[ImageJ-bugs] [Bug 1016] New: ERROR java.lang.IllegalArgumentException
bugzilla at fiji.sc
bugzilla at fiji.sc
Mon Mar 2 09:53:12 CST 2015
http://fiji.sc/bugzilla/show_bug.cgi?id=1016
Bug ID: 1016
Summary: ERROR java.lang.IllegalArgumentException
Product: Fiji
Version: unspecified
Hardware: Macintosh
OS: Mac OS
Status: NEW
Severity: normal
Priority: P4
Component: Plugins
Assignee: imagej-bugs at imagej.net
Reporter: deshpande.ojas at gmail.com
CC: deshpande.ojas at gmail.com
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
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