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Bug 642 - Opening of Zeiss lsm files in batch mode
Opening of Zeiss lsm files in batch mode
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-07-29 03:15 CDT by Antonio
Modified: 2013-07-29 03:40 CDT
1 user (show)

See Also:

Attachments
Example file (2.69 MB, application/octet-stream)
2013-07-29 03:18 CDT, Antonio

Description Antonio 2013-07-29 03:15:58 CDT 
setBatchMode(true); //no bug if we use false
open(lsmfile);

issues 
java.lang.NullPointerException: null
	 at org.imagearchive.lsm.reader.Reader.open(Reader.java:62)
	 at LSM_Reader.run(LSM_Reader.java:46)
	 at ij.IJ.runUserPlugIn(IJ.java:196)
	 at ij.IJ.runPlugIn(IJ.java:160)
	 at ij.IJ.runPlugIn(IJ.java:149)
	 at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:448)
	 at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:174)
	 at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:410)
	 at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	 at ij.IJ.runUserPlugIn(IJ.java:196)
	 at ij.IJ.runPlugIn(IJ.java:160)
	 at ij.IJ.runPlugIn(IJ.java:149)
	 at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:438)
	 at ij.io.Opener.openImage(Opener.java:310)
	 at ij.io.Opener.openImage(Opener.java:333)
	 at ij.io.Opener.open(Opener.java:143)
	 at ij.io.Opener.open(Opener.java:70)
	 at ij.IJ.open(IJ.java:1537)
	 at ij.macro.Functions.open(Functions.java:2433)
	 at ij.macro.Functions.doFunction(Functions.java:148)
	 at ij.macro.Interpreter.doStatement(Interpreter.java:219)
	 at ij.macro.Interpreter.doStatements(Interpreter.java:207)
	 at ij.macro.Interpreter.run(Interpreter.java:104)
	 at ij.macro.Interpreter.run(Interpreter.java:74)
	 at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	 at common.RefreshScripts.runScript(RefreshScripts.java:328)
	 at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1216)
	 at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1776)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Programs\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\Programs\Fiji.app

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Comment 1 Antonio 2013-07-29 03:18:54 CDT 
Created attachment 112
Example file