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Bug 1247 - Histogram don't working
Histogram don't working
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-03-14 05:52 CDT by Maya AL-SID-CHEIKH
Modified: 2016-03-14 05:52 CDT
1 user (show)

See Also:
Description Maya AL-SID-CHEIKH 2016-03-14 05:52:48 CDT 
I work with Nanodefine's plugin to characterize nanoparticles size from 5 or 10 SEM images, in function of the number of frame I have. The plugin work pretty well except for the histograms results. I obtained a table results but I can't plot no histogram for the size characterization. 

This message appear :

Rserve>/bin/sh: null: command not found
java.lang.NullPointerException
	at de.biomedical_imaging.ij.rplot.HistogramFrame.getNumberOfBins(HistogramFrame.java:374)
	at de.biomedical_imaging.ij.rplot.HistogramFrame.updateData(HistogramFrame.java:75)
	at de.biomedical_imaging.ij.rplot.HistogramFrame.<init>(HistogramFrame.java:59)
	at de.biomedical_imaging.ij.rplot.RPlot.hist(RPlot.java:87)
	at de.biomedical_imaging.ij.rplot.rHistogram_.run(rHistogram_.java:90)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at ij.IJ.run(IJ.java:292)
	at ij.macro.Functions.doRun(Functions.java:601)
	at ij.macro.Functions.doFunction(Functions.java:96)
	at ij.macro.Interpreter.doStatement(Interpreter.java:230)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.doStatement(Interpreter.java:272)
	at ij.macro.Interpreter.doIf(Interpreter.java:966)
	at ij.macro.Interpreter.doStatement(Interpreter.java:248)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.doStatement(Interpreter.java:272)
	at ij.macro.Interpreter.doIf(Interpreter.java:966)
	at ij.macro.Interpreter.doStatement(Interpreter.java:248)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.runFirstMacro(Interpreter.java:707)
	at ij.macro.Interpreter.doStatement(Interpreter.java:263)
	at ij.macro.Interpreter.doStatements(Interpreter.java:218)
	at ij.macro.Interpreter.run(Interpreter.java:115)
	at ij.macro.Interpreter.run(Interpreter.java:85)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	at HAADF_.run(HAADF_.java:8)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
	at de.biomedical_imaging.ij.rplot.HistogramFrame.getNumberOfBins(HistogramFrame.java:374)
	at de.biomedical_imaging.ij.rplot.HistogramFrame.updateData(HistogramFrame.java:75)
	at de.biomedical_imaging.ij.rplot.HistogramFrame.plotHist(HistogramFrame.java:390)
	at de.biomedical_imaging.ij.rplot.HistogramFrame.<init>(HistogramFrame.java:61)
	at de.biomedical_imaging.ij.rplot.RPlot.hist(RPlot.java:87)
	at de.biomedical_imaging.ij.rplot.rHistogram_.run(rHistogram_.java:90)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at ij.IJ.run(IJ.java:292)
	at ij.macro.Functions.doRun(Functions.java:601)
	at ij.macro.Functions.doFunction(Functions.java:96)
	at ij.macro.Interpreter.doStatement(Interpreter.java:230)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.doStatement(Interpreter.java:272)
	at ij.macro.Interpreter.doIf(Interpreter.java:966)
	at ij.macro.Interpreter.doStatement(Interpreter.java:248)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.doStatement(Interpreter.java:272)
	at ij.macro.Interpreter.doIf(Interpreter.java:966)
	at ij.macro.Interpreter.doStatement(Interpreter.java:248)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.runFirstMacro(Interpreter.java:707)
	at ij.macro.Interpreter.doStatement(Interpreter.java:263)
	at ij.macro.Interpreter.doStatements(Interpreter.java:218)
	at ij.macro.Interpreter.run(Interpreter.java:115)
	at ij.macro.Interpreter.run(Interpreter.java:85)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	at HAADF_.run(HAADF_.java:8)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
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Done: Checksummer

Thanks a lot for your help,
Maya

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.3
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b17
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b17
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /Applications/Fiji.app/java/macosx/jdk1.8.0_66/jre/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217160804)
Fiji: http://update.fiji.sc/ (last check:20160218145537)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160310173718)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20160313183422)
NanoDefine: http://sites.imagej.net/Ndef-psizer/ (last check:20160311090438)

Files not up-to-date:
  6505b48f (MODIFIED) 20160311154022 jars/ij-1.50e.jar
  127371d6 (LOCAL_ONLY) 20160215162349 plugins/jars/JavaScript.jar