[pymvpa] zcore issue/error?
Matthias Ekman
Matthias.Ekman at nf.mpg.de
Tue Dec 15 14:42:15 UTC 2009
Hi,
>> 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?
>
mh... hate to say so, but adding "dtype=N.float32" doesn't change the
result. Sorry if I get you wrong here...?
attr = SampleAttributes(os.path.join(ATTRIBUTES_PATH, ATTRIBUTES_FILE))
ds = NiftiDataset(samples=os.path.join(BOLD_PATH, BOLD_FILE),
labels=attr.labels,
chunks=attr.chunks,
mask=os.path.join(MASK_PATH, MASK_FILE),
dtype=N.float32)
Bests,
Matthias
> 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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>
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