Hi,<br>Thank you so much for the replies!! I now have 18 subject's datasets in
one file, but seem to still be missing something. Working through the
hyperalignment tutorial, after loading using h5load, zscoring
the individual datasets or inserting subject IDs to the individual datasets doesn't work with my combined dataset file (missing some attributes). It definitely works when using the example
hyperalignment dataset file though. <br>Pardon me for the repeated questions
on this. Would anyone please let me
know if there is something I am neglecting to do before saving all the
datasets into the one file? Thank you very much!<br>
<br>
Kimberly<br><br>>>> _ = [zscore(ds) for ds in ds_all]<br>
Traceback (most recent call last):<br>
File "<stdin>", line 1, in <module><br>
File "/usr/lib/pymodules/python2.7/mvpa2/mappers/zscore.py", line 286, in zscore<br>
zm.train(Dataset(ds))<br>
File "/usr/lib/pymodules/python2.7/mvpa2/base/dataset.py", line 214, in __init__<br>
"AttrDataset only supports dtypes as samples that have a "<br>
ValueError: AttrDataset only supports dtypes as samples that have a
`dtype` attribute that behaves similar to the one of an array-like.<br>
<br>>>> for i,sd in enumerate(ds_all):<br>
... <a href="http://sd.sa">sd.sa</a>['subject'] = np.repeat(i, len(sd))<br>
... <br>
Traceback (most recent call last):<br>
File "<stdin>", line 2, in <module><br>
AttributeError: 'str' object has no attribute 'sa'<br><br><div class="gmail_quote">On Fri, Jan 11, 2013 at 6:00 AM, <span dir="ltr"><<a href="mailto:pkg-exppsy-pymvpa-request@lists.alioth.debian.org" target="_blank">pkg-exppsy-pymvpa-request@lists.alioth.debian.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Multiple datasets in one hdf5 file (Kimberly Zhou)<br>
2. Re: Multiple datasets in one hdf5 file (Yaroslav Halchenko)<br>
3. Re: Multiple datasets in one hdf5 file (Michael Hanke)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 10 Jan 2013 12:57:07 -0600<br>
From: Kimberly Zhou <<a href="mailto:kyqzhou@gmail.com">kyqzhou@gmail.com</a>><br>
To: "<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>"<br>
<<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br>
Subject: [pymvpa] Multiple datasets in one hdf5 file<br>
Message-ID:<br>
<<a href="mailto:CA%2BydVYKCpdMRvtWhQfbpwtzOnZ8F_Pntfo5k%2BQBr%2B3Lr8L5LyA@mail.gmail.com">CA+ydVYKCpdMRvtWhQfbpwtzOnZ8F_Pntfo5k+QBr+3Lr8L5LyA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello,<br>
On the hyperalignment tutorial, the data (with attributes and everything<br>
already) for multiple subjects are all in one hdf5 file. Is there a page or<br>
something that shows how to save multiple datasets into one hdf5 file?<br>
Apologies<br>
for more noob questions. Thank you!!<br>
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<br>
Message: 2<br>
Date: Thu, 10 Jan 2013 14:01:03 -0500<br>
From: Yaroslav Halchenko <<a href="mailto:debian@onerussian.com">debian@onerussian.com</a>><br>
To: <a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br>
Subject: Re: [pymvpa] Multiple datasets in one hdf5 file<br>
Message-ID: <<a href="mailto:20130110190103.GG19929@onerussian.com">20130110190103.GG19929@onerussian.com</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
should be as simple as storing one since you can store (theoretically)<br>
any structure, so just try<br>
<br>
h5save('/tmp/out.h5', [ds1, ds2])<br>
<br>
and then load as<br>
<br>
ds1, ds2 = h5load('/tmp/out.h5')<br>
<br>
On Thu, 10 Jan 2013, Kimberly Zhou wrote:<br>
<br>
> Hello,?<br>
> On the hyperalignment tutorial, the data (with attributes and everything<br>
> already)?for multiple subjects are all in one hdf5 file. Is there a page<br>
> or something that shows how to save multiple datasets into one hdf5 file?<br>
> Apologies for more noob questions.?Thank you!!<br>
<br>
> _______________________________________________<br>
> Pkg-ExpPsy-PyMVPA mailing list<br>
> <a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br>
<br>
<br>
--<br>
Yaroslav O. Halchenko<br>
Postdoctoral Fellow, Department of Psychological and Brain Sciences<br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: <a href="tel:%2B1%20%28603%29%20646-9834" value="+16036469834">+1 (603) 646-9834</a> Fax: <a href="tel:%2B1%20%28603%29%20646-1419" value="+16036461419">+1 (603) 646-1419</a><br>
WWW: <a href="http://www.linkedin.com/in/yarik" target="_blank">http://www.linkedin.com/in/yarik</a><br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 10 Jan 2013 20:26:47 +0100<br>
From: Michael Hanke <<a href="mailto:michael.hanke@gmail.com">michael.hanke@gmail.com</a>><br>
To: Development and support of PyMVPA<br>
<<a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a>><br>
Subject: Re: [pymvpa] Multiple datasets in one hdf5 file<br>
Message-ID:<br>
<CAK-KoxRg0mQZjXQjXzB=<a href="mailto:F66WQ5MVMawxf6jUyMgFQDx262vdiQ@mail.gmail.com">F66WQ5MVMawxf6jUyMgFQDx262vdiQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
On Thu, Jan 10, 2013 at 8:01 PM, Yaroslav Halchenko<br>
<<a href="mailto:debian@onerussian.com">debian@onerussian.com</a>>wrote:<br>
<br>
> should be as simple as storing one since you can store (theoretically)<br>
> any structure, so just try<br>
><br>
> h5save('/tmp/out.h5', [ds1, ds2])<br>
><br>
> and then load as<br>
><br>
> ds1, ds2 = h5load('/tmp/out.h5')<br>
<br>
<br>
Or use a dict and access them by name:<br>
<br>
h5save('test.df5', dict(one=5, two=6))<br>
<br>
d = h5load('test.df5')<br>
d['one']<br>
5<br>
<br>
<br>
--<br>
GPG key: 1024D/3144BE0F Michael Hanke<br>
<a href="http://mih.voxindeserto.de" target="_blank">http://mih.voxindeserto.de</a><br>
Jabber: <a href="mailto:michael.hanke@gmail.com">michael.hanke@gmail.com</a><br>
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</blockquote></div><br>