[Insight-users] python prototyping advice

Thu Aug 18 19:25:36 EDT 2005

Hi,
This looks very interesting. However a stumbling block at the moment
appears to be the compilation of ITK with numarray support enabled -
my copy from cvs appears broken.

Any hints on getting it working?
Building object file wrap_itkPyBufferPython.o...
In file included from
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:105,
                 from
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/wrap_itkPyBuffer.cxx:17,
                 from
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:931:
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer()':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: there are no arguments to `import_libnumarray' that depend on a
template parameter, so a declaration of `import_libnumarray' must be
available
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: (if you use `-fpermissive', G++ will accept your code, but
allowing the use of an undeclared name is deprecated)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<unsigned char, 3u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<unsigned char,
3u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:2388:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: (Each undeclared identifier is reported only once for each
function it appears in.)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<short unsigned int, 3u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<short unsigned
int, 3u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:2531:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<unsigned char, 2u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<unsigned char,
2u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:2674:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<short unsigned int, 2u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<short unsigned
int, 2u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:2817:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<float, 2u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<float, 2u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:4150:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:
In constructor `itk::PyBuffer<TImage>::PyBuffer() [with TImage =
itk::Image<float, 3u>]':
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.h:57:
  instantiated from `static itk::SmartPointer<itk::PyBuffer<TImage> >
itk::PyBuffer<TImage>::New() [with TImage = itk::Image<float, 3u>]'
/scratch/richardb/Build/WebCVS/ITKBuild/Wrapping/CSwig/CommonA/wrap_itkPyBufferPython.cxx:6673:
  instantiated from here
/scratch/richardb/Build/WebCVS/Insight/Wrapping/CSwig/CommonA/itkPyBuffer.txx:32:
error: `import_libnumarray' undeclared (first use this function)
make[5]: *** [wrap_itkPyBufferPython.o] Error 1
make[4]: *** [default_target] Error 2
make[3]: *** [default_target_CommonA] Error 2
make[2]: *** [default_target] Error 2
make[1]: *** [default_target_Wrapping_CSwig] Error 2
make: *** [default_target] Error 2
On 8/18/05, Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
> On Wed, 17 Aug 2005 20:46:10 +0200, Einstein, Daniel R
> <daniel.einstein at pnl.gov> wrote:
> 
> > Gaetan,
> >
> > I am very much interested in prototyping with python as well. I have a
> > little experience with ITK now, and have worked somewhat with the
> > InsightToolkit module (unfortunately this is something I must do in my
> > spare time). I find the wrapping uneven. I was able to do it on one of
> > my machines but the other is being a bit more difficult.
> >
> > Anyway, could you clarify the comment you made to Richard about ipython?
> > What exactly does the ipython patch allow you to do?
> 
> Using dir() function on an ITK object to get the list of attributes return
> a list with attributes names and a non string object. This non string
> object was breaking completion of attributes in ipython... itk was
> impossible to use completion on ITK objects.
> The patch allow to use completion on ITK objects, which is very useful
> while prototyping with ITK because ITK names are very long.
> 
> Another great feature of ipython is the -qthread (or -wthread and
> -gthread) command line option. This option allows to use Qt gui without
> freezing the interperter. With that option, I have developed a small
> viewer with Qt and VTK which let me see in 3D the 3D images I have
> produced... really useful too for prototyping
> 
> >
> > Also, in terms of your public directory, I see all of the classes that
> > you have wrapped. But these won't these need to be re-wrapped on our
> > local machines? Or am I missing something?
> 
> There is only sources in public repository, you have to build binaries for
> your own system, but that build is very simple: you just need to install
> cableswig and to activate ITK_CSWIG_PYTHON in cmake
> 
> All comments about wrappers are very welcome :-)
> 
> Regards,
> 
> Gaetan
> 
> >
> > Thank you for your help
> >
> > Best Regards,
> > Dan
> >
> >
> > Daniel R Einstein, PhD
> > Biological Monitoring and Modeling
> > Pacific Northwest National Laboratory
> > P.O. Box 999; MSIN P7-59
> > Richland, WA 99352
> > Tel: 509/ 376-2924
> > Fax: 509/376-9064
> > daniel.einstein at pnl.gov
> >
> >
> > -----Original Message-----
> > From: insight-users-bounces+daniel.einstein=pnl.gov at itk.org
> > [mailto:insight-users-bounces+daniel.einstein=pnl.gov at itk.org] On Behalf
> > Of Gaetan Lehmann
> > Sent: Tuesday, August 16, 2005 11:58 PM
> > To: Richard.Beare at ieee.org
> > Cc: insight-users at itk.org
> > Subject: Re: [Insight-users] python prototyping advice
> >
> >
> > Hi Richard,
> >
> > I'm glad to see another ITK user who wants to do prototyping with python.
> > I'm not the only one ! ;-) Sadely prototyping with python is not a
> > priority for ITK developers, and there is lot of things which make
> > prototyping with python difficult (the small number of wrapped class to
> > begin).
> >
> > You may be interested in the work I have already done on wrapper. ITK is
> > a huge library, and wrapping all classes with a large set of types would
> > produce too large executables. To increase the number of wrapped
> > classes, I decided to wrap only unsigned short and float type, in 2 and
> > 3 dimensions (US2, US3, F2, F3). This way, I have wrapped lots more
> > filters with only a small increase of executables size.
> > This work is kept in sync with ITK CVS repository and is available in a
> > darcs repository at http://voxel.jouy.inra.fr/darcs/itk-mima2/
> > It also include some work done on mathematical morphology filters, and a
> > module for python (the module is named itk) which introduce facilities
> > for prototyping, especially with ipython.
> > If you are a ipython user, I advise you to checkout a fresh svn version
> > of
> > ipython: it contains a patch which allow completion to work with ITK.
> > That make prototyping really easier. If you're not a ipython user, you
> > should try it quickly ;-)
> >
> > If you're interested in improving ITK, you should consider joining the
> > developers mailing list which is the right list to talk about that. On
> > this list, we are also talking with Benoit Regrain of what can be done
> > to make ITK more usable with python and to improve wrap process. You are
> > welcome in the discussion if you're interested in :-)
> >
> > Gaetan
> >
> > On Wed, 17 Aug 2005 08:01:07 +0200, Richard Beare
> > <richard.beare at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> I'm trying to stick with prototyping using python for simpler trials.
> >> At the moment this includes mimicing a few old matlab scripts. This
> >> brings me to my two questions.
> >>
> >> Every time I've attempted to do something in python I've been slowed
> >> down by missing wrappers. Some of these are easy enough to add (I hope
> >> this is true - I'm waiting for the build to finish at the moment).
> >> Assuming I've done this successfully, is there any way I can commit
> >> these additions back to the repository? What is the protocol for this
> >> type of thing?
> >>
> >> The other question relates to certain types of operations that are
> >> often done in interactive interpreter environments like matlab or R.
> >> The particular matlab script I'm porting has a step where every pixel
> >> in a mask is weighted by the distance to the mask center of gravity.
> >>
> >> The approach in matlab is to generate coordinate images and operate on
> >> them e.g
> >>
> >> dist = sqrt((xcoords - xcog).^2 + (ycoords - ycog).^2);
> >>
> >> result = mask * dist
> >>
> >> How do I do something equivalent in python? Is this where the numarray
> >> stuff comes in?
> >>
> >> Thanks
> >> _______________________________________________
> >> Insight-users mailing list
> >> Insight-users at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-users
> >
> >
> >
> > --
> > Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr>
> > Tel: +33 1 34 65 29 66
> > Biologie du Développement et de la Reproduction INRA de Jouy-en-Josas
> > (France)
> > Web: http://voxel.jouy.inra.fr
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> 
> 
> 
> --
> Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr>
> Tel: +33 1 34 65 29 66
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> Web: http://voxel.jouy.inra.fr
>