[Insight-users] WrapITK and windows

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Mon May 11 14:51:39 EDT 2009 

Hi,

Sorry for the long time before reply.
I'm very interested in your project - I'm just quite busy with other  
things, like setting up a omero server for my team.

Le 5 mai 09 à 19:11, Badri Roysam a écrit :

> Hi Gaetan,
>
> FARSIGHT is a joint project involving Kitware, RPI, the University  
> of Wisconsin, and the Wadsworth center.
> You can get a quick feel for the project by visiting our 10-day old  
> wiki page www.farsight-toolkit.org.
> We are still working on it.
>
> In a nutshell, we are interested in building a toolkit for  
> biologists who need to make measurements
> from images of cells and tissue gathered from microscopes.
>
> I am very interested in your wrapITK project, and feel that it can  
> be extremely helpful to the FARSIGHT
> project. The main challenge that remains to be overcome is to make  
> it as simple as possible for non
> computer scientists to invoke ITK routines from Python. Ideally, I  
> would like it require just one
> line of Python code, kind of like MATLAB.

it's possible to use most of the python filters with a single line of  
code. For example:

   median = itk.MedianImageFilter.IUC3IUC3.New(reader, Radius=2)

Of course it is also possible to write python functions to make the  
usage simpler, or at least shorter, like matlab functions.
My feeling is that we may loose the pipeline architecture of ITK,  
which is quite nice and useful. And the ITK names, even if they are  
quite long, are also quite expressive.

Maybe a better approach than shortening names is to integrate nicely  
the name completion in the code editor, as well as the doc.

> At the same time, we need to devise ways to make the documentation
> accessible to end users - currently, it is aimed at computer  
> scientists.
>

there's lot of work on that point for sure

Regards,

Gaëtan

> Best Wishes,
>
>
> Badri Roysam
> Professor, Department of Electrical, Computer and Systems Engineering
> Associate Director, NSF Center for Subsurface Sensing & Imaging  
> Systems (CenSSIS ERC)
> Co-Director, Rensselaer Center for Open Source Software
> Rensselaer Polytechnic Institute
> 110 8th Street, Troy, New York 12180-3590, USA.
> Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC  
> 6308): 518-276-8207, Fax: 518-276-8715
> Email: roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam
>
>
>
> ----- Original Message -----
> From: Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr]
> To: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Cc: insight users [mailto:insight-users at itk.org], Zack Galbreath [mailto:zack.galbreath at kitware.com 
> ], farsight-developers at lists.kitware.com, Rick Giuly [mailto:rgiuly at gmail.com 
> ]
> Subject: Re: [Insight-users] WrapITK and windows
>
>
>>
>> Le 4 mai 09 à 17:14, Luis Ibanez a écrit :
>>
>>>
>>> Hi Gaetan,
>>>
>>>
>>> A Tutorial on how to build ITK+WrapITK for Python on Windows
>>> (and Linux) has been posted at:
>>>
>>>
>>> http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/ 
>>> Building_Software
>>>
>>>
>>> and it is linked from
>>>
>>>  http://www.itk.org/Wiki/ITK_Tutorials
>>>
>>>
>>> Also, a Windows binary installer containing
>>>
>>>   * ITK + WrapITK for Python
>>>
>>> is now available at:
>>>
>>>  http://public.kitware.com/pub/itk/InsightApplicationsBin/
>>>
>>> more precisely
>>>
>>>
>> http://public.kitware.com/pub/itk/InsightApplicationsBin/InsightToolkitWithPythonWrapping-3.13.0-win32.exe
>>>
>>>
>>> The Installer tutorial:
>>>
>>>
>> http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Just_Installing_Software
>>>
>>> describes how to configure the installation.
>>
>>
>> Nice :-)
>>
>> I didn't heard about farsight before. I see a reference of it in the
>> last TCon.
>> Is it a new project leaded by kitware?
>>
>> Regards,
>>
>> Gaëtan
>>
>>
>>>
>>>
>>>
>>>
>>>  Regards,
>>>
>>>
>>>      Luis
>>>
>>>
>>>
>>> -----------------------
>>> Gaëtan Lehmann wrote:
>>>> Le 17 avr. 09 à 20:39, Luis Ibanez a écrit :
>>>>>
>>>>> Hi Gaetan,
>>>>>
>>>>> My apologies for the misleading statement.
>>>>>
>>>>> It is not really that the installation produces an error,
>>>>> but the fact that once it is build, the user must setup
>>>>> a couple of environment variables. So, it took me  a couple
>>>>> of tries to find the right way to setup my environment.
>>>> Yes, you're right, that not really easy.
>>>> I'm not sure it can be made easier though - at least it should be
>>>> well  documented.
>>>>>
>>>>>
>>>>> This exercise was done with the current version of WrapITK
>>>>> inside ITK.  I have not tried yet the external version that
>>>>> you have in Google Code.
>>>> Would it be possible (and desirable) to have WrapITK tests in
>>>> itk's  dashboard, as it's done for the new statistics framework?
>>>>>
>>>>>
>>>>>
>>>>> Hope that helps to clarify,
>>>> Sure
>>>> Thanks,
>>>> Gaëtan
>>>>>
>>>>>
>>>>>
>>>>>   Thanks
>>>>>
>>>>>
>>>>>      Luis
>>>>>
>>>>>
>>>>> ---------------------
>>>>> Gaëtan Lehmann wrote:
>>>>>
>>>>>> Hi Luis,
>>>>>> Thanks for testing WrapITK. I never seen an error during
>>>>>> installation  on windows with the stable version - I'll look at
>>>>>> that.
>>>>>> However, I don't think your are talking about the stable
>>>>>> version   included in ITK, and not about the new version of
>>>>>> WrapITK which is   developed outside ITK.
>>>>>> http://code.google.com/p/wrapitk/
>>>>>> I think I had a similar error message than Rick the last time I
>>>>>> tried  to build this version.
>>>>>> Rick, I had no chance to look deeper in the error you have. I'm
>>>>>> quite  sure I won't have much time before next week.
>>>>>> Regards,
>>>>>> Gaëtan
>>>>>> Le 16 avr. 09 à 18:31, Luis Ibanez a écrit :
>>>>>>
>>>>>>>
>>>>>>> Hi Gaetan,
>>>>>>>
>>>>>>> I managed to build WrapITK with Visual Studio 7.1
>>>>>>> several weeks ago. (for Python wrapping).
>>>>>>>
>>>>>>> The compilation process proceeded without problem.
>>>>>>> It was the installation (setting up paths) what
>>>>>>> end up being tricky.
>>>>>>>
>>>>>>> I believe Zack has enabled a Nightly build with
>>>>>>> WrapITK for Windows. Let me double check on that...
>>>>>>>
>>>>>>>
>>>>>>> Luis
>>>>>>>
>>>>>>>
>>>>>>> ----------------------
>>>>>>> Gaëtan Lehmann wrote:
>>>>>>>
>>>>>>>> Le 15 avr. 09 à 14:45, Rick Giuly a écrit :
>>>>>>>>
>>>>>>>>> Hello All,
>>>>>>>>>
>>>>>>>>> Does WrapITK currently compile on Windows? If so what type
>>>>>>>>> of    compiler would work with it?
>>>>>>>>>
>>>>>>>>> Or, if I need the cutting edge versions of WrapITK, should I
>>>>>>>>> just   switch over to using Linux?
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>> My last try to build it on windows was not successful - that's
>>>>>>>> why  the  new wrapitk is still not released.
>>>>>>>> WrapITK builds without any problem on mac os with xcode, which
>>>>>>>> use  the  same kind of path that microsoft compilers, so there
>>>>>>>> shouldn't  be much  to fix.
>>>>>>>> I would appreciate the help of someone used to using
>>>>>>>> microsoft    compilers to help to debug the few remaining
>>>>>>>> problem.
>>>>>>>> Would you be ok to take this task?
>>>>>>>> Once the problems identified, I would be happy to work on a  
>>>>>>>> fix!
>>>>>>>> The other option is to switch to another environment - it is
>>>>>>>> tested  successfully on linux, mac and opensolaris.
>>>>>>>> Regards,
>>>>>>>> Gaëtan
>>>>>>>>
>> ------------------------------------------------------------------------
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>>
>> -- 
>> 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
>>
>>

-- 
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

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