[pymvpa] errors when running sphere_gnbsearchlight+balancer
Su Mei Lee
sumeilee at gmail.com
Sat Nov 1 16:57:53 UTC 2014
Hi Yaroslav,
Here's the complete output of the original code, error messages, and output
of mvpa2.wtf(). Thanks!
Su Mei
>>> from mvpa2.tutorial_suite import *
>>> ds=get_raw_haxby2001_data(roi='vt')
>>> part=ChainNode([NFoldPartitioner(),
Balancer(limit='partitions',apply_selection=True)], space='partitions')
>>> sl=sphere_gnbsearchlight(GNB(),part,postproc=mean_sample())
>>> map=sl(ds)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/home/user/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py",
line 259, in __call__
return super(Learner, self).__call__(ds)
File
"/home/user/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", line
121, in __call__
result = self._call(ds)
File
"/home/user/anaconda/lib/python2.7/site-packages/mvpa2/measures/searchlight.py",
line 143, in _call
results = self._sl_call(dataset, roi_ids, nproc)
File
"/home/user/anaconda/lib/python2.7/site-packages/mvpa2/measures/adhocsearchlightbase.py",
line 353, in _sl_call
if not (np.all(p.sa[targets_sa_name].value == labels)):
ValueError: shape mismatch: objects cannot be broadcast to a single shape
>>> print mvpa2.wtf()
Current date: 2014-11-01 12:51
PyMVPA:
Version: 2.3.1
Hash: $Format:%H$
Path:
/home/user/anaconda/lib/python2.7/site-packages/mvpa2/__init__.pyc
Version control (GIT):
GIT information could not be obtained due
"/home/user/anaconda/lib/python2.7/site-packages/mvpa2/.. is not under GIT"
SYSTEM:
OS: posix Linux 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25
19:59:55 UTC 2014
Distribution: centos/6.5/Final
EXTERNALS:
Present: cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_continuous._reduce_func(floc,fscale), good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, hdf5, ipython,
liblapack.so, libsvm, libsvm verbosity control, lxml, matplotlib, mock,
nibabel, nose, numpy, numpy_correct_unique, pylab, pylab plottable, scipy,
skl, statsmodels, weave
Absent: atlas_fsl, atlas_pymvpa, cran-energy, elasticnet, glmnet,
hcluster, lars, mass, mdp, mdp ge 2.4, nipy, nipy.neurospin, numpydoc,
openopt, pprocess, 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
Versions of critical externals:
ctypes : 1.1.0
h5py : 2.3.1
hdf5 : 1.8.13
ipython : 2.2.0
lxml : 3.4.0
matplotlib : 1.4.0
mock : 1.0.1
nibabel : 1.3.0
numpy : 1.9.0
scipy : 0.14.0
skl : 0.15.2
Matplotlib backend: Qt4Agg
RUNTIME:
PyMVPA Environment Variables:
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = no
have numpy = yes
have scipy = yes
have matplotlib = yes
have h5py = yes
have reportlab = no
have weave = yes
have good scipy.stats.rdist = yes
have good scipy.stats.rv_discrete.ppf = yes
have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes
have pylab = yes
have lars = no
have elasticnet = no
have glmnet = no
have skl = yes
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 nipy = no
have statsmodels = yes
have pywt = no
have cpickle = yes
have gzip = yes
have cran-energy = no
have griddata = yes
have nipy.neurospin = no
have lxml = yes
have pprocess = no
have atlas_fsl = no
have atlas_pymvpa = no
have hcluster = no
have hdf5 = yes
have ipython = yes
have liblapack.so = yes
have libsvm verbosity control = yes
have mass = no
have mock = yes
have nose = yes
have numpy_correct_unique = yes
have numpydoc = no
have pylab plottable = yes
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
Process Information:
Name: python
State: R (running)
Tgid: 9541
Pid: 9541
PPid: 9335
TracerPid: 0
Uid: 668400015 668400015 668400015 668400015
Gid: 668400015 668400015 668400015 668400015
Utrace: 0
FDSize: 256
Groups: 668400015 668400024 668400025 668400027 668400028
VmPeak: 1813844 kB
VmSize: 901476 kB
VmLck: 0 kB
VmHWM: 1081372 kB
VmRSS: 147476 kB
VmData: 205908 kB
VmStk: 92 kB
VmExe: 4 kB
VmLib: 129200 kB
VmPTE: 1464 kB
VmSwap: 0 kB
Threads: 9
SigQ: 0/1678307
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001004
SigCgt: 0000000180010002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ffff,ffffffff
Cpus_allowed_list: 0-47
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
Mems_allowed_list: 0-1
voluntary_ctxt_switches: 307
nonvoluntary_ctxt_switches: 69
On Thu, Oct 30, 2014 at 6:34 PM, Yaroslav Halchenko <yoh at onerussian.com>
wrote:
> Could you post output of
>
> print mvpa2.wtf()
>
> Embedded in your script to make sure you are using those versions
>
> On October 30, 2014 6:20:47 PM EDT, Su Mei Lee <sumeilee at gmail.com> wrote:
> >Yaroslav Halchenko <debian at ...> writes:
> >
> >>
> >>
> >> On Sun, 04 Aug 2013, Tren Huang wrote:
> >>
> >> > Good point Yaroslav! The snippet works with numpy 1.7.0 but not
> >1.2.1.
> >>
> >> wow -- 1.2.1, that is antique! even merely supported lucid has
> >1.3.0.
> >> so indeed -- upgrade of numpy is very advised!
> >>
> >
> >
> >Hi,
> >
> >I ran the same code from the top of this post and got the same error
> >when
> >using ChainNode with Balancer. I updated to Numpy 1.9.0, Python 2.7.8,
> >PyMVPA 2.3.1 but am still getting the error so I'm not sure why the
> >update
> >didn't work for me. Help?
> >
> >Thanks,
> >Su Mei
> >
> >
> >
> >_______________________________________________
> >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
>
> --
> Sent from a phone which beats iPhone.
>
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