherentObis/Maximum Laser Power [RO] = 0.0660
[ ] CoherentObis/Minimum Laser Power [RO] = 0.0010
[ ] CoherentObis/Name [RO] = CoherentObis
[ ] CoherentObis/Port = COM3
[ ] CoherentObis/PowerReadback [RO] = 1.0000
[ ] CoherentObis/PowerSetpoint = 1.0000
[ ] CoherentObis/State = 1
[ ] CoherentObis/Wavelength [RO] = 488.0000
[ ] HamamatsuHam_DCAM/Binning = 1x1
[ ] HamamatsuHam_DCAM/CONTRAST GAIN = 0
[ ] HamamatsuHam_DCAM/CONTRAST OFFSET = 0
[ ] HamamatsuHam_DCAM/Camera Bus [RO] = OHCI 1394
[ ] HamamatsuHam_DCAM/Camera Version [RO] = 1.01.02.G
[ ] HamamatsuHam_DCAM/CameraID [RO] = S/N: 000000
[ ] HamamatsuHam_DCAM/CameraName [RO] = Hamamatsu 1394 ORCA-ER
[ ] HamamatsuHam_DCAM/Description [RO] = Hamamatsu device adapter 1.8.10.49
[ ] HamamatsuHam_DCAM/Driver Version [RO] = 9.28.8.4643
[ ] HamamatsuHam_DCAM/EXPOSURE FULL RANGE = DISABLE
[ ] HamamatsuHam_DCAM/EXPOSURE TIME UNITS = MILLISECONDS
[ ] HamamatsuHam_DCAM/Exposure = 100.0980
[ ] HamamatsuHam_DCAM/LIGHT MODE = LOW LIGHT
[ ] HamamatsuHam_DCAM/MINIMUM ACQUISITION TIMEOUT = 60000
[ ] HamamatsuHam_DCAM/Module Version [RO] = 14.12.642.4643
[ ] HamamatsuHam_DCAM/Name [RO] = HamamatsuHam_DCAM
[ ] HamamatsuHam_DCAM/PixelType = 16bit
[ ] HamamatsuHam_DCAM/ReadoutTime [RO] = 0.1117
[ ] HamamatsuHam_DCAM/SENSOR MODE = AREA
[ ] HamamatsuHam_DCAM/TRIGGER ACTIVE = EDGE
[ ] HamamatsuHam_DCAM/TRIGGER SOURCE = INTERNAL
[ ] HamamatsuHam_DCAM/TransposeCorrection = 0
[ ] HamamatsuHam_DCAM/TransposeMirrorX = 0
[ ] HamamatsuHam_DCAM/TransposeMirrorY = 0
[ ] HamamatsuHam_DCAM/TransposeXY = 0
[ ] HamamatsuHam_DCAM/Trigger = NORMAL
[ ] HamamatsuHam_DCAM/TriggerPolarity = NEGATIVE
[ ] Picard Twister/Max = 32767
[ ] Picard Twister/Min = -32767
[ ] Picard Twister/Serial Number = 100
[ ] Picard Twister/StepSize = 1.0000
[ ] Picard Twister/Velocity = 1
[ ] Picard Z Stage/GoHome = 0
[ ] Picard Z Stage/Max = 7800
[ ] Picard Z Stage/Min = 0
[ ] Picard Z Stage/Serial Number = 296
[ ] Picard Z Stage/StepSize = 1.5000
[ ] Picard Z Stage/Velocity = 10
[ ] Picard XY Stage/Serial Number (X) = 294
[ ] Picard XY Stage/Serial Number (Y) = 295
[ ] Picard XY Stage/TransposeMirrorX = 0
[ ] Picard XY Stage/TransposeMirrorY = 0
[ ] Picard XY Stage/X-Max = 7800
[ ] Picard XY Stage/X-Min = 0
[ ] Picard XY Stage/X-StepSize = 1.5000
[ ] Picard XY Stage/X-Velocity = 10
[ ] Picard XY Stage/Y-Max = 7800
[ ] Picard XY Stage/Y-Min = 0
[ ] Picard XY Stage/Y-StepSize = 1.5000
[ ] Picard XY Stage/Y-Velocity = 10
[ ] Core/AutoFocus =
[ ] Core/AutoShutter = 1
[ ] Core/Camera = HamamatsuHam_DCAM
[ ] Core/ChannelGroup =
[ ] Core/Focus = Picard Z Stage
[ ] Core/Galvo =
[ ] Core/ImageProcessor =
[ ] Core/Initialize = 1
[ ] Core/SLM =
[ ] Core/Shutter = CoherentObis
[ ] Core/TimeoutMs = 5000
[ ] Core/XYStage = Picard XY Stage
2015-03-13T11:28:01.983254 tid4308 [IFO,App] ***** END Problem Report System Info *****
2015-03-13T11:28:02.037257 tid3832 [IFO,App] User has been prompted to reproduce problem
2015-03-13T11:28:07.247555 tid3832 [IFO,App] Plugin command: Acquire SPIM image
2015-03-13T11:28:07.266556 tid3832 [dbg,Core] Pixel size config: preset Uncalibrated: added setting : Core-Initialize = 1
2015-03-13T11:28:07.266556 tid3832 [dbg,Core] Pixel size config: preset Uncalibrated: set resolution to 1.00000 um/px
2015-03-13T11:28:07.266556 tid3832 [IFO,Core] Will initialize 6 devices
2015-03-13T11:28:07.266556 tid3832 [IFO,Core] Will initialize device COM3
2015-03-13T11:28:07.266556 tid3832 [IFO,Core] Did initialize device COM3
2015-03-13T11:28:07.266556 tid3832 [IFO,Core] Will initialize device CoherentObis
2015-03-13T11:28:07.267556 tid3832 [IFO,dev:CoherentObis] CoherentObis::Initialize()yes??
2015-03-13T11:28:07.267556 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SYST1:COMM:HAND On
2015-03-13T11:28:07.267556 tid3832 [dbg,dev:COM3] SetCommand -> SYST1:COMM:HAND On\r
2015-03-13T11:28:07.295558 tid3832 [dbg,dev:COM3] GetAnswer <- OK\r\n
2015-03-13T11:28:07.295558 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine OK
2015-03-13T11:28:07.295558 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SYST1:COMM:HAND?
2015-03-13T11:28:07.295558 tid3832 [dbg,dev:COM3] SetCommand -> SYST1:COMM:HAND?\r
2015-03-13T11:28:07.298558 tid3832 [dbg,dev:COM3] GetAnswer <- ON\r\n
2015-03-13T11:28:07.298558 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine ON
2015-03-13T11:28:07.298558 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SYST1:COMM:PROM Off
2015-03-13T11:28:07.298558 tid3832 [dbg,dev:COM3] SetCommand -> SYST1:COMM:PROM Off\r
2015-03-13T11:28:07.328560 tid3832 [dbg,dev:COM3] GetAnswer <- OK\r\n
2015-03-13T11:28:07.328560 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine OK
2015-03-13T11:28:07.328560 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SYST1:COMM:PROM?
2015-03-13T11:28:07.328560 tid3832 [dbg,dev:COM3] SetCommand -> SYST1:COMM:PROM?\r
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:COM3] GetAnswer <- OFF\r\n
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine OFF
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SYST1:ERR:CLE
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:COM3] SetCommand -> SYST1:ERR:CLE\r
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SOUR1:POW:LIM:HIGH?
2015-03-13T11:28:07.333560 tid3832 [dbg,dev:COM3] SetCommand -> SOUR1:POW:LIM:HIGH?\r
2015-03-13T11:28:07.338560 tid3832 [dbg,dev:COM3] GetAnswer <- OK\r\n
2015-03-13T11:28:07.338560 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine OK
2015-03-13T11:28:07.338560 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SOUR1:POW:LIM:HIGH?
2015-03-13T11:28:07.338560 tid3832 [dbg,dev:COM3] SetCommand -> SOUR1:POW:LIM:HIGH?\r
2015-03-13T11:28:07.342561 tid3832 [dbg,dev:COM3] GetAnswer <- 0.06600\r\n
2015-03-13T11:28:07.342561 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine 0.06600
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Did initialize device CoherentObis
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Default shutter set to CoherentObis
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Will initialize device HamamatsuHam_DCAM
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Did initialize device HamamatsuHam_DCAM
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Default camera set to HamamatsuHam_DCAM
2015-03-13T11:28:07.342561 tid3832 [IFO,Core] Will initialize device Picard Twister
2015-03-13T11:28:07.361562 tid3832 [IFO,Core] Did initialize device Picard Twister
2015-03-13T11:28:07.361562 tid3832 [IFO,Core] Will initialize device Picard Z Stage
2015-03-13T11:28:07.393564 tid3832 [IFO,Core] Did initialize device Picard Z Stage
2015-03-13T11:28:07.393564 tid3832 [IFO,Core] Will initialize device Picard XY Stage
2015-03-13T11:28:07.457567 tid3832 [IFO,Core] Did initialize device Picard XY Stage
2015-03-13T11:28:07.457567 tid3832 [IFO,Core] Default xy stage set to Picard XY Stage
2015-03-13T11:28:07.458567 tid3832 [IFO,Core] Finished initializing 6 devices
2015-03-13T11:28:07.458567 tid3832 [dbg,App] Notification for Device: Core Property: Initialize changed to value: 1
2015-03-13T11:28:07.458567 tid3832 [dbg,Core] Applied pixel size configuration preset Uncalibrated
2015-03-13T11:28:07.458567 tid3832 [IFO,App] Defined uncalibrated pixel size (1:1).
2015-03-13T11:28:07.590575 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SOUR1:POW:LIM:LOW?
2015-03-13T11:28:07.590575 tid3832 [dbg,dev:COM3] SetCommand -> SOUR1:POW:LIM:LOW?\r
2015-03-13T11:28:07.595575 tid3832 [dbg,dev:COM3] GetAnswer <- 0.00100\r\n
2015-03-13T11:28:07.595575 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine 0.00100
2015-03-13T11:28:07.595575 tid3832 [dbg,dev:CoherentObis] CoherentObis::Send SOUR1:POW:LIM:HIGH?
2015-03-13T11:28:07.595575 tid3832 [dbg,dev:COM3] SetCommand -> SOUR1:POW:LIM:HIGH?\r
2015-03-13T11:28:07.599575 tid3832 [dbg,dev:COM3] GetAnswer <- 0.06600\r\n
2015-03-13T11:28:07.599575 tid3832 [dbg,dev:CoherentObis] CoherentObis::ReceiveOneLine 0.06600
2015-03-13T11:28:07.599575 tid3832 [IFO,App] Uncaught exception in AWT/Swing event dispatch thread:
2015-03-13T11:28:07.599575 tid3832 [IFO,App] java.lang.IllegalArgumentException: invalid range properties
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.DefaultBoundedRangeModel.<init>(DefaultBoundedRangeModel.java:85)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.JSlider.<init>(JSlider.java:259)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.JSlider.<init>(JSlider.java:226)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at spim.SteppedSlider.<init>(SteppedSlider.java:63)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at spim.SPIMAcquisition$11.<init>(SPIMAcquisition.java:795)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at spim.SPIMAcquisition.initUI(SPIMAcquisition.java:795)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at spim.SPIMAcquisition.show(SPIMAcquisition.java:218)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at org.micromanager.pluginmanagement.PluginManager.displayPlugin(PluginManager.java:114)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at org.micromanager.pluginmanagement.PluginManager.access$100(PluginManager.java:22)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at org.micromanager.pluginmanagement.PluginManager$2.run(PluginManager.java:64)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at org.micromanager.utils.GUIUtils$3.actionPerformed(GUIUtils.java:348)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at java.awt.Component.processMouseEvent(Component.java:6289)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at java.awt.Component.processEvent(Component.java:6054)
2015-03-13T11:28:07.600575 tid3832 [IFO,App] at java.awt.Container.processEvent(Container.java:2041)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Component.dispatchEventImpl(Component.java:4652)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Container.dispatchEventImpl(Container.java:2099)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Component.dispatchEvent(Component.java:4482)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Container.dispatchEventImpl(Container.java:2085)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Window.dispatchEventImpl(Window.java:2478)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.Component.dispatchEvent(Component.java:4482)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue.access$000(EventQueue.java:85)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue$1.run(EventQueue.java:603)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue$1.run(EventQueue.java:601)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.security.AccessController.doPrivileged(Native Method)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue$2.run(EventQueue.java:617)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue$2.run(EventQueue.java:615)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.security.AccessController.doPrivileged(Native Method)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
2015-03-13T11:28:07.601575 tid3832 [IFO,App] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
2015-03-13T11:28:14.876992 tid3832 [IFO,App] User has stopped log capture
2015-03-13T11:28:14.890992 tid2344 [IFO,App] ***** BEGIN Problem Report System Info (incremental) *****
2015-03-13T11:28:14.891992 tid2344 [IFO,App] Total physical memory (caveats apply if JVM is 32-bit): 17121382400 (15.9 GiB)
[ ] Committed virtual memory size: 700473344 (668.0 MiB)
[ ] Free physical memory (may be meaningless if JVM is 32-bit): 14190235648 (13.2 GiB)
2015-03-13T11:28:14.891992 tid2344 [IFO,App] JVM heap memory usage: used = 37115312 (35.4 MiB); committed = 85000192 (81.1 MiB); max = 12832145408 (12.0 GiB)
[ ] JVM non-heap memory usage: used = 77787640 (74.2 MiB); committed = 137756672 (131.4 MiB); max = 184549376 (176.0 MiB)
2015-03-13T11:28:14.892993 tid2344 [IFO,App] All Java threads:
[ ] id 2 ("Reference Handler"): WAITING
[ ] id 3 ("Finalizer"): WAITING
[ ] id 5 ("Signal Dispatcher"): RUNNABLE
[ ] id 6 ("Attach Listener"): RUNNABLE
[ ] id 11 ("Java2D Disposer"): WAITING
[ ] id 12 ("AWT-Shutdown"): WAITING
[ ] id 13 ("AWT-Windows"): RUNNABLE
[ ] id 15 ("AWT-EventQueue-0"): RUNNABLE
[ ] id 17 ("SciJava-54cee271-Thread-0"): TIMED_WAITING
[ ] id 18 ("SciJava-54cee271-Thread-1"): TIMED_WAITING
[ ] id 21 ("DestroyJavaVM"): RUNNABLE
[ ] id 25 ("TimerQueue"): TIMED_WAITING
[ ] id 27 ("Thread-4"): TIMED_WAITING
[ ] id 28 ("BeanShell interpreter"): TIMED_WAITING
[ ] id 33 ("SwingWorker-pool-4-thread-1"): WAITING
[ ] id 34 ("SwingWorker-pool-4-thread-2"): RUNNABLE
[ ] (End all Java threads)
2015-03-13T11:28:14.892993 tid2344 [IFO,App] Deadlocked Java threads: none detected
2015-03-13T11:28:14.892993 tid2344 [IFO,App] MMCore version: MMCore version 7.0.2
[ ] Circular buffer size (MB): 250
2015-03-13T11:28:14.893993 tid2344 [IFO,App] Core property cache ("system state cache") contents:
[ ] COM3/AnswerTimeout = 500.0000
[ ] COM3/BaudRate = 115200
[ ] COM3/DataBits [RO] = 8
[ ] COM3/DelayBetweenCharsMs = 0.0000
[ ] COM3/Description [RO] = Serial port driver (boost:asio)
[ ] COM3/Handshaking = Off
[ ] COM3/Name [RO] = COM3
[ ] COM3/Parity = None
[ ] COM3/StopBits = 1
[ ] COM3/Verbose = 1
[ ] CoherentObis/Description [RO] = CoherentObis Laser
[ ] CoherentObis/Head Usage Hours [RO] = 44
[ ] CoherentObis/HeadID [RO] = M140606003
[ ] CoherentObis/Maximum Laser Power = 0.0660
[ ] CoherentObis/Minimum Laser Power = 0.0010
[ ] CoherentObis/Name [RO] = CoherentObis
[ ] CoherentObis/Port = COM3
[ ] CoherentObis/PowerReadback [RO] = 1.0000
[ ] CoherentObis/PowerSetpoint = 1.0000
[ ] CoherentObis/State = 1
[ ] CoherentObis/Wavelength [RO] = 488.0000
[ ] HamamatsuHam_DCAM/Binning = 1x1
[ ] HamamatsuHam_DCAM/CONTRAST GAIN = 0
[ ] HamamatsuHam_DCAM/CONTRAST OFFSET = 0
[ ] HamamatsuHam_DCAM/Camera Bus [RO] = OHCI 1394
[ ] HamamatsuHam_DCAM/Camera Version [RO] = 1.01.02.G
[ ] HamamatsuHam_DCAM/CameraID [RO] = S/N: 000000
[ ] HamamatsuHam_DCAM/CameraName [RO] = Hamamatsu 1394 ORCA-ER
[ ] HamamatsuHam_DCAM/Description [RO] = Hamamatsu device adapter 1.8.10.49
[ ] HamamatsuHam_DCAM/Driver Version [RO] = 9.28.8.4643
[ ] HamamatsuHam_DCAM/EXPOSURE FULL RANGE = DISABLE
[ ] HamamatsuHam_DCAM/EXPOSURE TIME UNITS = MILLISECONDS
[ ] HamamatsuHam_DCAM/Exposure = 100.0980
[ ] HamamatsuHam_DCAM/LIGHT MODE = LOW LIGHT
[ ] HamamatsuHam_DCAM/MINIMUM ACQUISITION TIMEOUT = 60000
[ ] HamamatsuHam_DCAM/Module Version [RO] = 14.12.642.4643
[ ] HamamatsuHam_DCAM/Name [RO] = HamamatsuHam_DCAM
[ ] HamamatsuHam_DCAM/PixelType = 16bit
[ ] HamamatsuHam_DCAM/ReadoutTime [RO] = 0.1117
[ ] HamamatsuHam_DCAM/SENSOR MODE = AREA
[ ] HamamatsuHam_DCAM/TRIGGER ACTIVE = EDGE
[ ] HamamatsuHam_DCAM/TRIGGER SOURCE = INTERNAL
[ ] HamamatsuHam_DCAM/TransposeCorrection = 0
[ ] HamamatsuHam_DCAM/TransposeMirrorX = 0
[ ] HamamatsuHam_DCAM/TransposeMirrorY = 0
[ ] HamamatsuHam_DCAM/TransposeXY = 0
[ ] HamamatsuHam_DCAM/Trigger = NORMAL
[ ] HamamatsuHam_DCAM/TriggerPolarity = NEGATIVE
[ ] Picard Twister/Max = 32767
[ ] Picard Twister/Min = -32767
[ ] Picard Twister/Serial Number = 100
[ ] Picard Twister/StepSize = 1.0000
[ ] Picard Twister/Velocity = 1
[ ] Picard Z Stage/GoHome = 0
[ ] Picard Z Stage/Max = 7800
[ ] Picard Z Stage/Min = 0
[ ] Picard Z Stage/Serial Number = 296
[ ] Picard Z Stage/StepSize = 1.5000
[ ] Picard Z Stage/Velocity = 10
[ ] Picard XY Stage/Serial Number (X) = 294
[ ] Picard XY Stage/Serial Number (Y) = 295
[ ] Picard XY Stage/TransposeMirrorX = 0
[ ] Picard XY Stage/TransposeMirrorY = 0
[ ] Picard XY Stage/X-Max = 7800
[ ] Picard XY Stage/X-Min = 0
[ ] Picard XY Stage/X-StepSize = 1.5000
[ ] Picard XY Stage/X-Velocity = 10
[ ] Picard XY Stage/Y-Max = 7800
[ ] Picard XY Stage/Y-Min = 0
[ ] Picard XY Stage/Y-StepSize = 1.5000
[ ] Picard XY Stage/Y-Velocity = 10
[ ] Core/AutoFocus =
[ ] Core/AutoShutter = 1
[ ] Core/Camera = HamamatsuHam_DCAM
[ ] Core/ChannelGroup =
[ ] Core/Focus = Picard Z Stage
[ ] Core/Galvo =
[ ] Core/ImageProcessor =
[ ] Core/Initialize = 1
[ ] Core/SLM =
[ ] Core/Shutter = CoherentObis
[ ] Core/TimeoutMs = 5000
[ ] Core/XYStage = Picard XY Stage
2015-03-13T11:28:14.893993 tid2344 [IFO,App] ***** END Problem Report System Info (incremental) *****
2015-03-13T11:28:14.893993 tid2344 [IFO,App] Problem Report: End of log capture
2015-03-13T11:28:14.894993 tid2344 [IFO,LogManager] Removing secondary log file C:\Users\biolpc2829\MMProblemReport\CoreLogCapture.txt
***** END Captured Log *****
***** END OF PROBLEM REPORT *****
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