MMStudio in MATLAB

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MMStudio in MATLAB

Vanessa King
Hi,

I seem to be having issues using MMStudio in MATLAB. My current script is simply:

MMsetup_javaclasspath('C:\Program Files\Micro-Manager-1.4')

import mmcorej.*

import org.micromanager.MMStudio;

 

gui = MMStudio(false);

gui.show;

mmc = gui.getCore;

acq = gui.getAcquisitionEngine;



But this gives the error: 


May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences WindowsRegOpenKey1

WARNING: Trying to recreate Windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences openKey

WARNING: Could not open windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002. Windows RegOpenKey(...) returned error code 2.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences WindowsRegOpenKey1

WARNING: Trying to recreate Windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences openKey

WARNING: Could not open windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002. Windows RegOpenKey(...) returned error code 2.

Error using trialMicroGUI (line 7)
Java exception occurred:
java.lang.NoClassDefFoundError: org/fife/ui/rsyntaxtextarea/RSyntaxTextArea

at org.micromanager.utils.MMKeyDispatcher.<init>(MMKeyDispatcher.java:48)

at org.micromanager.MainFrame.<init>(MainFrame.java:148)

at org.micromanager.MMStudio.<init>(MMStudio.java:330)


Thread 120 (Pipeline Class loading thread) terminated with uncaught exception
java.lang.NoClassDefFoundError: clojure/lang/IFn
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Class.java:264)
  at org.micromanager.MMStudio$1.run(MMStudio.java:582)
Caused by exception:
java.lang.ClassNotFoundException: clojure.lang.IFn
  at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
  at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Class.java:264)
  at org.micromanager.MMStudio$1.run(MMStudio.java:582)


Apologies if this is something that has already been asked before, but I couldn't find any reference to someone else who found this.  I am also new to scripting Micro-Manager. My operating system is Windows 7 and the things I've added to my static javaclasspath are:


C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar                                      
C:\Program Files\Micro-Manager-1.4\ij.jar                                                                 
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMAcqEngine.jar                                  
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMJ_.jar                                         
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\clojure.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\bsh-2.0b4.jar                                    
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\swingx-0.9.5.jar                                 
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\swing-layout-1.0.4.jar                           
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\commons-math-2.0.jar                             
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\ome-xml.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\scifio.jar                                       
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\guava-17.0.jar   

Please let me know if you have any suggestions for why this error is being thrown and what I could do to resolve it, it would be greatly appreciated! Thanks,

Vanessa


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Re: MMStudio in MATLAB

Nico Stuurman-2
Hi Vanessa,


On 5/15/18 1:44 PM, Vanessa King wrote:

> I seem to be having issues using MMStudio in MATLAB. My current script
> is simply:
>
> MMsetup_javaclasspath('C:\Program Files\Micro-Manager-1.4')
>
> import mmcorej.*
>
> import org.micromanager.MMStudio;
>
> gui = MMStudio(false);
>
> gui.show;
>
> mmc = gui.getCore;
>
> acq = gui.getAcquisitionEngine;
>
>
>
> But this gives the error:
>
>
> Error using trialMicroGUI (line 7)
> Java exception occurred:
> java.lang.NoClassDefFoundError:
> org/fife/ui/rsyntaxtextarea/RSyntaxTextArea
>
> at org.micromanager.utils.MMKeyDispatcher.<init>(MMKeyDispatcher.java:48)
>
> at org.micromanager.MainFrame.<init>(MainFrame.java:148)
>
> at org.micromanager.MMStudio.<init>(MMStudio.java:330)

Looks like rsyntaxtextarea.jar is not found on the classpath.
  the things I've added to my static javaclasspath are:

>
>
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar
> C:\Program Files\Micro-Manager-1.4\ij.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMAcqEngine.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMJ_.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\clojure.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\bsh-2.0b4.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\swingx-0.9.5.jar
> C:\Program
> Files\Micro-Manager-1.4\plugins\Micro-Manager\swing-layout-1.0.4.jar
> C:\Program
> Files\Micro-Manager-1.4\plugins\Micro-Manager\commons-math-2.0.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\ome-xml.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\scifio.jar
> C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\guava-17.0.jar

Yes, it is not on your classpath.  You will need to add most (all ?)
jars that you find in plugins/Micro-Manager to the classpath.  They will
be used at one time or another.

Best,

Nico



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Re: Camera Capable of Live Plot Profile in MM 1.4

Geoff Pickford
In reply to this post by Vanessa King

Hi,

I am trying to find and then purchase a 5 to 10 MP camera less than around USD800 that is able to achieve "Live Plot Profile" in ImageJ wishing MM 1.4. 

I only need monochrome camera, but if it is color, then I must be able to run software in monochrome. 

My preference is for 8 bit grey-levels. I have found a Tucsen camera that can use MM, but it cannot use the "Live Plot Profile" function. 

Many thanks, GeoffP




On 16 May 2018, at 6:44 AM, Vanessa King <[hidden email]> wrote:

Hi,

I seem to be having issues using MMStudio in MATLAB. My current script is simply:

MMsetup_javaclasspath('C:\Program Files\Micro-Manager-1.4')
import mmcorej.*
import org.micromanager.MMStudio;

 

gui = MMStudio(false);
gui.show;
mmc = gui.getCore;
acq = gui.getAcquisitionEngine;


But this gives the error: 


May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences WindowsRegOpenKey1

WARNING: Trying to recreate Windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences openKey

WARNING: Could not open windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002. Windows RegOpenKey(...) returned error code 2.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences WindowsRegOpenKey1

WARNING: Trying to recreate Windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002.

May 15, 2018 4:36:29 PM java.util.prefs.WindowsPreferences openKey

WARNING: Could not open windows registry node Software\JavaSoft\Prefs\org\micromanager at root 0x80000002. Windows RegOpenKey(...) returned error code 2.

Error using trialMicroGUI (line 7)
Java exception occurred:
java.lang.NoClassDefFoundError: org/fife/ui/rsyntaxtextarea/RSyntaxTextArea

at org.micromanager.utils.MMKeyDispatcher.<init>(MMKeyDispatcher.java:48)

at org.micromanager.MainFrame.<init>(MainFrame.java:148)

at org.micromanager.MMStudio.<init>(MMStudio.java:330)


Thread 120 (Pipeline Class loading thread) terminated with uncaught exception
java.lang.NoClassDefFoundError: clojure/lang/IFn
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Class.java:264)
  at org.micromanager.MMStudio$1.run(MMStudio.java:582)
Caused by exception:
java.lang.ClassNotFoundException: clojure.lang.IFn
  at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
  at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Class.java:264)
  at org.micromanager.MMStudio$1.run(MMStudio.java:582)


Apologies if this is something that has already been asked before, but I couldn't find any reference to someone else who found this.  I am also new to scripting Micro-Manager. My operating system is Windows 7 and the things I've added to my static javaclasspath are:


C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar                                      
C:\Program Files\Micro-Manager-1.4\ij.jar                                                                 
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMAcqEngine.jar                                  
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMCoreJ.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\MMJ_.jar                                         
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\clojure.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\bsh-2.0b4.jar                                    
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\swingx-0.9.5.jar                                 
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\swing-layout-1.0.4.jar                           
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\commons-math-2.0.jar                             
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\ome-xml.jar                                      
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\scifio.jar                                       
C:\Program Files\Micro-Manager-1.4\plugins\Micro-Manager\guava-17.0.jar   

Please let me know if you have any suggestions for why this error is being thrown and what I could do to resolve it, it would be greatly appreciated! Thanks,

Vanessa

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