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--></style></head><body lang="EN-US" link="blue" vlink="purple"><div class="gmail_quote">On September 20, 2016 3:46:40 PM EDT, "Liang, Guangsheng" <guangsheng.liang@ttu.edu> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hello,<p></p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><p> </p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you very much for your kindly response.<p></p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Which function that I can remove them?<p></p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><p> </p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks again!<p></p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Carl<p></p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><p> </p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Pkg-ExpPsy-PyMVPA [mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu.edu@lists.alioth.debian.org]
<b>On Behalf Of </b>Richard Dinga<br />
<b>Sent:</b> Tuesday, September 20, 2016 3:50 AM<br />
<b>To:</b> Development and support of PyMVPA <pkg-exppsy-pymvpa@lists.alioth.debian.org><br />
<b>Subject:</b> Re: [pymvpa] ENET error<p></p></span></p>
<p class="MsoNormal"></p><p> </p>
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<p class="MsoNormal">I guess you have invariant features in your dataset, therefore you will get problems when trying to divide by 0. There is a function to remove them.
</p><p></p>
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<p class="MsoNormal"></p><p> </p>
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<p class="MsoNormal">On Fri, Sep 16, 2016 at 8:01 PM, Liang, Guangsheng <<a href="mailto:guangsheng.liang@ttu.edu" target="_blank">guangsheng.liang@ttu.edu</a>> wrote:</p><p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello PyMVPA community,</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am currently working on a fMRI data applying an ENET classifier.
</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">My PyMVPA is running under Linux environment, with python 2.7.12.
</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The design of the data is a repeated measurement with pre and post conditions. </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">In my understanding, in my case, chunk value should store subject ID, target value should store the time conditions.
</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am using the classifier code that I found in the maillist:
<a href="http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2009q1/000412.html" target="_blank">
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2009q1/000412.html</a></p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">clf = FeatureSelectionClassifier(\</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> ENET(lm=1.0,max_steps=500,trace=False,normalize=False),\</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> SensitivityBasedFeatureSelection(\</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> CorrStability(),\</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> FixedNElementTailSelector(5000,mode='select',tail='upper')),\</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> descr="ENET on 5K best(CorrStability) features")</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am also using 1000 times of permutation to test the null hypothesis, which are almost the same as those in the tutorial:
<a href="http://www.pymvpa.org/tutorial_significance.html#the-following-content-is-incomplete-and-experimental" target="_blank">
http://www.pymvpa.org/tutorial_significance.html#the-following-content-is-incomplete-and-experimental</a> (section: Avoiding the trap OR Advanced magic 101)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However, errors suspend my program:</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value encountered in divide</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0))</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
/lustre/work/apps/anaconda/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in y - mu : non-numeric argument to binary operator</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
warnings.warn(x, RRuntimeWarning)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
Traceback (most recent call last):</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
File "15subj_enet.py", line 68, in <module></p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
err_fds = cv_mc_corr_fds(fds)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", line 258, in __call__</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
return super(Learner, self).__call__(ds)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", line 136, in __call__</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
self._precall(ds)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/base.py", line 120, in _precall</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
self.__null_dist.fit(measure, ds)</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/clfs/stats.py", line 427, in fit</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
% (measure, skipped))</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
RuntimeError: Failed to obtain any value from <CrossValidation>. 1000 measurements were skipped. Check above warnings, and your code/data</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I was wondering if someone could kindly explain what are those mean, and how do I resolve this?</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you very much!</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Carl</p><p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p><p></p>
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<p class="MsoNormal"><br />
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<p class="MsoNormal"></p><p> </p>
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<p style="margin-top: 2.5em; margin-bottom: 1em; border-bottom: 1px solid #000"></p><pre class="k9mail"><hr /><br />Pkg-ExpPsy-PyMVPA mailing list<br />Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<br /><a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a></pre></blockquote></div><br clear="all"><a href="http://www.pymvpa.org/faq.html#is-there-an-easy-way-to-remove-invariant-features-from-a-dataset">http://www.pymvpa.org/faq.html#is-there-an-easy-way-to-remove-invariant-features-from-a-dataset</a><br>
;-)<br>
-- <br>
Sent from a phone which beats iPhone.</body></html>