<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi Melissa,</div><div>Thanks a lot for the info. I was using the exporter in my macro. I tried the trunk build, and got the following error:</div><div><br></div><div><div>java.lang.NullPointerException</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.out.Exporter.run(Exporter.java:357)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.LociExporter.run(LociExporter.java:73)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:249)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)</div><div><span class="Apple-tab-span"
style="white-space:pre"> </span>at ij.IJ.runUserPlugIn(IJ.java:185)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.IJ.runPlugIn(IJ.java:150)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.Executer.runCommand(Executer.java:124)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.Executer.run(Executer.java:61)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.IJ.run(IJ.java:249)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Functions.doRun(Functions.java:561)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Functions.doFunction(Functions.java:79)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:203)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at
ij.macro.Interpreter.doBlock(Interpreter.java:518)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:239)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doIf(Interpreter.java:852)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:215)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doIf(Interpreter.java:865)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:215)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doBlock(Interpreter.java:518)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:239)</div><div><span
class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doIf(Interpreter.java:852)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:215)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doBlock(Interpreter.java:518)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:239)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doIf(Interpreter.java:852)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:215)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doBlock(Interpreter.java:518)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at
ij.macro.Interpreter.doStatement(Interpreter.java:239)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doFor(Interpreter.java:464)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:221)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doBlock(Interpreter.java:518)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.runUserFunction(Interpreter.java:278)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatement(Interpreter.java:206)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.doStatements(Interpreter.java:191)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.run(Interpreter.java:102)</div><div><span
class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.Interpreter.run(Interpreter.java:72)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.macro.MacroRunner.run(MacroRunner.java:124)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.lang.Thread.run(Thread.java:619)</div></div><div><br></div><div>The same macro runs the stable build fine. Any suggestion? Thanks a lot.<br></div><div><br></div><div>Best,</div><div>Liang</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Melissa Linkert <melissa@glencoesoftware.com><br><b><span style="font-weight: bold;">To:</span></b> "cail@rocketmail" <cail@rocketmail.com><br><b><span style="font-weight: bold;">Cc:</span></b>
ome-users@lists.openmicroscopy.org.uk<br><b><span style="font-weight: bold;">Sent:</span></b> Fri, January 7, 2011 6:29:50 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [ome-users] very slow LOCI bio-format exporter<br></font><br>
Hi Cail,<br><br>Thank you for reporting this problem.<br><br>We have received similar reports from a few other people, and have recently made<br>several changes that hopefully improve the OME-TIFF export performance.<br>Could you please try using the latest trunk build of loci_tools.jar and<br>see if you notice any difference?<br><br>Regards,<br>-Melissa<br><br>On Wed, Jan 05, 2011 at 11:21:48AM -0800, cail@rocketmail wrote:<br>> Dear All,<br>> I have a xyzct stack with a total of 1800 planes. When I use LOCI bio-format <br>> exporter to save it as ome.tif file, it starts with 10-20 planes per second, but <br>> when it is saving the >900 planes (e.g saving plan 1001/1800), the speed drops <br>> to 1-5 second per plane, which is extremely slow. If I directly save the entire <br>> stack as a TIF file, it totally costs less than 10 second, but it is not ome.tif <br>> format. I want the ome.tif format.<br>> I have used the lasted
stable build of loci_tools.jar and 1.44m ImageJ on 32bit <br>> Java.<br>> Any suggestion on improving the file saving process is really appreciated.<br>> Thank you very much for your time,<br>> Best,<br>> cail<br>> <br>> <br>> <br><br>> _______________________________________________<br>> ome-users mailing list<br>> <a ymailto="mailto:ome-users@lists.openmicroscopy.org.uk" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br><span>> <a target="_blank" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></span><br><br></div></div><div style="position:fixed"></div>
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