startup error micromanager gamma

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Z H
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startup error micromanager gamma

Z H
I recently updated PVCAM drivers and now the micro-manager gamma plugin (190324 and 190321 builds tried) fails to start. Build 190321 worked great before the PVCAM upgrade. Reverting PVCAM does nothing, and micromanager beta still works fine (an early 2018 build). I'm at a loss to diagnose the problem and would love to get it fixed because gamma has some advantages for us. The command line output (windows 64-bit; windows 10) follows.

Zach

C:\Program Files\Micro-Manager-2.0gamma>jre\bin\java -cp ij.jar ij.ImageJ
2019-03-25T16:20:05.256117 tid8668 [IFO,LogManager] Enabled logging to stderr
java.io.IOException: com.google.gson.JsonSyntaxException: java.lang.IllegalStateException: Expected BEGIN_OBJECT but was STRING at line 1 column 1
        at org.micromanager.internal.propertymap.PropertyMapJSONSerializer.fromJSON(PropertyMapJSONSerializer.java:871)
        at org.micromanager.PropertyMaps.loadJSON(PropertyMaps.java:71)
        at org.micromanager.profile.internal.UserProfileAdmin.readFile(UserProfileAdmin.java:491)
        at org.micromanager.profile.internal.UserProfileAdmin.getProfileImpl(UserProfileAdmin.java:269)
        at org.micromanager.profile.internal.UserProfileAdmin.getAutosavingProfile(UserProfileAdmin.java:261)
        at org.micromanager.internal.utils.UserProfileStaticInterface.getInstance(UserProfileStaticInterface.java:62)
        at org.micromanager.internal.dialogs.OptionsDlg.getIsDebugLogEnabled(OptionsDlg.java:378)
        at org.micromanager.internal.MMStudio.initializeLogging(MMStudio.java:387)
        at org.micromanager.internal.MMStudio.<init>(MMStudio.java:239)
        at MMStudioPlugin$1.run(MMStudioPlugin.java:79)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
        at java.awt.EventQueue.access$500(EventQueue.java:97)
        at java.awt.EventQueue$3.run(EventQueue.java:709)
        at java.awt.EventQueue$3.run(EventQueue.java:703)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: com.google.gson.JsonSyntaxException: java.lang.IllegalStateException: Expected BEGIN_OBJECT but was STRING at line 1 column 1
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:176)
        at com.google.gson.Gson.fromJson(Gson.java:803)
        at com.google.gson.Gson.fromJson(Gson.java:768)
        at com.google.gson.Gson.fromJson(Gson.java:717)
        at com.google.gson.Gson.fromJson(Gson.java:689)
        at org.micromanager.internal.propertymap.PropertyMapJSONSerializer.fromJSONImpl(PropertyMapJSONSerializer.java:829)
        at org.micromanager.internal.propertymap.PropertyMapJSONSerializer.fromJSON(PropertyMapJSONSerializer.java:865)
        ... 23 more
Caused by: java.lang.IllegalStateException: Expected BEGIN_OBJECT but was STRING at line 1 column 1
        at com.google.gson.stream.JsonReader.beginObject(JsonReader.java:374)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:165)
        ... 29 more

java.lang.NullPointerException in Thread[AWT-EventQueue-0,6,main]
  at org.micromanager.internal.dialogs.OptionsDlg.getIsDebugLogEnabled(OptionsDlg.java:378)
  at org.micromanager.internal.MMStudio.initializeLogging(MMStudio.java:387)
  at org.micromanager.internal.MMStudio.<init>(MMStudio.java:239)
  at MMStudioPlugin$1.run(MMStudioPlugin.java:79)
  at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
  at java.awt.EventQueue.access$500(EventQueue.java:97)
  at java.awt.EventQueue$3.run(EventQueue.java:709)
  at java.awt.EventQueue$3.run(EventQueue.java:703)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
  at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
  at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)


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Re: startup error micromanager gamma

Stuurman, Nico
Hi Zach,


> I recently updated PVCAM drivers and now the micro-manager gamma
> plugin (190324 and 190321 builds tried) fails to start. Build 190321
> worked great before the PVCAM upgrade. Reverting PVCAM does nothing,
> and micromanager beta still works fine (an early 2018 build). I'm at a
> loss to diagnose the problem and would love to get it fixed because
> gamma has some advantages for us. The command line output (windows
> 64-bit; windows 10) follows.

Looks to me that the (default) profile went bad.  You can test this by
renaming ~/Appdata/Local/Micro-Manager.  If that indeed fixes things, it
would be great if you could send me the faulty profiles files, so that I
can harden the code to survive this bad input.

B.t.w., a couple of nightly build's installer had a problem when
installing into an existing installation (multiple versions of the same
jar could end up in the plugins/Micro-Manager directory) causing runtime
errors, and the UI not appearing).  20190324 should fix that one.


Best,

Nico



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