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

[cail@rocketmail]

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


      
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