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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I now use the remove_invariant_features() on my full dataset first, and then run the program again.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">But I still got the same error message:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value encountered
in divide<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0))<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">/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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">And warning message:
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">WARNING: Failed to obtain value from <CrossValidation> due to Failed to predict on <Dataset: 4956x5000@float64, <sa: chunks,partitions,targets,time_coords,time_indices>,
<fa: voxel_indices>, <a: imgaffine,imghdr,imgtype,lastpartitionset,lastsplit,mapper,partitions_set,repetitons...> using <ENET>. Exceptions was: Error in y - mu : non-numeric argument to binary operator<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">. Measurement was skipped, which could lead to unstable and/or incorrect assessment of the null_dist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I did not use any mask this time.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Any thoughts on that? Any help will be appreciated!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<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"> Yaroslav Halchenko [mailto:yoh@onerussian.com]
<br>
<b>Sent:</b> Tuesday, September 20, 2016 4:43 PM<br>
<b>To:</b> Development and support of PyMVPA <pkg-exppsy-pymvpa@lists.alioth.debian.org>; Liang, Guangsheng <guangsheng.liang@ttu.edu><br>
<b>Subject:</b> Re: [pymvpa] ENET error<o:p></o:p></span></p>
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</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On September 20, 2016 3:46:40 PM EDT, "Liang, Guangsheng" <<a href="mailto:guangsheng.liang@ttu.edu">guangsheng.liang@ttu.edu</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hello,<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> <o:p></o: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.<o:p></o: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?<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks again!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Carl<o:p></o:p></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> <o:p></o: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 [</span><a href="mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu.edu@lists.alioth.debian.org"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu.edu@lists.alioth.debian.org</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<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 <</span><a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">pkg-exppsy-pymvpa@lists.alioth.debian.org</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b> Re: [pymvpa] ENET error<o:p></o:p></span></p>
<p> <o:p></o:p></p>
<div>
<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.
<o:p></o:p></p>
</div>
<div>
<p> <o:p></o:p></p>
<div>
<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:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt">
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello PyMVPA community,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o: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.
<o:p></o: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.
<o:p></o: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. <o:p></o: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.
<o:p></o: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><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">clf = FeatureSelectionClassifier(\<o:p></o: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),\<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> SensitivityBasedFeatureSelection(\<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> CorrStability(),\<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> FixedNElementTailSelector(5000,mode='select',tail='upper')),\<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> descr="ENET on 5K best(CorrStability) features")<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o: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)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However, errors suspend my program:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o: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<o:p></o: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))<o:p></o: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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
warnings.warn(x, RRuntimeWarning)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
Traceback (most recent call last):<o:p></o: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><o:p></o: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)<o:p></o: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__<o:p></o: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)<o:p></o: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__<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
self._precall(ds)<o:p></o: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<o:p></o: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)<o:p></o: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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
% (measure, skipped))<o:p></o: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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o: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?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you very much!<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Carl<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><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><o:p></o:p></p>
</blockquote>
</div>
<p> <o:p></o:p></p>
</div>
<pre style="text-align:center"><hr size="2" width="100%" align="center"></pre>
<pre><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">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><o:p></o:p></pre>
</blockquote>
</div>
<p class="MsoNormal"><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.<o:p></o:p></p>
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