[pymvpa] IndexError from gnbsearchlight analysis

[Zhen Zonglei]

Wow, this is my version information.


Current date:   2011-07-26 10:30
PyMVPA:
 Version:       0.6.0~rc2
 Hash:          abd29b48d0d585cc8ba91d800a6e884d586c4027
 Path:
/usr/local/neurosoft/lib/python2.6/site-packages/mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/usr/local/neurosoft/lib/python2.6/site-packages/mvpa/.. is not under GIT"
SYSTEM:
 OS:            posix Linux 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT
2009
 Distribution:  redhat/5.4/Final
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, libsvm, libsvm verbosity
control, matplotlib, nibabel, nose, numpy, pylab, pylab plottable, running
ipython env, scipy, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, hcluster, lars,
lxml, mass, mdp, mdp ge 2.4, nipy, openopt, pprocess, pywt, pywt wp
reconstruct, pywt wp reconstruct fixed, reportlab, rpy2, 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     : 0.10.1
  scipy       : 0.8.0
  numpy       : 1.5.1
  matplotlib  : 1.0.1
  ctypes      : 1.1.0
  matplotlib  : 1.0.1
  nifti       : failed to query due to "nifti is not a known dependency
key."
  numpy       : 1.5.1
 Matplotlib backend: TkAgg

Zonglei Zhen

On Tue, Jul 26, 2011 at 10:24 AM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> please share the output of mvpa.wtf() which would answer
> "version" question
>
> because with rc4 (although seems to be reported as rc3 :-/ ) and current
> master everything seems to be ok on my box:
>
> In [1]: from mvpa.suite import *
> h5load/usr/lib/pymodules/python2.6/nose/plugins/manager.py:405:
> UserWarning: Module paste was already imported from None, but
> /usr/lib/python2.6/dist-packages is being added to sys.path
>  import pkg_resources
>
> In [2]: dataset = h5load('att.gzipped.hdf5')
>
> In [3]: print dataset.summary()
> Dataset: 72x821 at float32, <sa: chunks,targets,time_coords,time_indices>,
> <fa: voxel_indices>, <a: imghdr,mapper,voxel_dim,voxel_eldim>
>  stats: mean=-5.2752e-08 std=0.999996 var=0.999993 min=-3.02555
> max=3.05246
>
> Counts of targets in each chunk:
>  chunks\targets attf attm
>                  ---  ---
>       0.0         6    6
>       1.0         6    6
>       2.0         6    6
>       3.0         6    6
>       4.0         6    6
>       5.0         6    6
>
> Summary for targets across chunks
>  targets mean std min max #chunks
>   attf     6   0   6   6     6
>   attm     6   0   6   6     6
>
> Summary for chunks across targets
>  chunks mean std min max #targets
>    0      6   0   6   6      2
>    1      6   0   6   6      2
>    2      6   0   6   6      2
>    3      6   0   6   6      2
>    4      6   0   6   6      2
>    5      6   0   6   6      2
> Sequence statistics for 72 entries from set ['attf', 'attm']
> Counter-balance table for orders up to 2:
> Targets/Order O1     |  O2     |
>    attf:     30  6  |  24 12  |
>    attm:      5 30  |  10 24  |
> Correlations: min=-1 max=1 mean=-0.014 sum(abs)=35
>
> In [4]: gnbsl =
> sphere_gnbsearchlight(GNB(),NFoldPartitioner(),radius=3,postproc=mean_sample())
>
> In [5]: slmap = gnbsl(dataset)
>
> In [6]: print slmap.summary()
> Dataset: 1x821 at float64, <a: mapper> stats: mean=0.473186 std=0.0686585
> var=0.00471399 min=0.319444 max=0.652778
>
>
> In [7]: print mvpa.__version__
> 0.6.0~rc3
>
> In [8]: print mvpa.wtf()
> Current date:   2011-07-25 22:19
> PyMVPA:
>  Version:       0.6.0~rc3
>  Hash:          fd0f2809300cc25e81ee21a3a876d00d524402c1
>  Path:          /usr/lib/pymodules/python2.6/mvpa/__init__.pyc
>  Version control (GIT):
>  GIT information could not be obtained due
> "/usr/lib/pymodules/python2.6/mvpa/.. is not under GIT"
> SYSTEM:
>  OS:            posix Linux 2.6.38-2-amd64 #1 SMP Thu Apr 7 04:28:07 UTC
> 2011
>  Distribution:  debian/wheezy/sid
> EXTERNALS:
>  Present:       atlas_fsl, atlas_pymvpa, cPickle
> ....
>
> On Mon, 25 Jul 2011, Yaroslav Halchenko wrote:
>
> > ah -- that is why mailman refused first to post -- kind you shared the
> > 1MB dataset  with the list ;)  ok -- will have a look
>
> > On Tue, 26 Jul 2011, Zhen Zonglei wrote:
>
> > >    Thanks very much, Yarik.
>
> > >    The fellowing the summary of dataset. For hdf5 file, please see
> > >    attachments.
> --
> =------------------------------------------------------------------=
> Keep in touch                                     www.onerussian.com
> Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic
>
> _______________________________________________
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> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
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>
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