[pymvpa] zcore issue/error?

[Matthias Ekman]

Hi,

I am using pymvpa 0.4.3 and getting the following issue/error on both
linux and windows machines.

In the case of only two samples in a chunk and using zscore with
"perchunk=True" the zscoring is not working properly for me. Instead of
returning (float) z-values I am getting only integers (either -1 or +1).

This behavior occurs with my own data and also with the sample data
shipped with PyMVPA. So you might be able to reproduce it.

attr = SampleAttributes(os.path.join(pymvpa_dataroot, 'attributes.txt'))
dataset = NiftiDataset(samples=os.path.join(pymvpa_dataroot, 'bold.nii.gz'),
                       labels=attr.labels,
                       chunks=attr.chunks,
                       mask=os.path.join(pymvpa_dataroot, 'mask.nii.gz'))

zscore(dataset, perchunk=True, targetdtype='float32')
dataset.map2Nifti(dataset).save('tmp.nii.gz')

Instead of the original attributes.txt-file I used a faked one with only
two samples in the first chunk.

I am aware of the fact that it might be not "useful" to calculate
chunkwise z-values with only two samples per chunk, but I just wanted to
let you know about this issue.

Best regards,
Matthias

what the f*ck info:

PyMVPA:
 Version:       0.4.3
 Path:
/daten/mekman/3rd/local_pymvpa_installations/043/lib64/python2.5/site-packages/mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/daten/mekman/3rd/local_pymvpa_installations/043/lib64/python2.5/site-packages/mvpa/..
is not under GIT"
SYSTEM:
 OS:            posix Linux 2.6.27.7-134.fc10.x86_64 #1 SMP Mon Dec 1
22:21:35 EST 2008
 Distribution:  redhat/10/Cambridge
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rv_discrete.ppf, gzip,
libsvm, libsvm verbosity control, nifti, nifti ge 0.20090205.1, numpy,
reportlab, scipy, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good
scipy.stats.rdist, griddata, hcluster, lars, lxml, matplotlib, mdp, mdp
ge 2.4, openopt, pylab, pylab plottable, pywt, pywt wp reconstruct, pywt
wp reconstruct fixed, rpy, running ipython env, sg ge 0.6.4,
sg_fixedcachesize, shogun, shogun.lightsvm, shogun.mpd, shogun.svrlight
 Versions of critical externals:
  ctypes      : 1.0.3
  nifti       : 0.20090303.1
  numpy       : 1.2.0
  scipy       : 0.7.0
RUNTIME:
 PyMVPA Environment Variables:
  PYTHONPATH          :
"/daten/mekman/3rd/local_pymvpa_installations/043/lib64/python2.5/site-packages"
 PyMVPA Runtime Configuration:
  [externals]
  have griddata = no
  have good scipy.stats.rdist = no
  have pylab plottable = no
  have pywt wp reconstruct = no
  have pywt = no
  have lxml = no
  have running ipython env = no
  have ctypes = yes
  have sg_fixedcachesize = no
  have elasticnet = no
  have shogun.mpd = no
  have matplotlib = no
  have pywt wp reconstruct fixed = no
  have scipy = yes
  have reportlab = yes
  have openopt = no
  have libsvm = yes
  have nifti ge 0.20090205.1 = yes
  have weave = yes
  have atlas_fsl = no
  have mdp = no
  have hcluster = no
  have sg ge 0.6.4 = no
  have good scipy.stats.rv_discrete.ppf = yes
  have libsvm verbosity control = yes
  have mdp ge 2.4 = no
  have shogun.svrlight = no
  have rpy = no
  have shogun = no
  have glmnet = no
  have lars = no
  have atlas_pymvpa = no
  have nifti = yes
  have cpickle = yes
  have numpy = yes
  have pylab = no
  have shogun.lightsvm = no
  have gzip = yes

  [general]
  verbose = 1
 Process Information:
  Name: python
  State:        R (running)
  Tgid: 7499
  Pid:  7499
  PPid: 6796
  TracerPid:    0
  Uid:  1515    1515    1515    1515
  Gid:  113     113     113     113
  FDSize:       256
  Groups:       113 6150
  VmPeak:         393496 kB
  VmSize:         392476 kB
  VmLck:               0 kB
  VmHWM:           36236 kB
  VmRSS:           36200 kB
  VmData:          28948 kB
  VmStk:             256 kB
  VmExe:               4 kB
  VmLib:           43336 kB
  VmPTE:             724 kB
  Threads:      1
  SigQ: 1/135168
  SigPnd:       0000000000000000
  ShdPnd:       0000000000000000
  SigBlk:       0000000000000000
  SigIgn:       0000000001001000
  SigCgt:       0000000180000002
  CapInh:       0000000000000000
  CapPrm:       0000000000000000
  CapEff:       0000000000000000
  CapBnd:       ffffffffffffffff
  Cpus_allowed: 00000000,0000000f
  Cpus_allowed_list:    0-3
  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:      2397
  nonvoluntary_ctxt_switches:   39