Okay, that error means your chunks are of the form 1.0 and similar, not 'A', 'B', 'C' and 'D'.
If you look in your $path/attributes.txt file, what does the first line look like? I'm going to guess, for some X: X 1 X is your target, 1 is your chunk (and PyMVPA interprets it as a float, so prints 1.0). If X is among 'A'..'D', then what you probably want to use is targets instead of chunks. fds.sa['runtype'] = [rnames[target] for target in fds.sa.targets] If not, you'll need to figure out where you 'A'..'D' are coming from. On the other hand, this doesn't seem like a necessary step, as runtype is not referenced in the later code. Cheers, Chris On Sat, Jan 4, 2014 at 2:42 PM, Jessica Goold <[email protected]> wrote: > Hi Chris, > > Thanks for getting back to me so fast. When i try to run that I get this > error: > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > KeyError: 1.0 > > I also changed the code a little because I saw the differences in > preprocessing for wanting to run an nfoldpartitioner. I think it could have > to do with what you think though because when i run either LinearNuSVMC or > SMLR it gives me way too many samples back of accuracies. Here's the > slightly changed code: > > from mvpa2.suite import * > import numpy as np > import scipy.stats as sp > import scipy.io > import nibabel > import random > path = '/home/menglab/JG/AP/concat/Session 1' > attr = SampleAttributes(os.path.join(path, 'attributes.txt')) > > fds = fmri_dataset(samples=os.path.join(path, 'ap_all.nii'), targets = > attr.targets, chunks=attr.chunks, mask = os.path.join(path, 'rFFA_AP1.nii')) > > poly_detrend(fds, polyord=1, chunks_attr='chunks') > fds = fds[fds.sa.targets != 'none'] > > rnames = {'A': 'Face', 'B': 'High_Face', 'C': 'Low_Face', 'D': 'Non_Face'} > fds.sa['runtype'] = [rnames[chunks] for chunks in fds.sa.chunks] > #error happens here > > clf = LinearCSVMC() > cvte = CrossValidation(clf, NFoldPartitioner(), errorfx=lambda p, t: > np.mean(p == t)) > cv_results = cvte(fds) > > Thanks! > Jessica > > > On Sat, Jan 4, 2014 at 2:23 PM, Chris Johnson <[email protected]> wrote: >> >> This line is setting fds.sa['runtype'] to a list with a single boolean >> (probably [False]). >> >> > fds.sa['runtype'] = [rnames in fds.sa.chunks] >> >> I would guess what you want is: >> >> > fds.sa['runtype'] = [rnames[chunk] for chunk in fds.sa.chunks] >> >> Hopefully that's all the problem is. Otherwise the code looks like it >> should run. >> >> Chris >> >> >> On Sat, Jan 4, 2014 at 2:13 PM, Jessica Goold <[email protected]> >> wrote: >> > Hello, >> > >> > I'm trying to run my first classification analysis on my own data, and >> > every >> > classification type seems to work except LinearCSVMC(). I'm attaching my >> > python file of code and I've pasted the error I get at the bottom of it. >> > Any >> > help on why this is happening would be great! >> > >> > Thank you, >> > Jessica >> > >> > _______________________________________________ >> > Pkg-ExpPsy-PyMVPA mailing list >> > [email protected] >> > >> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa >> >> _______________________________________________ >> Pkg-ExpPsy-PyMVPA mailing list >> [email protected] >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
