[pymvpa] Problem with tutorial data

[Andrej Schoeke]

Hi there,

I installed PyMVPA from github. I try to run through the tutorial, but
it seems like I am missing the data:

Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on
darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from mvpa2.tutorial_suite import *
>>> ds = get_haxby2001_data()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/mvpa2/tutorial_suite.py", line
42, in get_haxby2001_data
    ds = get_raw_haxby2001_data(roi=roi)
  File "/Library/Python/2.7/site-packages/mvpa2/tutorial_suite.py", line
37, in get_raw_haxby2001_data
    return load_datadb_tutorial_data(path=path, roi=roi)
  File
"/Library/Python/2.7/site-packages/mvpa2/misc/data_generators.py", line
376, in load_datadb_tutorial_data
    attr = SampleAttributes(os.path.join(path, 'attributes.txt'))
  File "/Library/Python/2.7/site-packages/mvpa2/misc/io/base.py", line
408, in __init__
    sep=None, dtype=dtypes)
  File "/Library/Python/2.7/site-packages/mvpa2/misc/io/base.py", line
118, in __init__
    dtype=dtype, skiplines=skiplines)
  File "/Library/Python/2.7/site-packages/mvpa2/misc/io/base.py", line
214, in _from_file
    file_ = open(filename, 'r')
IOError: [Errno 2] No such file or directory: './data/attributes.txt'


>>> wtf()
Current date:   2012-04-05 13:45
PyMVPA:
 Version:       2.0.0
 Hash:          $Format:%H$
 Path:          /Library/Python/2.7/site-packages/mvpa2/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/Library/Python/2.7/site-packages/mvpa2/.. is not under GIT"
SYSTEM:
 OS:            posix Darwin 11.3.0 Darwin Kernel Version 11.3.0: Thu
Jan 12 18:47:41 PST 2012; root:xnu-1699.24.23~1/RELEASE_X86_64
 Distribution:   10.7.3/x86_64
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, gzip, ipython, libsvm, libsvm verbosity
control, nibabel, numpy, scipy, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, griddata,
h5py, hcluster, lars, lxml, mass, matplotlib, mdp, mdp ge 2.4, nipy,
nipy.neurospin, nose, openopt, pprocess, pylab, pylab plottable, pywt,
pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy2, running
ipython env, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun,
shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svmocas,
shogun.svrlight, skl
 Versions of critical externals:
  ipython     : 0.12
  nibabel     : 1.1.0
  scipy       : 0.11.0.dev-0fbfdbc
  numpy       : 1.5.1
  ctypes      : 1.1.0
  nifti       : failed to query due to "nifti is not a known dependency
key."
  numpy       : 1.5.1
RUNTIME:
 PyMVPA Environment Variables:
   PyMVPA Runtime Configuration:
  [general]
  verbose = 1

  [externals]
  have running ipython env = no
  have numpy = yes
  have scipy = yes
  have matplotlib = no
  have h5py = no
  have reportlab = no
  have weave = yes
  have good scipy.stats.rdist = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have pylab = no
  have lars = no
  have elasticnet = no
  have glmnet = no
  have skl = no
  have ctypes = yes
  have libsvm = yes
  have shogun = no
  have openopt = no
  have nibabel = yes
  have mdp = no
  have mdp ge 2.4 = no
  have pywt = no
  have cpickle = yes
  have gzip = yes
  have nipy.neurospin = no
  have lxml = no
  have atlas_fsl = no
  have atlas_pymvpa = no
  have griddata = no
  have hcluster = no
  have ipython = yes
  have libsvm verbosity control = yes
  have mass = no
  have nipy = no
  have nose = no
  have pprocess = no
  have pylab plottable = no
  have pywt wp reconstruct = no
  have pywt wp reconstruct fixed = no
  have rpy2 = no
  have sg ge 0.6.4 = no
  have sg ge 0.6.5 = no
  have sg_fixedcachesize = no
  have shogun.krr = no
  have shogun.lightsvm = no
  have shogun.mpd = no
  have shogun.svmocas = no
  have shogun.svrlight = no

>>> ^D

➜  data  pwd
/Library/Python/2.7/site-packages/mvpa2/data
➜  data  ls
README                 bold.nii.gz            eep.bin
glm.mat                smpl_attr.txt          v73.mat
attributes.txt         bold_mc.par            example4d.nii.gz
mask.nii.gz            tueb_meg.dat.gz        xavr1010.dat
attributes_literal.txt bv

Any idea what went wrong? I changed in python to the install directory,
but it seems like it tries to access the data with relatives path which
doesn't work very well.

Andrej

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