[ome-users] very slow LOCI bio-format exporter

[Melissa Linkert]

Hi Liang,

> Thanks a lot for the info. I was using the exporter in my macro. I tried the 
> trunk build, and got the following error:

Thank you for the update - that problem should be fixed now.

Can you please update to the latest trunk build again and let us know how it goes?

Regards,
-Melissa

On Fri, Jan 07, 2011 at 10:01:15AM -0800, cail at rocketmail wrote:
> Hi Melissa,
> Thanks a lot for the info. I was using the exporter in my macro. I tried the 
> trunk build, and got the following error:
> 
> java.lang.NullPointerException
> at loci.plugins.out.Exporter.run(Exporter.java:357)
> at loci.plugins.LociExporter.run(LociExporter.java:73)
> at 
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:249)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.Executer.runCommand(Executer.java:124)
> at ij.Executer.run(Executer.java:61)
> at ij.IJ.run(IJ.java:249)
> at ij.macro.Functions.doRun(Functions.java:561)
> at ij.macro.Functions.doFunction(Functions.java:79)
> at ij.macro.Interpreter.doStatement(Interpreter.java:203)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.doStatement(Interpreter.java:239)
> at ij.macro.Interpreter.doIf(Interpreter.java:852)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doIf(Interpreter.java:865)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.doStatement(Interpreter.java:239)
> at ij.macro.Interpreter.doIf(Interpreter.java:852)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.doStatement(Interpreter.java:239)
> at ij.macro.Interpreter.doIf(Interpreter.java:852)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.doStatement(Interpreter.java:239)
> at ij.macro.Interpreter.doFor(Interpreter.java:464)
> at ij.macro.Interpreter.doStatement(Interpreter.java:221)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.runUserFunction(Interpreter.java:278)
> at ij.macro.Interpreter.doStatement(Interpreter.java:206)
> at ij.macro.Interpreter.doStatements(Interpreter.java:191)
> at ij.macro.Interpreter.run(Interpreter.java:102)
> at ij.macro.Interpreter.run(Interpreter.java:72)
> at ij.macro.MacroRunner.run(MacroRunner.java:124)
> at java.lang.Thread.run(Thread.java:619)
> 
> The same macro runs the stable build fine. Any suggestion? Thanks a lot.
> 
> 
> Best,
> Liang
> 
> 
> 
> ________________________________
> From: Melissa Linkert <melissa at glencoesoftware.com>
> To: "cail at rocketmail" <cail at rocketmail.com>
> Cc: ome-users at lists.openmicroscopy.org.uk
> Sent: Fri, January 7, 2011 6:29:50 AM
> Subject: Re: [ome-users] very slow LOCI bio-format exporter
> 
> Hi Cail,
> 
> Thank you for reporting this problem.
> 
> We have received similar reports from a few other people, and have recently made
> several changes that hopefully improve the OME-TIFF export performance.
> Could you please try using the latest trunk build of loci_tools.jar and
> see if you notice any difference?
> 
> Regards,
> -Melissa
> 
> On Wed, Jan 05, 2011 at 11:21:48AM -0800, cail at rocketmail wrote:
> > Dear All,
> > I have a xyzct stack with a total of 1800 planes. When I use LOCI bio-format 
> > exporter to save it as ome.tif file, it starts with 10-20 planes per second, 
> >but 
> >
> > when it is saving the >900 planes (e.g saving plan 1001/1800), the speed drops 
> 
> > to 1-5 second per plane, which is extremely slow. If I directly save the entire 
> >
> > stack as a TIF file, it totally costs less than 10 second, but it is not 
> >ome.tif 
> >
> > format. I want the ome.tif format.
> > I have used the lasted stable build of loci_tools.jar and 1.44m ImageJ on 32bit 
> >
> > Java.
> > Any suggestion on improving the file saving process is really appreciated.
> > Thank you very much for your time,
> > Best,
> > cail
> > 
> > 
> >      
> 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 
> 
>