[pymvpa] MVPA .4 and multi-feature RBF

Fri Dec 16 05:58:06 UTC 2011

I've tried adapting 5-6 examples to my trial's data, but other than 
the <http://v04.pymvpa.org/examples/smellit.html>Simple 
Data-Exploration example they all throw  exceptions and access 
violation 0x0000000 errors...
I got past the numerix.ma error but the ctypes errors stumped me.
I should try the .6 branch I suppose.
Other ideas? Please?

The data exploration:

import numpy
import pylab as P
from mvpa.suite import *
from mvpa.misc.plot import plotFeatureHist, plotSamplesDistance

fh = open('con4.csv', 'r')
lines = fh.readlines()
fh.close()
features = lines[0].split(',')[1:]

labels = numpy.zeros((len(lines)-1), dtype=numpy.float32)

data = numpy.zeros((len(lines)-1, len(features)-1), dtype=numpy.float32)
print 'data shape', data.shape
for smp in range(1,len(lines)-1):
     d = lines[smp].split(',')[1:]
     labels[smp] = d[1]
     data[smp, :] = lines[smp].split(',')[2:]

ds = MaskedDataset(samples=data, labels=labels,  chunks=1)

# next only works with floating point data
ds.setSamplesDType('float')

# look at sample similiarity
# Note, the decreasing similarity with increasing temporal distance
# of the samples
P.subplot(121)
plotSamplesDistance(ds, sortbyattr='chunks')
P.title('Sample distances (sorted by chunks)')

P.subplot(122)
plotSamplesDistance(ds, sortbyattr='labels')
P.title('Sample distances (sorted by labels)')
if cfg.getboolean('examples', 'interactive', True):
     P.show()

# z-score features individually per chunk
print 'Detrending data'
detrend(ds, perchunk=True, model='regress', polyord=2)
print 'Z-Scoring data'
zscore(ds)

P.subplot(121)
plotSamplesDistance(ds, sortbyattr='chunks')
P.title('Distances: z-scored, detrended (sorted by chunks)')
P.subplot(122)
plotSamplesDistance(ds, sortbyattr='labels')
P.title('Distances: z-scored, detrended (sorted by labels)')
if cfg.getboolean('examples', 'interactive', True):
     P.show()

Ray Schumacher
Programmer/Consultant  
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SWG,0,1.25,0.75,19.47289463,-18.86017207,9789.579278,-632.1815788,4,1.416828128,1.25,0.75,19.08041088,-17.54145854,5101.649764,-332.633099,3,1.366545703,1.5,0.5,7.797273643,-19.43983349,754.7271888,-2.590727081,2,1.892164102,1.25,0.5,13.88477282,-30.30156714,-599.4409431,185.693049,4,2.263159347,1.75,1.5,9999,-28.99435021,1232.579495,-53.12689015,2,2.281950327,1.25,0.5,18.91376792,-29.2637392,17874.05266,-952.5126422,2,2.053347093
TJS,0,2.75,1.75,16.43935349,-6.804923937,12353.01503,-786.9828084,4,1.709430204,3.5,1.75,3.879413199,-6.379459208,7655.321593,-524.2941293,3,1.756066899,2,1,7.689336673,-6.284365649,1605.427464,-70.23601662,4,2.513126806,2,0.75,6.987375911,-9.428204605,345.1886471,-5.671336241,6,2.050413236,2.25,0.75,8.08018834,-8.496833601,568.1201703,-26.55411586,6,1.288187755,2.25,1,5.943177093,-8.174226686,1337.929703,-20.33541248,4,1.864744902
VGM,0,4.5,3.25,10.57762178,-3.544721656,15835.54328,-903.0921925,3,2.211584757,4,3,9.864631355,-10.57431866,9599.456361,-628.885797,2,1.612338817,4.5,4,9999,-8.728745023,-3499.745972,429.6281113,0,0,4.25,2.75,9999,-3.698256437,2055.213232,204.2482935,3,2.162788774,1.5,0,9999,-4.362706457,-6406.529081,691.1825168,3,1.377621145,4,2,3.287676114,-14.50410021,-97203.53872,10492.30547,3,1.629254485
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Subject,Condition,SLJ1bw6,SLJ1bw3,SLJ1sL,SLJ1sR,SLJ2a,SLJ2b,SLJ3n,SLJ3mx,SRJ1bw6,SRJ1bw3,SRJ1sL,SRJ1sR,SRJ2a,SRJ2b,SRJ3n,SRJ3mx,ALJ1bw6,ALJ1bw3,ALJ1sL,ALJ1sR,ALJ2a,ALJ2b,ALJ3n,ALJ3mx,ARJ1bw6,ARJ1bw3,ARJ1sL,ARJ1sR,ARJ2a,ARJ2b,ARJ3n,ARJ3mx,BKJ1bw6,BKJ1bw3,BKJ1sL,BKJ1sR,BKJ2a,BKJ2b,BKJ3n,BKJ3mx,TPJ1bw6,TPJ1bw3,TPJ1sL,TPJ1sR,TPJ2a,TPJ2b,TPJ3n,TPJ3mx
DJSM2,1,1.75,0.75,9999,-3.946831699,4634.370738,-228.424548,4,1.654530255,1.5,0.75,9999,-4.946325276,5410.350607,-268.8718961,6,1.710138974,2.25,0.75,9999,-3.785189616,6948.230711,-397.704205,6,1.843566482,5,4.75,9999,-12.81083508,21930.55614,-1384.114778,3,1.367001587,3.5,2,9999,-2.996900928,9468.470118,-571.5634936,6,1.539143648,1.25,0.5,14.26458952,-13.21848625,53305.22524,-3204.169118,3,1.559347195
STM,1,2.25,0.75,8.399133372,-4.788717106,4480.868889,-161.236025,2,1.642841513,2.25,0.75,7.470112676,-5.214834721,3601.847459,-126.6547928,2,1.698144263,1.25,0.25,14.05644535,-9.199833081,-375.4174704,85.62757263,4,1.429483178,4.25,2.75,14.44039583,-3.804048794,-1712.456385,235.7130989,4,1.348794903,1,0.5,10.47858759,-12.09096366,658.7787483,-36.03173908,4,1.36354968,2.75,1.75,19.67157815,-7.282620252,-11309.21584,1370.262711,4,1.811259937
TKG,1,2.5,1.25,13.18333627,-5.285312205,4702.743197,-273.8909233,2,2.232127365,2.5,1.25,13.92449568,-5.167472097,1981.590131,-123.3490981,0,0,3.5,2.5,9999,-4.796728222,117.121599,42.03618377,1,2.174767388,4,2.25,9999,-2.742826484,-1850.267926,258.6318556,4,1.90095475,2.75,2.25,9999,-7.418952262,-613.5575301,103.0158456,5,1.568939561,3.75,2.75,15.6722649,-9.624195883,-529.2710082,383.0475131,3,1.812087946
TWL,1,0.75,0.5,9999,-16.64823806,5668.906688,-96.38954564,3,1.820285991,0.75,0.5,9999,-15.82833276,2634.412159,-154.3845173,4,1.532061608,2.5,1,8.741697808,-0.853621552,22158.74508,-1179.844422,5,1.943920585,2.5,1,11.16710812,-3.807662418,15071.64119,-853.1824898,3,1.871640655,2.75,1,6.556155589,-2.027046901,14317.54591,-830.6492898,3,1.842539997,2.5,1,10.57847731,-3.662062335,48295.88485,-2689.427689,4,1.329002776
ARO,0,4.25,2,3.280951971,-4.311233238,20894.79513,-1366.828691,2,1.909116937,4,1.75,3.480445346,-4.211002805,8730.785342,-560.665588,2,1.476034411,3.75,2.5,9999,-4.025572681,3670.41306,-167.8996653,5,1.436649174,5,3,9999,-0.630856385,4494.709459,-155.2792431,4,2.022039078,3.5,2.5,8.538205088,-7.056226385,1252.807828,-6.395534462,4,2.431981567,4.5,3.25,9.473051119,-6.206733965,-526.2691133,336.1614166,4,1.887584203
AXK-PS,0,2.25,1.25,12.99957379,-9.506729864,16972.47147,-1049.68814,5,1.703091984,2.25,1.25,13.10148625,-8.873181615,15535.94827,-988.6166422,4,1.634884524,2.25,1.5,15.40020089,-16.03263123,720.4408515,-17.37092402,4,1.750157582,2.25,0.75,4.273409113,-13.25753273,8622.138297,-361.9927092,5,1.723521645,2.25,1.25,15.59161828,-14.50288664,1332.960602,-54.43380046,5,1.924909876,2.25,1.25,15.85333205,-13.22521893,2219.586286,-112.9267404,4,1.540008834
BAM,0,2.75,1.25,8.992127543,-6.259273449,14316.87644,-748.9303938,5,2.075734923,2.5,1.25,9.849072959,-5.521240515,9838.863364,-615.8617552,5,1.720924271,4.25,3,9999,-3.285634833,-109.1698291,78.63041732,3,1.961039078,3.25,1.75,7.75820911,-4.221856682,1634.409791,-58.63071001,4,2.153264803,3.25,3,9999,-13.25109919,1380.538143,-67.00627621,6,1.318197574,2.5,0.75,5.450285973,-8.98284729,17847.1102,-925.873951,3,1.512358212
CDR,0,3.5,2.5,9.783343566,-8.148190681,514.6790923,20.39516094,3,1.75934749,3.5,2.5,10.34965243,-7.987568461,559.7218185,20.19850647,2,1.718872496,1.75,0.25,13.20287,-6.345448743,-36.69320681,107.4182634,7,1.451001681,1,0.5,9999,-12.69434975,2883.157892,-115.758986,7,1.678352782,1,0.5,9999,-12.71403,3024.53758,-58.20154477,7,1.674699889,2,0.25,10.17368327,-7.329917112,8252.307566,-377.3044572,5,1.791382709
DJM,0,4.75,3.25,6.200913667,-5.494181196,5838.82839,-366.3373956,4,1.7867329,5,3.75,12.00190493,-4.214517868,5832.877965,-353.1826883,3,1.808005783,3.25,0.75,4.470650025,-2.517071312,3413.493419,-49.41406975,3,2.078334506,3,0.75,5.277538039,-3.210622818,1629.957149,140.0181975,3,3.646904548,3,0.75,4.442420216,-2.986927492,1441.794071,142.0163835,3,3.077569557,3.25,1.5,10.29414823,-3.531899252,-11808.52388,1537.263687,3,3.351633148
DLK,0,1,0,16.58687176,-17.2132687,2204.37691,-114.3506625,3,2.947844887,1,0,17.23746443,-19.76038688,1026.183319,-6.05076672,4,3.448038009,0.75,0.25,27.7150303,-22.7549022,6560.995262,-412.9062449,3,2.512039449,0.75,0.25,28.76197018,-22.9487526,8355.773429,-541.8068544,2,1.506887726,0.75,0.25,27.42112078,-22.68897975,5583.814586,-345.4957086,2,1.796149648,0.75,0.25,28.99334009,-22.92172906,31682.94851,-1937.813938,3,2.4543453
EEM,0,1.5,0.5,12.68866568,-13.26398751,7454.074254,-468.9744334,3,2.39406853,1.5,0.5,11.43573589,-13.59902227,2234.278454,-117.3815026,3,1.914861717,0.5,0,9999,-23.00275197,5288.083644,-274.3187416,4,1.924659186,0.5,0,9999,-24.92822352,1622.32314,-27.76521488,6,1.427279223,0.5,0,9999,-24.5410921,3627.868587,-200.9859623,5,1.811353234,2.75,0.5,4.631019554,-8.967437467,13847.99661,-473.2508864,4,1.919579246
GET-PS,0,2,0.5,13.13047592,-5.079069622,2169.665527,-136.3883385,2,1.587728338,2,0.75,16.38039648,-3.244446943,2568.583893,-158.1018075,2,1.993147274,3.75,0.5,5.06714958,-1.624041473,1749.570549,35.3250423,2,3.031985525,0.5,0.25,9999,-14.47138066,4038.359691,-232.9751771,2,2.669533153,0.5,0.25,9999,-13.87933967,986.3134665,-40.93178001,2,2.354075638,4.25,3,9999,-4.969498841,6198.742137,-301.4862909,2,2.700316503
GXA,0,1.5,0.75,24.28891674,-11.82614725,6918.746449,-312.5265772,5,2.369175042,1.5,0.5,21.91370783,-8.249569009,6474.578216,-335.9224132,4,2.438946082,1.25,0.5,17.84156338,-27.93196036,3272.701177,-16.87550742,4,2.038247528,1.25,0.5,20.73044382,-24.42385467,7181.667731,-267.4010441,5,1.533080483,1.25,0.5,12.53609156,-28.45961474,3194.919274,-131.9523066,6,1.654469538,1.25,1,18.74866264,9999,7563.398255,-106.2516649,4,1.574422505
HCF,0,4.5,3.75,9999,-6.137996322,4173.417576,-249.9400039,3,1.782707684,4,3.5,9999,-8.897527792,2794.503988,-158.9258733,4,1.524976996,4,1.75,9999,-2.489511209,1685.685316,-35.02090533,4,1.650701434,2.5,2,9999,-8.470875379,678.9510343,37.34858425,6,1.5623322,4.25,3.75,9999,-7.73002628,1371.981927,36.43538532,7,1.438784185,2,0.75,6.878356116,-9.432694795,15636.9182,-655.2863102,5,1.443880833
JRW,0,1.5,0.25,12.54111844,-8.761744285,5643.876619,-308.9039329,3,2.052735173,1.25,0.25,15.00508836,-13.61194707,6083.699521,-320.829991,3,2.633743441,5,5,9999,9999,1961.855655,51.59969305,6,1.258427556,3,0.75,9999,-2.45469281,4953.419388,-252.2379912,3,2.119419502,2.75,2.25,9999,-8.708126867,2343.770564,-131.3284421,3,1.340850244,1,0.5,19.76063941,-17.04469285,9251.103089,-464.0983091,5,1.426925801
LWL,0,1.75,0.5,9.910485159,-11.57660179,6660.392264,-398.6096326,4,2.2947648,1.75,0.75,10.41672936,-11.8572631,5308.861431,-320.2203449,4,2.233114718,3.25,0.75,6.262633133,-3.482552077,1702.076416,-78.56818869,3,1.708561403,3.75,2.75,14.26451105,-11.42202063,3972.360398,-217.8391346,3,1.904967555,3.5,0.75,4.156420292,-4.537613099,2918.136548,-105.9842519,3,1.859153455,2.5,1.5,11.2931503,-11.97167614,28834.38107,-1426.455698,3,2.2367539
MJC-PS,0,1,0.25,20.85264514,-12.67229392,404.571772,16.50044018,3,1.799240937,1.75,0.25,15.94792004,-7.550811606,966.0060405,-33.0918602,2,1.513815984,0.25,0,9999,-33.51320773,-391.7151043,66.31176425,4,2.167886402,1.5,0.5,4.292912919,-18.81215701,7178.583739,-180.8614549,2,2.191630981,1,0.25,18.19007114,-24.27724309,209.3152068,55.17541492,2,2.227119249,1,0.5,22.38055169,-26.48002104,1245.983433,-43.46106755,2,2.515786256
MKS-PS,0,1,0.25,16.29408575,-31.31021741,18230.87526,-933.1959875,4,1.877269205,1,0.25,15.16016901,-30.79719695,4482.302418,-284.7671623,3,1.935709599,2,1.5,12.03667952,9999,10255.36432,-545.1497973,3,1.714019065,0.75,0.25,8.19975839,9999,20506.18098,-1107.458695,4,1.99178696,1,0.25,24.79781141,-12.19870113,7979.775526,-409.6098121,4,1.796750594,1.5,0.5,12.4725974,-9.009909753,17381.60584,-869.116711,5,1.849315435
MMA,0,2.5,0.75,3.148200099,-11.09177076,3593.301343,-220.3100634,4,2.955791735,2.5,0.75,3.323251403,-11.59979973,2970.691583,-183.5859569,3,2.906701398,2.25,1.5,8.774483039,-18.1797041,1637.953039,-18.57508212,3,1.831275254,1.25,1,9999,-22.39439891,8142.204642,-487.3726547,4,2.12399649,2.5,1.75,13.5581789,-18.95684964,7310.053526,-411.4239641,5,1.541503283,5,2,4.695639402,-1.776121956,0.431406871,-0.007106317,8,1.383427418
MTN,0,2.25,0.5,5.869509674,-7.374752085,7786.923613,-291.6874482,4,3.08361388,3.75,2.25,5.687932625,-5.978332258,5153.488081,-153.2511933,5,1.511460969,5,2.5,9999,-0.973924343,1123.888118,157.2067386,4,1.645951344,5,2.25,9999,-0.518999984,-10525.7248,1645.204462,5,1.714548903,3.5,1.5,17.10293189,-2.896745581,-15272.47995,2896.304913,3,1.853568443,3.5,1.25,13.97013476,-2.621626635,-14468.82232,6373.717545,3,2.066186909
NAO,0,1,0.25,19.0072303,-18.24273831,5924.13208,-396.4927017,2,2.346503631,1,0.25,20.48288837,-21.90264772,3608.635537,-247.6462497,1,2.545476955,1.25,1,9999,-27.32378897,613.2162241,-25.46742479,4,2.204613091,1.25,0.25,6.190405321,-28.23948188,2209.958937,-133.6767321,6,1.944461341,1.25,1,9999,-27.77271167,-35.90875333,41.00841875,5,1.84213655,1.25,0.5,19.09456938,-17.34835737,14723.00613,-711.9745327,5,2.366272801
PIH-PS,0,2.25,1,7.14131422,-10.83995702,3996.406492,-257.2383391,4,1.856422729,2.25,1,7.684719911,-10.34669632,3763.981434,-243.8004652,3,1.93158067,3.25,2.75,9999,-10.96339245,-515.3094939,94.17368804,3,2.402916383,0.75,0.25,9999,-16.87345903,-318.8906056,103.1445868,3,2.673261254,0.75,0.25,9999,-15.38294659,-947.7840787,161.7617738,4,2.4891082,1.25,0.5,9999,-8.1101731,-152.8195707,87.4537146,4,1.794656928
RFD,0,1.25,0.25,19.16012884,-17.25218063,15396.36323,-1028.914498,1,3.552638207,1.25,0.25,18.89441738,-16.25191362,14572.69247,-1006.973767,1,5.67984127,1,0.5,15.09558383,9999,9226.72071,-629.6483447,1,10.9108836,1,0.5,16.11006821,-20.11560098,1734.430164,-105.5941606,1,2.680387161,0.75,0.5,14.69985667,9999,7960.309208,-536.0775607,1,3.333900687,1,0.25,19.77287864,-23.5122034,4211.246932,-55.20038833,2,2.240271298
SAJ,0,2.5,1.75,21.4842118,-7.455760978,3519.181374,-59.08772458,2,3.060927973,1,0.25,22.69895311,-12.49585471,4956.284788,-258.8424943,3,2.218920017,1.25,0.25,15.69391467,-16.83077328,1325.977696,141.3735674,4,1.71805052,1.5,0.25,14.81866536,-7.124046534,10310.76287,-250.0594324,8,1.643065567,1.25,0.25,16.52703508,-16.9186608,2811.382042,5.545974258,4,1.818893912,1.25,0.25,18.44005357,-16.69981616,25693.48501,-651.4291454,4,2.326193894
SBR,0,1,0.5,23.5378452,-31.06595859,10400.30543,-514.8073254,3,4.407602976,1,0.5,24.71836021,-34.63714539,5405.811279,-314.3408243,3,3.277627955,1,0.5,29.16161975,-32.55860514,186.8196322,2.122260386,5,1.819890254,0.75,0.25,22.37875938,-35.11078507,1790.457351,-89.31380545,4,3.311462944,0.75,0.25,20.59223079,-33.85657157,205.1383987,1.875415364,4,2.117140243,1,0.25,23.72542674,-29.42611994,1554.847844,178.7690701,4,2.242122056
SJL,0,3,2,15.23037477,-12.26118872,9090.362627,-555.676749,2,2.401199016,2,1,11.13728513,-10.84515466,5429.282504,-341.6346909,3,2.711224802,3.25,2.75,9999,-13.12194404,2540.956691,-32.60031955,3,2.338747258,4.5,3.5,9999,-3.689441051,-5755.192617,812.3372479,6,1.531641795,3.25,2.75,9999,-11.96127984,445.0630516,104.684652,3,2.065697083,3.25,0.5,4.357768233,-3.490763774,10113.59718,159.6431549,3,2.20037545
SWG,0,1.25,0.75,19.47289463,-18.86017207,9789.579278,-632.1815788,4,1.416828128,1.25,0.75,19.08041088,-17.54145854,5101.649764,-332.633099,3,1.366545703,1.5,0.5,7.797273643,-19.43983349,754.7271888,-2.590727081,2,1.892164102,1.25,0.5,13.88477282,-30.30156714,-599.4409431,185.693049,4,2.263159347,1.75,1.5,9999,-28.99435021,1232.579495,-53.12689015,2,2.281950327,1.25,0.5,18.91376792,-29.2637392,17874.05266,-952.5126422,2,2.053347093
TJS,0,2.75,1.75,16.43935349,-6.804923937,12353.01503,-786.9828084,4,1.709430204,3.5,1.75,3.879413199,-6.379459208,7655.321593,-524.2941293,3,1.756066899,2,1,7.689336673,-6.284365649,1605.427464,-70.23601662,4,2.513126806,2,0.75,6.987375911,-9.428204605,345.1886471,-5.671336241,6,2.050413236,2.25,0.75,8.08018834,-8.496833601,568.1201703,-26.55411586,6,1.288187755,2.25,1,5.943177093,-8.174226686,1337.929703,-20.33541248,4,1.864744902
VGM,0,4.5,3.25,10.57762178,-3.544721656,15835.54328,-903.0921925,3,2.211584757,4,3,9.864631355,-10.57431866,9599.456361,-628.885797,2,1.612338817,4.5,4,9999,-8.728745023,-3499.745972,429.6281113,0,0,4.25,2.75,9999,-3.698256437,2055.213232,204.2482935,3,2.162788774,1.5,0,9999,-4.362706457,-6406.529081,691.1825168,3,1.377621145,4,2,3.287676114,-14.50410021,-97203.53872,10492.30547,3,1.629254485