[pymvpa] LinearCSVMC() error with python 2.7 but not 2.6?
Edmund Chong
edmund.w.chong at gmail.com
Fri Sep 7 17:01:49 UTC 2012
Hi Yarik,
For both systems:
issubclass(LinearCSVMC,libsvm.SVM)
is True,
and issubclass(LinearCSVMC,sg.SVM)
is False.
another thing you could if that was under ipython,
> enable debug mode by entering
>
> pdb
>
> so it would jump into pdb whenever failure occurs... and then share output
> of
>
> print dist_samples.shape
> print shape
>
ipdb> print dist_samples.shape
(0, 1)
ipdb> print shape
(0,)
could you share complete snippet of your code and the dataset (check --
> may be it fails also with a small portion of it, e.g. fds1[:, :10]).
> you can easily share it by saving via h5save
>
This is where it gets a little strange: so I saved my fds1 to hdf5 format.
When I loaded it back, the classifier actually works (on the non-working
system)! So in my script I added a few lines that saved and then loaded the
dataset just before applying the classifier -- I obtain exactly the same
results as on the working system. So I guess it would not make sense to
share the hdf5 file with you -- would you like the .nii instead? And here's
the code i used for the classifier:
repeater = Repeater(count=200)
partitioner=ChainNode([NFoldPartitioner(cvtype=1),
Balancer(attr='targets',
count=1, # for real data > 1
limit='partitions',
apply_selection=True
)],
space='partitions')
clf = LinearCSVMC() #choice of classifier
permutator = AttributePermutator('targets', limit={'partitions': 1},
count=1)
null_cv = CrossValidation(
clf,
ChainNode([partitioner, permutator], space=partitioner.get_space()),
errorfx=mean_mismatch_error)
distr_est = MCNullDist(repeater, tail='left', measure=null_cv,
enable_ca=['dist_samples'])
cvte = CrossValidation(clf, partitioner,
errorfx=mean_mismatch_error,
null_dist=distr_est,
enable_ca=['stats'])
also what is the output of
>
> mvpa2.wtf() # where fails
>
>
for the working system:
Current date: 2012-09-07 12:59
PyMVPA:
Version: 2.1.0
Hash: 828f4b4bea2488f8c7e3f6c2446a445d77325338
Path: /usr/lib/pymodules/python2.6/mvpa2/__init__.pyc
Version control (GIT):
GIT information could not be obtained due
"/usr/lib/pymodules/python2.6/mvpa2/.. is not under GIT"
SYSTEM:
OS: posix Linux 2.6.32-25-generic #45-Ubuntu SMP Sat Oct 16
19:52:42 UTC 2010
Distribution: Ubuntu/10.04/lucid
EXTERNALS:
Present: atlas_fsl, cPickle, ctypes, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, liblapack.so,
libsvm, libsvm verbosity control, lxml, matplotlib, nibabel, nose, numpy,
pylab, pylab plottable, pywt, pywt wp reconstruct, reportlab, running
ipython env, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun,
shogun.krr, shogun.mpd, shogun.svmocas, skl, weave
Absent: atlas_pymvpa, cran-energy, elasticnet, glmnet, good
scipy.stats.rdist, hcluster, lars, mass, mdp, mdp ge 2.4, nipy,
nipy.neurospin, openopt, pprocess, pywt wp reconstruct fixed, rpy2,
shogun.lightsvm, shogun.svrlight, statsmodels
Versions of critical externals:
shogun:full : 0.9.1_r4481_2009-11-16_10:14_
shogun:rev : 4481
reportlab : 2.4
shogun : 0.9.1
nibabel : 1.2.2
matplotlib : 0.99.1.1
scipy : 0.7.0
ipython : 0.10
skl : 0.11
numpy : 1.3.0
ctypes : 1.1.0
matplotlib : 0.99.1.1
lxml : 2.2.4
nifti : failed to query due to "nifti is not a known dependency
key."
numpy : 1.3.0
pywt : 0.1.7
shogun : v0.9.1_r4481_2009-11-16_10:14_
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PyMVPA Runtime Configuration:
[externals]
have griddata = yes
have pprocess = no
have ipython = yes
have cran-energy = no
have good scipy.stats.rdist = no
have pylab plottable = yes
have pywt wp reconstruct = yes
have ctypes = yes
have lxml = yes
have running ipython env = yes
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 = yes
have h5py = yes
have liblapack.so = yes
have weave = yes
have atlas_fsl = yes
have mdp = no
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 skl = yes
have mdp ge 2.4 = no
have shogun.svrlight = no
have shogun = yes
have shogun.svmocas = yes
have nipy = no
have glmnet = no
have nose = yes
have mass = no
have lars = no
have libsvm verbosity control = yes
have atlas_pymvpa = no
have shogun.krr = yes
have cpickle = yes
have numpy = yes
have pylab = yes
have rpy2 = no
have shogun.lightsvm = no
have pywt = yes
have statsmodels = no
have gzip = yes
have nipy.neurospin = no
[general]
verbose = 1
Process Information:
Name: ipython
State: R (running)
Tgid: 3040
Pid: 3040
PPid: 1691
TracerPid: 0
Uid: 1001 1001 1001 1001
Gid: 1001 1001 1001 1001
FDSize: 256
Groups: 4 20 21 24 26 29 30 44 46 103 104 112 115 120 1001
VmPeak: 697704 kB
VmSize: 614156 kB
VmLck: 0 kB
VmHWM: 235484 kB
VmRSS: 131248 kB
VmData: 118084 kB
VmStk: 244 kB
VmExe: 2160 kB
VmLib: 84924 kB
VmPTE: 1156 kB
Threads: 2
SigQ: 0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: fff
Cpus_allowed_list: 0-11
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 801
nonvoluntary_ctxt_switches: 2002
******************************************
for the non-working system:
Current date: 2012-09-07 13:00
PyMVPA:
Version: 2.1.0
Hash: 828f4b4bea2488f8c7e3f6c2446a445d77325338
Path: /usr/lib/pymodules/python2.7/mvpa2/__init__.py
Version control (GIT):
GIT information could not be obtained due
"/usr/lib/pymodules/python2.7/mvpa2/.. is not under GIT"
SYSTEM:
OS: posix Linux 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27
17:03:23 UTC 2012
Distribution: Ubuntu/12.04/precise
EXTERNALS:
Present: cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, liblapack.so,
libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp ge 2.4,
nibabel, nose, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct,
reportlab, running ipython env, scipy, sg ge 0.6.4, sg ge 0.6.5,
sg_fixedcachesize, shogun, shogun.krr, shogun.mpd, shogun.svmocas, skl,
weave
Absent: atlas_fsl, atlas_pymvpa, cran-energy, elasticnet, glmnet,
hcluster, lars, mass, nipy, nipy.neurospin, openopt, pprocess, pywt wp
reconstruct fixed, rpy2, shogun.lightsvm, shogun.svrlight, statsmodels
Versions of critical externals:
shogun:full : 1.1.0_02ce3cd_2011-12-12_08:17_
shogun:rev : 2941901
reportlab : 2.5
shogun : 1.1.0
nibabel : 1.2.2
matplotlib : 1.1.1rc
scipy : 0.9.0
ipython : 0.12.1
skl : 0.11
mdp : 3.3
numpy : 1.6.1
ctypes : 1.1.0
matplotlib : 1.1.1rc
lxml : 2.3.2
nifti : failed to query due to "nifti is not a known dependency
key."
numpy : 1.6.1
pywt : 0.2.0
shogun : v1.1.0_02ce3cd_2011-12-12_08:17_
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH :
":/home/shim/.python27_compiled:/usr/lib/python2.7/plat-linux2:/usr/bin:/usr/lib/python2.7/dist-packages/ubuntuone-couch:/data/projects/09dec11er:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/PIL:/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/lib/python2.7/dist-packages/ubuntuone-client:/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/lib/python2.7/dist-packages/ubuntuone-control-panel:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/gst-0.10"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = yes
have numpy = yes
have scipy = yes
have matplotlib = yes
have h5py = yes
have reportlab = yes
have weave = yes
have good scipy.stats.rdist = yes
have good scipy.stats.rv_discrete.ppf = yes
have pylab = yes
have lars = no
have elasticnet = no
have glmnet = no
have skl = yes
have ctypes = yes
have libsvm = yes
have shogun = yes
have sg ge 0.6.5 = yes
have shogun.mpd = yes
have shogun.lightsvm = no
have shogun.svrlight = no
have shogun.krr = yes
have shogun.svmocas = yes
have sg_fixedcachesize = yes
have openopt = no
have nibabel = yes
have mdp = yes
have mdp ge 2.4 = yes
have statsmodels = no
have pywt = yes
have cpickle = yes
have gzip = yes
have cran-energy = no
have griddata = yes
have nipy.neurospin = no
have lxml = yes
have atlas_fsl = no
have atlas_pymvpa = no
have hcluster = no
have ipython = yes
have liblapack.so = yes
have libsvm verbosity control = yes
have mass = no
have nipy = no
have nose = yes
have pprocess = no
have pylab plottable = yes
have pywt wp reconstruct = yes
have pywt wp reconstruct fixed = no
have rpy2 = no
have sg ge 0.6.4 = yes
Process Information:
Name: python
State: R (running)
Tgid: 3346
Pid: 3346
PPid: 2453
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 4 24 27 30 46 109 124 1000
VmPeak: 875080 kB
VmSize: 793920 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 249916 kB
VmRSS: 145868 kB
VmData: 274428 kB
VmStk: 264 kB
VmExe: 2500 kB
VmLib: 85992 kB
VmPTE: 1240 kB
VmSwap: 0 kB
Threads: 3
SigQ: 0/127910
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 627
nonvoluntary_ctxt_switches: 1414
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