[pymvpa] Advice for input to SampleAttributes? Text file may have too many columns?

Nick Oosterhof n.n.oosterhof at googlemail.com
Wed Mar 22 17:44:48 UTC 2017

> On 21 Mar 2017, at 16:53, Lauren Nelson <lmnelson at bu.edu> wrote:
> I'm having trouble passing a text file to SampleAttributes, and I -think- what my problem might be is that my text file has more columns than I thought it did. Vim seems to think it has 3894 columns.

What makes you think that? Do you mean columns as in (1) strings separated by some separator string (e.g. whitespace), or (2) columns as in characters?

> I have a couple questions. Does the following error message seem consistent with this?
> And if so, is there a possible way to fix this? Even better, is there a way to read in an Excel spreadsheet? That's the file format I'm starting with.
> >>> attr = SampleAttributes(attr_fname)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.7/dist-packages/mvpa2/misc/io/base.py", line 426, in __init__
>     sep=None, dtype=dtypes)
>   File "/usr/lib/python2.7/dist-packages/mvpa2/misc/io/base.py", line 118, in __init__
>     dtype=dtype, skiplines=skiplines)
>   File "/usr/lib/python2.7/dist-packages/mvpa2/misc/io/base.py", line 258, in _from_file
>     "of columns in header [%i]." % (len(l), len(hdr))
> RuntimeError: Number of entries in line [3] does not match number of columns in header [2].

Can you provide the output of the first few lines of your text file? PyMVPA seems to think there are either 2 or 3 columns (with meaning (1), separated by some separator string)

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