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Bugzilla – Bug 1016 |
ERROR java.lang.IllegalArgumentException |
Last modified: 2015-03-02 10:13:01 CST |
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NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug. The Fiji project now uses GitHub Issues for issue tracking. Please file all new issues there. |
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ERROR (Fiji Is Just) ImageJ 2.0.0-rc-25/1.49m; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.5; 37MB of 5991MB (<1%) java.lang.IllegalArgumentException at java.nio.Buffer.position(Buffer.java:216) at io.scif.io.NIOFileHandle.buffer(NIOFileHandle.java:544) at io.scif.io.NIOFileHandle.seek(NIOFileHandle.java:246) at io.scif.io.RandomAccessInputStream.seek(RandomAccessInputStream.java:139) at io.scif.formats.tiff.TiffParser.getSamples(TiffParser.java:839) at io.scif.formats.tiff.TiffParser.getSamples(TiffParser.java:746) at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:627) at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:537) at io.scif.AbstractReader.openPlane(AbstractReader.java:167) at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170) at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151) at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:304) at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208) at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225) at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191) at io.scif.img.ImgOpener.read(ImgOpener.java:805) at io.scif.img.ImgOpener.read(ImgOpener.java:771) at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:758) at io.scif.img.ImgOpener.openImgs(ImgOpener.java:361) at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257) at io.scif.img.ImgOpener.openImgs(ImgOpener.java:146) at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:123) at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:109) at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75) at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50) at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135) at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327) at ij.IJ.open(IJ.java) at ij.macro.Functions.open(Functions.java:2478) at ij.macro.Functions.doFunction(Functions.java:149) at ij.macro.Interpreter.doStatement(Interpreter.java:226) at ij.macro.Interpreter.doBlock(Interpreter.java:598) at ij.macro.Interpreter.doStatement(Interpreter.java:268) at ij.macro.Interpreter.doIf(Interpreter.java:956) at ij.macro.Interpreter.doStatement(Interpreter.java:244) at ij.macro.Interpreter.doBlock(Interpreter.java:598) at ij.macro.Interpreter.doStatement(Interpreter.java:268) at ij.macro.Interpreter.doFor(Interpreter.java:525) at ij.macro.Interpreter.doStatement(Interpreter.java:250) at ij.macro.Interpreter.doStatements(Interpreter.java:214) at ij.macro.Interpreter.run(Interpreter.java:111) at ij.macro.Interpreter.run(Interpreter.java:81) at ij.macro.Interpreter.run(Interpreter.java:92) 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:794) at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116) at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:160) 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) MACRO ----------------------------------- NoChannels= 2 // Define the no of channels NoZStacks= 35 // Define the no of Z sections // Define the directories Input = getDirectory("/Users/odeshpande/Documents/20141218_foroptimisingmacro_20150112_63517 PM/"); Output = getDirectory("/Users/odeshpande/Documents/20141218_foroptimisingmacro_20150112_63517 PM/output/"); list_Input = getFileList(Input); //hyperstack and spilt into individual channel files for each time point for every input image for(i=0; i<list_Input.length; i++){ if(endsWith(list_Input[i], ".tif")){ open(Input+list_Input[i]); Title1 = getTitle(); N = nSlices; NoFrames = N/(NoChannels*NoZStacks); run("Stack to Hyperstack...", "order=xyczt(default) channels=NoChannels slices=NoZStacks frames=NoFrames display=Color"); run("Split Channels"); selectWindow("C1-"+Title1); Title2 = getTitle(); saveAs("Tiff", Output+Title2+"_C1"); selectWindow("C2-"+Title1); Title3 = getTitle(); saveAs("Tiff", Output+Title3+"_C1"); run("Close All"); } } Information about your version of Java: os.arch => x86_64 os.name => Mac OS X os.version => 10.9.5 java.version => 1.6.0_65 java.vendor => Apple Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_65-b14-462-11M4609 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 20.65-b04-462 java.vm.vendor => Apple Inc. java.vm.info => mixed mode java.awt.graphicsenv => apple.awt.CGraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 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: null imagej.dir => /Applications/Fiji.app Information about the version of each plugin: Activated update sites: ImageJ: http://update.imagej.net/ (last check:20150302042523) Fiji: http://fiji.sc/update/ (last check:20150302131317) Files not up-to-date: 200a30ac (MODIFIED) 20150302154002 Contents/Info.plist b6bf3817 (OBSOLETE_UNINSTALLED) 20141120053514 jars/edu_mines_jtk.jar 25895ad6 (OBSOLETE_UNINSTALLED) 20141120053514 jars/imglib2-ops-2.0.0-beta-26.jar 8c636e50 (OBSOLETE_UNINSTALLED) 20141120053514 jars/jai_codec.jar 717dd8e0 (OBSOLETE_UNINSTALLED) 20141120053514 jars/jai_core.jar 1ad3be0d (LOCAL_ONLY) 20141120053514 jars/jpedalSTD.jar a2677f69 (LOCAL_ONLY) 20150113191609 macros/BatchMacro.ijm