<html>
<head>
<base href="http://fiji.sc/bugzilla/" />
</head>
<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - ERROR java.lang.IllegalArgumentException"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1016">1016</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>ERROR java.lang.IllegalArgumentException
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>normal
</td>
</tr>
<tr>
<th>Priority</th>
<td>P4
</td>
</tr>
<tr>
<th>Component</th>
<td>Plugins
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>deshpande.ojas@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>deshpande.ojas@gmail.com
</td>
</tr></table>
<p>
<div>
<pre>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: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150302042523)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (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</pre>
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