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<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
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<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - java.io.IOException: io.scif.FormatException: Invalid TIFF file"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=902">902</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>java.io.IOException: io.scif.FormatException: Invalid TIFF file
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>PC
</td>
</tr>
<tr>
<th>OS</th>
<td>Windows
</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>sweel@uci.edu
</td>
</tr>
<tr>
<th>CC</th>
<td>sweel@uci.edu
</td>
</tr></table>
<p>
<div>
<pre>Running an imageJ script which uses the function:
run("Image Sequence...", "open=["someTifFile"] number="+numofPics+" starting=1
increment=1 scale=100 file=BF sort");
which used to work in the IJ1-Fiji version now throws this exception:
(Fiji Is Just) ImageJ 2.0.0-rc-13/1.49e; Java 1.6.0_24 [64-bit]; Windows 7 6.1;
213MB of 9189MB (2%)
java.io.IOException: io.scif.img.ImgIOException: java.io.IOException:
io.scif.FormatException: Invalid TIFF file at
net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:273) at
net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250) at
net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78) at
net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50) at
net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:136)
at
net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:335)
at ij.plugin.FolderOpener.run(FolderOpener.java:190) at
ij.IJ.runPlugIn(IJ.java:172) at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64) at ij.IJ.run(IJ.java:272) at
ij.macro.Functions.doRun(Functions.java:591) at
ij.macro.Functions.doFunction(Functions.java:89) at
ij.macro.Interpreter.doStatement(Interpreter.java:227) at
ij.macro.Interpreter.doBlock(Interpreter.java:599) at
ij.macro.Interpreter.doStatement(Interpreter.java:269) at
ij.macro.Interpreter.doIf(Interpreter.java:957) at
ij.macro.Interpreter.doStatement(Interpreter.java:245) 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:783) 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$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662) Caused by:
io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException:
Invalid TIFF file at io.scif.img.ImgOpener.createReader(ImgOpener.java:551)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144) at
net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266) ...
41 more Caused by: java.io.IOException: io.scif.FormatException: Invalid TIFF
file at io.scif.AbstractReader.setSource(AbstractReader.java:274) at
io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:542) ... 43 more
Caused by: io.scif.FormatException: Invalid TIFF file at
io.scif.formats.MinimalTIFFFormat$Parser.typedParse(MinimalTIFFFormat.java:412)
at
io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:867)
at io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:849)
at io.scif.AbstractParser.parse(AbstractParser.java:252) at
io.scif.AbstractParser.parse(AbstractParser.java:335) at
io.scif.AbstractParser.parse(AbstractParser.java:52) at
io.scif.AbstractReader.setSource(AbstractReader.java:270) ... 45 more
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: CHECK_TURNED_OFF
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to:
C:\Users\sweel\Desktop\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Users\sweel\Desktop\FIJI-W~1\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:20140814090445)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140813115223)
Files not up-to-date:
ba8c13c5 (LOCAL_ONLY) 20140716220023 macros/StartupMacros.ijm
d78d6380 (LOCAL_ONLY) 20140625032732 macros/StartupMacrosold.ijm</pre>
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