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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 - plugin register virtual stack slices"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1007">1007</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>plugin register virtual stack slices
</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>unnitsu@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>unnitsu@gmail.com
</td>
</tr></table>
<p>
<div>
<pre>I have 3325MB of RAM and a core 2 duo 64 bit windows system running windows 7
ultimate OS.
When I use the plugin "plugin register virtual stack slices", I observe that
the registered slices are
saved one by one in my selected output directory but the saving order is not
numerically sequential.
It saved files NEF1, NEF2,NEF3,NEF4 and suddenly becomes NEF10,NEF11,etc. The
screen shot
of the directory , I will try to upload. It shows the sequence of saving. There
were 60 files in the input directory
each of 23MB Tiff format. When the 59th file was saved, I saw a log window as
below:
<span class="quote">>>>>>>>>>>>>>>>>>>>>>>>>>>></span >
<Out of memory>
<All available memory (2995MB) has been>
<used. To make more available, use the>
<Edit>Options>Memory & Threads command.>
<span class="quote">>>>>>>>>>>>>>>>>>>>>>>>>>>></span >
My queries :
1. Being virtual stack, I hoped that there is no memory limit and I could
process 100 or 200 such files. Am I right ?
2. Why the files are not saved in the numerical order ? If so, file NEF5 would
not have got distorted.
3. I feel that as the processing of about 40 files were over, memory trouble
began and subsequent files were
wrongly processed before giving out the memory shortage error in log
window.
4. I tried the virtual stack in some of the other menus but the effect is the
same.
5. My requirement is to process 100 or 200 such files for use in focus
stacking. Since I did not find a method to
combine the stack , I use the aligned images from FIJI as input in a
program COMBINE ZP and the results are
excellent.
6. So I processed only 45 files using virtual stack method instead of my
available 70 files. There was no error.
Using the normal method of stacking into RAM, I can process only 24 files
maximum, in my system. (Linear stack
alignment with SIFT)
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: UPDATEABLE
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: E:\Fiji64/java/win64/jdk1.6.0_24//jre
imagej.dir => E:\Fiji64
Information about the version of each plugin:
Activated update sites:
ImageJ: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20141015224008)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20141023202357)
Files not up-to-date:
4c694223 (MODIFIED) 20150217210320 jars/imagej-common-0.12.1.jar
28763c96 (MODIFIED) 20141025210702 jars/imagej-common-0.9.0.jar
56ab750a (MODIFIED) 20140920133924 jars/imagej-ops-0.5.0.jar
771f88d5 (MODIFIED) 20150217210326 jars/imagej-ops-0.9.0.jar
c8af6461 (MODIFIED) 20141025210705 jars/imagej-updater-0.6.2.jar
a6077b46 (MODIFIED) 20150217210328 jars/imagej-updater-0.7.0.jar
6e22d9dd (MODIFIED) 20140920133924 jars/imglib2-2.0.0-beta-26.jar
225b3943 (MODIFIED) 20150217210314 jars/imglib2-2.2.0.jar
fd37b4cc (LOCAL_ONLY) 20150217210331 jars/imglib2-algorithm-0.2.0.jar
ba955d64 (MODIFIED) 20140920133924
jars/imglib2-realtransform-2.0.0-beta-26.jar
c0b8f2de (MODIFIED) 20150217210329
jars/imglib2-realtransform-2.0.0-beta-28.jar
5be1fcae (LOCAL_ONLY) 20150217210329 jars/imglib2-roi-0.2.0.jar
68d72328 (MODIFIED) 20140920133928 jars/scijava-common-2.33.0.jar
cde753a7 (MODIFIED) 20150217210317 jars/scijava-common-2.38.0.jar
a15062e7 (LOCAL_ONLY) 20140920225015 plugins/ExtendedDepthField.txt
a5908c2b (LOCAL_ONLY) 20140921071831 plugins/edf_3D.jar
a66e53c8 (LOCAL_ONLY) 20140921071839 plugins/ijtools.jar</pre>
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