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

[alex gouaillard]

I successfully built the bf-cpp after a svn up.
thanks

i move on to itk-wrapping.

alex.



On May 21, 2009, at 1:12 PM, Curtis Rueden wrote:

> Hi Alex,
>
> * 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.
>
> Good points, I will add to the documentation when I get a chance.
>
> 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?
>
> This is the problem I mentioned to you about support for Windows DLL  
> symbol export breaking compilation on Mac & Linux. It should be  
> fixed with r5116 from two days ago. Did you update to the latest  
> trunk?
>
> -Curtis
>
> 2009/5/21 alex gouaillard <alexandre_gouaillard at hms.harvard.edu>
> 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>
>
>
>

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