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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 - Headless mode incorect macro parsing (grid stitching)"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=900">900</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Headless mode incorect macro parsing (grid stitching)
</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>stanislaw@wdidevice.com
</td>
</tr>
<tr>
<th>CC</th>
<td>stanislaw@wdidevice.com
</td>
</tr></table>
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<pre>I start app like this:
Fiji.app\\ImageJ-win64.exe -macro ..\\..\\tmp\\scan.ijm
or like this:
Fiji.app\\ImageJ-win64.exe --headless -macro ..\\..\\tmp\\scan.ijm
Results are different.
Macro file is:
run("Grid/Collection stitching", "type=[Positions from file] order=[Defined by
TileConfiguration] directory=tmp layout_file=scan.pos fusion_method=[Linear
Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50
absolute_displacement_threshold=3.50 compute_overlap=[false]
computation_parameters=[Save computation time (but use more RAM)]
image_output=[Fuse and display]");
saveAs("Jpeg", "map.jpg");
run("Quit");
In standard mode Fiji works as expected.
In headless mode Fiji automatically activates option "Compute overlap",
although it is not specified.
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:\BADZIE~1\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\BADZIE~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:20140802105300)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20140730140634)</pre>
</div>
</p>
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