[Insight-users] Bio-Formats in ITK (was: Re: ITK for fluorescence microscopy - BioImageXD)

[alex gouaillard]

hi guys,

I'm painfully going through bf-cpp compiling on my mac.

I write here a few comments for others not to bump on the same stones:

* boost on mac: I ended up using port for that ("sudo port install  
bosst"
* jace root:  do NOT use relative path. Java is going to handle it ok,  
but the cmake part is going to fail in the IS_DIRECTORY test.

Now I'm stuck in the C++ compiation.  The compilator complains about  
JACE_PROXY_API not being defined. I attached the build log to this e- 
maill, could you take a look and tell me what I did wrong?

thanks



alex.


On May 21, 2009, at 12:11 AM, Curtis Rueden wrote:

> Hi Gaëtan,
>
> I don't get that error with a zvi file. Great!
>
> Great. And we will eliminate the problem for TIFF files soon as well.
>
> However, the performances don't seem that good: with my simple  
> python wrapper for bioformats, I open the image in 39 seconds.
> With itk-plugin, at 39 second, only 6 plans are open on the 51 plans  
> of the image.
>
> That is bad news. I was planning on doing some benchmarks comparing  
> with Bio-Formats + Ice, but was not expecting to see such bad  
> performance with JNI. I will look into it and see what I can find  
> out. It should be possible to do much better.
>
> I'll continue my investigations and will continue to report my  
> progress.
>
> Thank you.
>
> -Curtis
>
> 2009/5/20 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 20 mai 09 à 14:58, Curtis Rueden a écrit :
>
>
> Hi Gaëtan,
>
> -      "jace-runtime.jar:bio-formats.jar:loci_tools.jar"
> +      "jace.jar:jace-runtime.jar:bio-formats.jar:loci_tools.jar"
>
> Interesting; this library is not supposed to be necessary. But I'm  
> glad you got it working.
>
> Any idea about what is wrong with the threads?
> Also, do you now why it tries to start AWT? A GUI shouldn't be  
> useful in that case!
>
> We are aware of the AWT error messages on Mac OS X, and are working  
> to fix them. It is basically a matter of removing references to the  
> java.awt.Rectangle class, which we use for convenience reasons right  
> now, but can easily be changed.
>
> In the meantime, would you mind trying to read a file in a non-TIFF- 
> based format? The AWT errors mainly happen with TIFF-based formats  
> with the current codebase.
>
>
> I don't get that error with a zvi file. Great!
>
> However, the performances don't seem that good: with my simple  
> python wrapper for bioformats, I open the image in 39 seconds.
> With itk-plugin, at 39 second, only 6 plans are open on the 51 plans  
> of the image.
>
> I'll continue my investigations and will continue to report my  
> progress.
>
>
> Regards,
>
> Gaëtan
>
>
> -- 
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr  http://www.mandriva.org
> http://www.itk.org  http://www.clavier-dvorak.org
>
>
> <ATT00001.txt>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20090521/2c0d2f54/attachment-0002.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: log
Type: application/octet-stream
Size: 189831 bytes
Desc: not available
URL: <http://www.itk.org/pipermail/insight-users/attachments/20090521/2c0d2f54/attachment-0001.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20090521/2c0d2f54/attachment-0003.htm>