roiManager("measure") NullPointerException

[pradeep kota]

Dear all,

I am trying to write a macro to export line ROIs from many tif overlays in a directory, one at a time, into roiManager and then measure lengths and angles of the lines. Each tif file contains 4-8 such lines. Here's the relevant part of the macro that processes each file in a given directory.

open(inputList[fNo]); //Array holding files in a given directory

if(!isOpen("ROI Manager")) {

run("ROI Manager...");

} else {

clearROIManager(); //User-defined utility function to clear all elements of the ROIManager

}

run("To ROI Manager");

if(isOpen("Results")) {

run("Clear Results");

}

run("Set Measurements...", "bounding redirect=None decimal=3");

roiManager("Measure");

This part runs fine, except that it throws a NullPointerException sporadically. Here's the exception returned when I run the macro

(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49g; Java 1.6.0_65 [64-bit]; Mac OS X 10.8.5; 161MB of 4087MB (3%)

 

java.lang.NullPointerException

at ij.gui.Line.getPixels(Line.java:404)

at ij.gui.ProfilePlot.getStraightLineProfile(ProfilePlot.java:169)

at ij.gui.ProfilePlot.<init>(ProfilePlot.java:56)

at ij.gui.ProfilePlot.<init>(ProfilePlot.java:34)

at ij.plugin.filter.Analyzer.measureLength(Analyzer.java:412)

at ij.plugin.filter.Analyzer.measure(Analyzer.java:244)

at ij.plugin.filter.Analyzer.run(Analyzer.java:92)

at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)

at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)

at ij.IJ.runPlugIn(IJ.java:174)

at ij.Executer.runCommand(Executer.java:131)

at ij.Executer.run(Executer.java:64)

at ij.IJ.run(IJ.java:272)

at ij.IJ.run(IJ.java:250)

at ij.plugin.frame.RoiManager.measure(RoiManager.java:853)

at ij.plugin.frame.RoiManager.runCommand(RoiManager.java:1797)

at ij.macro.Functions.roiManager(Functions.java:2559)

at ij.macro.Functions.getFunctionValue(Functions.java:223)

at ij.macro.Interpreter.getFactor(Interpreter.java:1376)

at ij.macro.Interpreter.getTerm(Interpreter.java:1347)

at ij.macro.Interpreter.getStringExpression(Interpreter.java:1487)

at ij.macro.Interpreter.getStringTerm(Interpreter.java:1306)

at ij.macro.Interpreter.getString(Interpreter.java:1263)

at ij.macro.Interpreter.doStatement(Interpreter.java:278)

at ij.macro.Interpreter.doBlock(Interpreter.java:599)

at ij.macro.Interpreter.doStatement(Interpreter.java:269)

at ij.macro.Interpreter.doFor(Interpreter.java:526)

at ij.macro.Interpreter.doStatement(Interpreter.java:251)

at ij.macro.Interpreter.doStatements(Interpreter.java:215)

at ij.macro.Interpreter.run(Interpreter.java:112)

at ij.macro.Interpreter.run(Interpreter.java:82)

at ij.macro.Interpreter.run(Interpreter.java:93)

at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)

at ij.IJ.runMacro(IJ.java:119)

at ij.IJ.runMacro(IJ.java:108)

at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:782)

at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)

at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:156)

at org.scijava.script.ScriptModule.run(ScriptModule.java:175)

at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)

at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)

at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)

at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)

at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)

at java.util.concurrent.FutureTask.run(FutureTask.java:138)

at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)

at java.lang.Thread.run(Thread.java:695)

It does not throw the exception with the same file in the directory every time, making it harder for me to track it down. Any pointers are greatly appreciated.

best

Pradeep