[pymvpa] installation

Wed Mar 2 12:14:20 UTC 2011

Hi, thanks for the reply. 

i had already typed in import nibabel and it was accepted but when i type  >>>> ds = get_haxby2001_data()
i get RuntimeError: Required external 'nibabel' was not found. so no change from before.

Also when i do the same in ubuntu i always get the same error as shown below

 IOError: [Errno 2] No such file or directory: './data/attributes.txt'

i have also added such directory to the path so it should be able to find it.

>>> sys.path.append("/home/amit/tutorial_data/data")

thanks in advance

Amit

>>> ds = get_haxby2001_data()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/amit/tutorial_data/tutorial_lib.py", line 44, in get_haxby2001_data
    ds = get_raw_haxby2001_data(roi=roi)
  File "/home/amit/tutorial_data/tutorial_lib.py", line 39, in get_raw_haxby2001_data
    return load_datadb_demo_blockfmri(path=path, roi=roi)
  File "mvpa/misc/data_generators.py", line 375, in load_datadb_tutorial_data
    attr = SampleAttributes(os.path.join(path, 'attributes.txt'))
  File "mvpa/misc/io/base.py", line 408, in __init__
    sep=None, dtype=dtypes)
  File "mvpa/misc/io/base.py", line 118, in __init__
    dtype=dtype, skiplines=skiplines)
  File "mvpa/misc/io/base.py", line 214, in _from_file
    file_ = open(filename, 'r')
IOError: [Errno 2] No such file or directory: './data/attributes.txt'

>>> mvpa.wtf()
Current date:   2011-03-01 14:10
PyMVPA:
 Version:       0.6.0~rc1
 Hash:          feda3f526efd71a5ae34f0c1fd3d8f2334d5f412
 Path:          mvpa/__init__.py
 Version control (GIT):
 GIT information could not be obtained due "mvpa/.. is not under GIT"
SYSTEM:
 OS:            posix Linux 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010
 Distribution:  Ubuntu/10.10/maverick
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, gzip, matplotlib, mdp, mdp ge 2.4, nibabel, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct, reportlab, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.mpd, shogun.svmocas
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, h5py, hcluster, lars, libsvm, libsvm verbosity control, lxml, mass, nipy, nose, openopt, pprocess, pywt wp reconstruct fixed, rpy2, running ipython env, shogun.lightsvm, shogun.svrlight, skl, weave
 Versions of critical externals:
  shogun:full : 0.9.3_r4889_2010-05-27_20:52_
  shogun:rev  : 4889
  reportlab   : 2.4
  shogun      : 0.9.3
  matplotlib  : 0.99.3
  scipy       : 0.7.2
  mdp         : 2.6
  numpy       : 1.3.0
  ctypes      : 1.1.0
  matplotlib  : 0.99.3
  nifti       : failed to query due to "nifti is not a known dependency key."
  numpy       : 1.3.0
  pywt        : 0.2.0
  shogun      : v0.9.3_r4889_2010-05-27_20:52_
 Matplotlib backend: TkAgg
RUNTIME:
 PyMVPA Environment Variables:
   PyMVPA Runtime Configuration:
  [externals]
  have griddata = yes
  have pprocess = no
  have good scipy.stats.rdist = yes
  have pylab plottable = yes
  have pywt wp reconstruct = yes
  have h5py = no
  have lxml = no
  have running ipython env = no
  have nibabel = yes
  have sg_fixedcachesize = yes
  have elasticnet = no
  have shogun.mpd = yes
  have matplotlib = yes
  have pywt wp reconstruct fixed = no
  have scipy = yes
  have reportlab = yes
  have openopt = no
  have libsvm = no
  have nose = no
  have weave = no
  have atlas_fsl = no
  have ctypes = yes
  have hcluster = no
  have sg ge 0.6.4 = yes
  have sg ge 0.6.5 = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have libsvm verbosity control = no
  have mdp ge 2.4 = yes
  have shogun.svrlight = no
  have shogun = yes
  have shogun.svmocas = yes
  have nipy = no
  have glmnet = no
  have mass = no
  have lars = no
  have shogun.krr = yes
  have atlas_pymvpa = no
  have cpickle = yes
  have mdp = yes
  have numpy = yes
  have pylab = yes
  have rpy2 = no
  have shogun.lightsvm = no
  have pywt = yes
  have skl = no
  have gzip = yes

> Date: Tue, 1 Mar 2011 13:38:55 -0500
> From: michael.hanke at gmail.com
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Subject: Re: [pymvpa] (no subject)
> 
> Hey,
> 
> On Tue, Mar 01, 2011 at 05:56:43PM +0000, Daniel Agger wrote:
> > 
> > Dear pymvpa helper
> >  
> > Im trying to install pymvpa and i start the tutorial, and i run into
> > this problem.It says nibabel not found,and it requires external
> > nibabel but i have nibabel in my path. so i don't what to do, please
> > help.
> 
> It doesn't look like you have it in the path.
> 
> > >>> ds = get_haxby2001_data()
> 
> Can you do a
> 
> 	import nibabel
> 
> right in front of that line. I guess it doesn't work and nibabel is not
> available.
> 
> Michael
> 
> -- 
> Michael Hanke
> http://mih.voxindeserto.de
> 
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa

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