[pymvpa] zcore issue/error?

[Yaroslav Halchenko]

Hi Matthias,

> 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.
yeap ;) thanks!

and I guess everything works fine if dataset.samples.dtype is of some
float, right?

On Tue, 15 Dec 2009, Matthias Ekman wrote:

> 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

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