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

[Curtis Rueden]

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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