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<head>
<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Gaussian Blur Filter in headless mode broken"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1002">1002</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Gaussian Blur Filter in headless mode broken
</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>tensionheadx@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>tensionheadx@gmail.com
</td>
</tr></table>
<p>
<div>
<pre>So in short, when running a macro in headless mode from the command line, the
sigma parameter of the standard Gaussian Filter seems not to be captured by the
macro interpreter.
Here is a dummy example:
open('path-to-image');
name = getTitle()
run("Duplicate...", "title=Dup");
run("Gaussian Blur...", "sigma=5");
save('gaussian1.tif');
selectImage(name)
run("Gaussian Blur...", "sigma=1");
save('gaussian2.tif');
When calling this macro from the Fiji in Gui (so normal) mode, everything works
as expected.
But when calling this macro from the commandline like 'ImageJ-macosx --headless
-macro dummy.ijm'
the two produced images will be the same, meaning that sigma most likely was
set to a default value.
See also my post and the replies on
<a href="http://imagej.1557.x6.nabble.com/Gaussian-Blur-Filter-in-headless-mode-broken-td5011489.html#a5011505">http://imagej.1557.x6.nabble.com/Gaussian-Blur-Filter-in-headless-mode-broken-td5011489.html#a5011505</a>
Information about your version of Java:
os.arch => x86_64
os.name => Mac OS X
os.version => 10.10.1
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-b14-466.1-11M4716
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 20.65-b04-466.1
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: READ_ONLY
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: null
imagej.dir => /Volumes/Fiji/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:20150122044514)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150127132630)</pre>
</div>
</p>
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