[pymvpa] smvc_wrap.cpp error?

[Yaroslav Halchenko]

Hi Koji,

I hope it is ok if I replied to the list since it might be of interest
to other users of the proprietary operating system in question.

my google supplement of the brain was even more useful today -- I have
managed to dig into the memories of Michael without asking him ;)

this issue is of the same origin -- outdated swig
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pynifti/2010q1/000127.html
but now for pynifti -- so you would need to rebuild it as well with
freshier smvc_wrap.cpp  -- find both generated .py and .c attached
(compressed to get posted)

Alternatively (and actually somewhat recommended) -- you could simply
use nibabel as the interface to nifti files from pymvpa:
https://github.com/nipy/nibabel/

if nibabel is available (pure python so not much of building needed --
just point PYTHONPATH to it or install system-wide), it should
take precedence of pynifti in the version of pymvpa you are using.

P.S. what was exactly the problem with posting to the list? are you
     subscribed with jimura at austin.utexas.edu email (or whichever you
     used to post)

Cheers,
Yarik

On Thu, 03 Mar 2011, Koji Jimura wrote:

> Dear Yaroslav,

> I repeatedly failed to post a message to Pkg-ExpPsy-PyMVPA list
> and please allow me to directly inquire you.

> I come across trouble probably with smvc_wrap.cpp

> I am running on python 2.7.1 (built by gcc445 on 64-bit
> Linux). I had to update smvc_wrap.cpp to v1.3.40,
> given a compile error with libsvm as Russ asked you.
> http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2010q2/001164.html

> But I am then having the following error
> ----
>  File "<stdin>", line 6, in <module>
>  File "/corral/utexas/poldracklab/software_lonestar/mvpa/lib/python/mvpa/datasets/mri.py",
> line 233, in fmri_dataset
>  imgdata, imghdr = _load_anyimg(samples, ensure=True, enforce_dim=4)
>  File "/corral/utexas/poldracklab/software_lonestar/mvpa/lib/python/mvpa/datasets/mri.py",
> line 380, in _load_anyimg
>  data = _img2data(src)
>  File "/corral/utexas/poldracklab/software_lonestar/mvpa/lib/python/mvpa/datasets/mri.py",
> line 121, in _img2data
>  return _get_txyz_shaped(data.T), img.header
>  File "/corral/utexas/poldracklab/software_lonestar/mvpa/lib/python/nifti/format.py",
> line 274, in asDict
>  ret = nhdr2dict(nhdr, extensions=self.extensions)
>  File "/corral/utexas/poldracklab/software_lonestar/mvpa/lib/python/nifti/utils.py",
> line 254, in nhdr2dict
>  h['xyz_unit'] = ncl.xyzt2space(nhdr.xyzt_units)
> TypeError: in method 'xyzt2space', argument 1 of type 'char'
> ---
> which should have been resolved by the new svmc_wrap.cpp.
> http://lists.alioth.debian.org/pipermail/pkg-exppsy-pynifti/2010q1/000127.html

> Can you tell any critical installation procedure that I might have missed?
> I am working with pymvpa 0.5.0 dev version (72b8f6c).

> Any suggestion would be greatly appreciated.

> Best wishes,
> Koji

-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        
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