bonej java problem

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bonej java problem

Anovitz, Lawrence {Larry} M.
I am trying to run bonej on a stack of images from and X-ray CT on a Mac Pro (12 core, 64 GB)
There are 2293 slices, each 1360 x 1360 pixesl, all 8 bit – total 3.9 GB
FIJI/ImageJ had about 44GB of memory available, but watching activity monitor it never called for more than 11GB

I was running the fractal dimension calculation, and it threw and exception.

Have I made some error or is this some limit with java?
Please let me know if this is do-able and if so how.

Thanks.

--Larry


Here is the output from the console

[ERROR] Module threw exception
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at net.imagej.ops.thread.chunker.DefaultChunker.run(DefaultChunker.java:103)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel.compute(MapUnaryComputers.java:101)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel.compute(MapUnaryComputers.java:87)
                at net.imagej.ops.special.chain.UHCFViaUC.compute(UHCFViaUC.java:65)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
                at net.imagej.ops.convert.ConvertNamespace.bit(ConvertNamespace.java:132)
                at org.bonej.wrapperPlugins.wrapperUtils.Common.toBitTypeImgPlus(Common.java:80)
                at org.bonej.wrapperPlugins.FractalDimensionWrapper.run(FractalDimensionWrapper.java:172)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
                at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
                at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
                at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
                at java.util.concurrent.FutureTask.run(FutureTask.java:266)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
                at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at java.util.concurrent.FutureTask.report(FutureTask.java:122)
                at java.util.concurrent.FutureTask.get(FutureTask.java:192)
                at net.imagej.ops.thread.chunker.DefaultChunker.run(DefaultChunker.java:97)
                ... 24 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at net.imglib2.img.basictypeaccess.array.AbstractByteArray.getValue(AbstractByteArray.java:61)
                at net.imglib2.type.numeric.integer.GenericByteType.getByte(GenericByteType.java:127)
                at net.imglib2.type.numeric.integer.UnsignedByteType.get(UnsignedByteType.java:151)
                at net.imglib2.type.numeric.integer.UnsignedByteType.getIntegerLong(UnsignedByteType.java:168)
                at net.imagej.ops.convert.ConvertTypes$IntegerToBit.compute(ConvertTypes.java:102)
                at net.imagej.ops.convert.ConvertTypes$IntegerToBit.compute(ConvertTypes.java:89)
                at net.imagej.ops.map.Maps.map(Maps.java:297)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel$1.execute(MapUnaryComputers.java:106)
                at net.imagej.ops.thread.chunker.DefaultChunker$1.run(DefaultChunker.java:77)
                at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                ... 4 more


And here is the output from the exception window

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_192 [64-bit]; Mac OS X 10.13.6; 5676MB of 44619MB (12%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
                at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
                at ij.IJ.runPlugIn(IJ.java)
                at ij.Executer.runCommand(Executer.java:137)
                at ij.Executer.run(Executer.java:66)
                at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at java.util.concurrent.FutureTask.report(FutureTask.java:122)
                at java.util.concurrent.FutureTask.get(FutureTask.java:192)
                at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:299)
                ... 5 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at net.imagej.ops.thread.chunker.DefaultChunker.run(DefaultChunker.java:103)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel.compute(MapUnaryComputers.java:101)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel.compute(MapUnaryComputers.java:87)
                at net.imagej.ops.special.chain.UHCFViaUC.compute(UHCFViaUC.java:65)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
                at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
                at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
                at net.imagej.ops.convert.ConvertNamespace.bit(ConvertNamespace.java:132)
                at org.bonej.wrapperPlugins.wrapperUtils.Common.toBitTypeImgPlus(Common.java:80)
                at org.bonej.wrapperPlugins.FractalDimensionWrapper.run(FractalDimensionWrapper.java:172)
                at org.scijava.command.CommandModule.run(CommandModule.java:199)
                at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
                at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
                at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
                at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
                at java.util.concurrent.FutureTask.run(FutureTask.java:266)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
                ... 1 more
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at java.util.concurrent.FutureTask.report(FutureTask.java:122)
                at java.util.concurrent.FutureTask.get(FutureTask.java:192)
                at net.imagej.ops.thread.chunker.DefaultChunker.run(DefaultChunker.java:97)
                ... 24 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1997687038
                at net.imglib2.img.basictypeaccess.array.AbstractByteArray.getValue(AbstractByteArray.java:61)
                at net.imglib2.type.numeric.integer.GenericByteType.getByte(GenericByteType.java:127)
                at net.imglib2.type.numeric.integer.UnsignedByteType.get(UnsignedByteType.java:151)
                at net.imglib2.type.numeric.integer.UnsignedByteType.getIntegerLong(UnsignedByteType.java:168)
                at net.imagej.ops.convert.ConvertTypes$IntegerToBit.compute(ConvertTypes.java:102)
                at net.imagej.ops.convert.ConvertTypes$IntegerToBit.compute(ConvertTypes.java:89)
                at net.imagej.ops.map.Maps.map(Maps.java:297)
                at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel$1.execute(MapUnaryComputers.java:106)
                at net.imagej.ops.thread.chunker.DefaultChunker$1.run(DefaultChunker.java:77)
                at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                ... 4 more

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