[pymvpa] Problem About running mvpa2 tutorial

[Ceyhun Çakar]

Hello Yaroslav,

I think I've understood and solved the problem. Because issue is about
Turkish Localization of Linux, only Turkish user can see this problem.
Nevertheless I am sending my solution.

I Turkish capital of i is different than English as below.
Capital of  'i' is 'İ' in Turkish (Unicode Number 0x130)
Lower case of 'I' is 'ı' in Turkish (Unicode Number 0x131)

So, 'aligned' does not match with 'ALIGNED' in Turkish. But code
assumes this in mvpa2/clfs/libsmlrc/ctypes_helper.py

When I use below patch to this file, problem solved.

*** ctypes_helper_original.py	2012-10-15 21:39:35.807810206 +0300
--- ctypes_helper.py	2012-10-15 21:28:24.496481350 +0300
***************
*** 12,21 ****
  import ctypes as C

  # define an array type to help with wrapping
! c_darray = np.ctypeslib.ndpointer(dtype=np.float64,
flags='aligned,contiguous')
! c_larray = np.ctypeslib.ndpointer(dtype=np.int64, flags='aligned,contiguous')
! c_farray = np.ctypeslib.ndpointer(dtype=np.float32,
flags='aligned,contiguous')
! c_iarray = np.ctypeslib.ndpointer(dtype=np.int32, flags='aligned,contiguous')

  def extend_args(*args):
      """Turn ndarray arguments into dims and arrays."""
--- 12,21 ----
  import ctypes as C

  # define an array type to help with wrapping
! c_darray = np.ctypeslib.ndpointer(dtype=np.float64,
flags='ALIGNED,CONTIGUOUS')
! c_larray = np.ctypeslib.ndpointer(dtype=np.int64, flags='ALIGNED,CONTIGUOUS')
! c_farray = np.ctypeslib.ndpointer(dtype=np.float32,
flags='ALIGNED,CONTIGUOUS')
! c_iarray = np.ctypeslib.ndpointer(dtype=np.int32, flags='ALIGNED,CONTIGUOUS')

  def extend_args(*args):
      """Turn ndarray arguments into dims and arrays."""

Thank you for your immediate help.
Ceyhun Çakar


On Mon, Oct 15, 2012 at 5:31 AM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
>
> On Sun, 14 Oct 2012, Ceyhun Çakar wrote:
>> PyMVPA:
>>  Version:       2.0.0
>
> before we explore much more -- could you please upgrade to 2.2.0
> packages for which we provide from NeuroDebian http://neuro.debian.net/
>
>>   PYTHONPATH          :
>> ":/home/ceyhun:/usr/lib/python2.7/plat-linux2:/usr/local/lib/python2.7/dist-packages/PyBrain-0.3.1-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-control-panel:/usr/lib/python2.7/dist-packages/ubuntuone-couch:/usr/local/lib/python2.7/dist-packages/Orange/orng:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode:/usr/local/lib/python2.7/dist-packages/setproctitle-1.1.6-py2.7-linux-x86_64.egg:/usr/lib/python2.7/dist-packages/PIL:/usr/local/lib/python2.7/dist-packages/FuncDesigner-0.42-py2.7.egg:/usr/local/lib/python2.7/dist-packages/openopt-0.42-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-dynload:/usr/lib/python2.7/dist-packages/ubuntu-sso-client:/usr/local/lib/python2.7/dist-packages/Kivy-1.3.0-py2.7-linux-x86_64.egg:/usr/lib/python2.7/dist-packages/ubuntuone-client:/usr/local/lib/python2.7/dist-packages/DerApproximator-0.42-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-installer:/usr/lib/python2.7/lib-old:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/local/lib/python2.7/dist-packages/SpaceFuncs-0.42-py2.7.egg:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/gst-0.10"
>
> although unlikely,  but still possible -- the number of modules of
> /usr/local gives a feeling that problem might be  coming from  there...
>
> what if you run
>
> grep -R ALiGNED /usr 2>/dev/null
>
> and then if nothing appears
>
> grep -R ALiGNED /home/ceyhun 2>/dev/null
>
> may be we could spot a bad cow ;)
>
> --
> 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
>
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa



-- 
Ceyhun Çakar
cakar.ceyhun at gmail.com