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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 - ClassCastException when using Process>Batch>Convert..."
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1086">1086</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>ClassCastException when using Process>Batch>Convert...
</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>jan.eglinger@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>jan.eglinger@gmail.com
</td>
</tr></table>
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<pre>When trying to convert a folder of czi files to TIFF using 'Process > Batch >
Convert...', the exception below [2] is thrown. The czi files contain
hyperstacks of 3 channels and 19 z-slices and they open correctly when opened
normally (i.e. via drag-and-drop or using the Bio-Formats Importer).
A workaround is to use 'Process > Batch > Macro...' and entering just an empty
comment ('//') into the macro text field.
Looking at ImageWriter.java [1], it seems that the nImages<=1 for the
associated FileInfo opbject.
Cheers,
Jan
[1]:<a href="https://github.com/imagej/ImageJA/blob/wayne/ij/io/ImageWriter.java#L281">https://github.com/imagej/ImageJA/blob/wayne/ij/io/ImageWriter.java#L281</a>
[2]:
(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49t; Java 1.8.0_40 [64-bit]; Windows 7 6.1;
1492MB of 96000MB (1%)
java.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [S
at ij.io.ImageWriter.write(ImageWriter.java:281)
at ij.io.TiffEncoder.write(TiffEncoder.java:129)
at ij.io.TiffEncoder.write(TiffEncoder.java:150)
at ij.io.FileSaver.saveAsTiff(FileSaver.java:114)
at ij.plugin.BatchConverter.run(BatchConverter.java:93)
at ij.IJ.runPlugIn(IJ.java:169)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:745)
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: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\UTILIT~1\FIJI-D~1.APP/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\UTILIT~1\FIJI-D~1.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:20150602035708)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150605150752)</pre>
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