Re: [pymvpa] ENET error
Thanks! I now use the remove_invariant_features() on my full dataset first, and then run the program again. But I still got the same error message: /lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value encountered in divide covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0)) /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 And warning message: WARNING: Failed to obtain value from due to Failed to predict on , , using . Exceptions was: Error in y - mu : non-numeric argument to binary operator . Measurement was skipped, which could lead to unstable and/or incorrect assessment of the null_dist I did not use any mask this time. Any thoughts on that? Any help will be appreciated! From: Yaroslav Halchenko [mailto:y...@onerussian.com] Sent: Tuesday, September 20, 2016 4:43 PM To: Development and support of PyMVPA ; Liang, Guangsheng Subject: Re: [pymvpa] ENET error On September 20, 2016 3:46:40 PM EDT, "Liang, Guangsheng" mailto:guangsheng.li...@ttu.edu>> wrote: Hello, Thank you very much for your kindly response. Which function that I can remove them? Thanks again! Carl From: Pkg-ExpPsy-PyMVPA [mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu@lists.alioth.debian.org] On Behalf Of Richard Dinga Sent: Tuesday, September 20, 2016 3:50 AM To: Development and support of PyMVPA mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org>> Subject: Re: [pymvpa] ENET error 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. On Fri, Sep 16, 2016 at 8:01 PM, Liang, Guangsheng mailto:guangsheng.li...@ttu.edu>> wrote: Hello PyMVPA community, I am currently working on a fMRI data applying an ENET classifier. My PyMVPA is running under Linux environment, with python 2.7.12. The design of the data is a repeated measurement with pre and post conditions. In my understanding, in my case, chunk value should store subject ID, target value should store the time conditions. I am using the classifier code that I found in the maillist: http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2009q1/000412.html clf = FeatureSelectionClassifier(\ ENET(lm=1.0,max_steps=500,trace=False,normalize=False),\ SensitivityBasedFeatureSelection(\ CorrStability(),\ FixedNElementTailSelector(5000,mode='select',tail='upper')),\ descr="ENET on 5K best(CorrStability) features") I am also using 1000 times of permutation to test the null hypothesis, which are almost the same as those in the tutorial: http://www.pymvpa.org/tutorial_significance.html#the-following-content-is-incomplete-and-experimental (section: Avoiding the trap OR Advanced magic 101) However, errors suspend my program: /lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value encountered in divide covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0)) /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 warnings.warn(x, RRuntimeWarning) Traceback (most recent call last): File "15subj_enet.py", line 68, in err_fds = cv_mc_corr_fds(fds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", line 136, in __call__ self._precall(ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/base.py", line 120, in _precall self.__null_dist.fit(measure, ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/clfs/stats.py", line 427, in fit % (measure, skipped)) RuntimeError: Failed to obtain any value from . 1000 measurements were skipped. Check above warnings, and your code/data I was wondering if someone could kindly explain what are those mean, and how do I resolve this? Thank you very much! Carl ___ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa http://www.pymvpa.o
Re: [pymvpa] ENET error
On September 20, 2016 3:46:40 PM EDT, "Liang, Guangsheng" wrote: >Hello, > >Thank you very much for your kindly response. >Which function that I can remove them? > >Thanks again! >Carl > >From: Pkg-ExpPsy-PyMVPA >[mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu@lists.alioth.debian.org] >On Behalf Of Richard Dinga >Sent: Tuesday, September 20, 2016 3:50 AM >To: Development and support of PyMVPA > >Subject: Re: [pymvpa] ENET error > >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. > >On Fri, Sep 16, 2016 at 8:01 PM, Liang, Guangsheng >mailto:guangsheng.li...@ttu.edu>> wrote: >Hello PyMVPA community, > >I am currently working on a fMRI data applying an ENET classifier. >My PyMVPA is running under Linux environment, with python 2.7.12. >The design of the data is a repeated measurement with pre and post >conditions. >In my understanding, in my case, chunk value should store subject ID, >target value should store the time conditions. >I am using the classifier code that I found in the maillist: >http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2009q1/000412.html > >clf = FeatureSelectionClassifier(\ > ENET(lm=1.0,max_steps=500,trace=False,normalize=False),\ >SensitivityBasedFeatureSelection(\ >CorrStability(),\ > FixedNElementTailSelector(5000,mode='select',tail='upper')),\ >descr="ENET on 5K best(CorrStability) features") > > >I am also using 1000 times of permutation to test the null hypothesis, >which are almost the same as those in the tutorial: >http://www.pymvpa.org/tutorial_significance.html#the-following-content-is-incomplete-and-experimental >(section: Avoiding the trap OR Advanced magic 101) > >However, errors suspend my program: > >/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: >RuntimeWarning: invalid value encountered in divide > covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0)) >/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 > > warnings.warn(x, RRuntimeWarning) >Traceback (most recent call last): > File "15subj_enet.py", line 68, in >err_fds = cv_mc_corr_fds(fds) >File >"/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", >line 258, in __call__ >return super(Learner, self).__call__(ds) >File >"/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", >line 136, in __call__ >self._precall(ds) >File >"/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/base.py", >line 120, in _precall >self.__null_dist.fit(measure, ds) >File >"/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/clfs/stats.py", >line 427, in fit >% (measure, skipped)) >RuntimeError: Failed to obtain any value from . 1000 >measurements were skipped. Check above warnings, and your code/data > > >I was wondering if someone could kindly explain what are those mean, >and how do I resolve this? > >Thank you very much! >Carl > > >___ >Pkg-ExpPsy-PyMVPA mailing list >Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org> >http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > > > > > >___ >Pkg-ExpPsy-PyMVPA mailing list >Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org >http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa http://www.pymvpa.org/faq.html#is-there-an-easy-way-to-remove-invariant-features-from-a-dataset ;-) -- Sent from a phone which beats iPhone.___ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
Re: [pymvpa] ENET error
Hello, Thank you very much for your kindly response. Which function that I can remove them? Thanks again! Carl From: Pkg-ExpPsy-PyMVPA [mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu@lists.alioth.debian.org] On Behalf Of Richard Dinga Sent: Tuesday, September 20, 2016 3:50 AM To: Development and support of PyMVPA Subject: Re: [pymvpa] ENET error 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. On Fri, Sep 16, 2016 at 8:01 PM, Liang, Guangsheng mailto:guangsheng.li...@ttu.edu>> wrote: Hello PyMVPA community, I am currently working on a fMRI data applying an ENET classifier. My PyMVPA is running under Linux environment, with python 2.7.12. The design of the data is a repeated measurement with pre and post conditions. In my understanding, in my case, chunk value should store subject ID, target value should store the time conditions. I am using the classifier code that I found in the maillist: http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2009q1/000412.html clf = FeatureSelectionClassifier(\ ENET(lm=1.0,max_steps=500,trace=False,normalize=False),\ SensitivityBasedFeatureSelection(\ CorrStability(),\ FixedNElementTailSelector(5000,mode='select',tail='upper')),\ descr="ENET on 5K best(CorrStability) features") I am also using 1000 times of permutation to test the null hypothesis, which are almost the same as those in the tutorial: http://www.pymvpa.org/tutorial_significance.html#the-following-content-is-incomplete-and-experimental (section: Avoiding the trap OR Advanced magic 101) However, errors suspend my program: /lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value encountered in divide covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0)) /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 warnings.warn(x, RRuntimeWarning) Traceback (most recent call last): File "15subj_enet.py", line 68, in err_fds = cv_mc_corr_fds(fds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", line 136, in __call__ self._precall(ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/base.py", line 120, in _precall self.__null_dist.fit(measure, ds) File "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/clfs/stats.py", line 427, in fit % (measure, skipped)) RuntimeError: Failed to obtain any value from . 1000 measurements were skipped. Check above warnings, and your code/data I was wondering if someone could kindly explain what are those mean, and how do I resolve this? Thank you very much! Carl ___ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa ___ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
Re: [pymvpa] ENET error
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. On Fri, Sep 16, 2016 at 8:01 PM, Liang, Guangsheng wrote: > Hello PyMVPA community, > > > > I am currently working on a fMRI data applying an ENET classifier. > > My PyMVPA is running under Linux environment, with python 2.7.12. > > The design of the data is a repeated measurement with pre and post > conditions. > > In my understanding, in my case, chunk value should store subject ID, > target value should store the time conditions. > > I am using the classifier code that I found in the maillist: > http://lists.alioth.debian.org/pipermail/pkg-exppsy- > pymvpa/2009q1/000412.html > > > > clf = FeatureSelectionClassifier(\ > > ENET(lm=1.0,max_steps=500,trace=False,normalize=False),\ > > SensitivityBasedFeatureSelection(\ > > CorrStability(),\ > > FixedNElementTailSelector( > 5000,mode='select',tail='upper')),\ > > descr="ENET on 5K best(CorrStability) features") > > > > > > I am also using 1000 times of permutation to test the null hypothesis, > which are almost the same as those in the tutorial: http://www.pymvpa.org/ > tutorial_significance.html#the-following-content-is- > incomplete-and-experimental (section: Avoiding the trap OR Advanced magic > 101) > > > > However, errors suspend my program: > > > > /lustre/work/apps/anaconda/lib/python2.7/site-packages/ > mvpa2/measures/corrstability.py:94: RuntimeWarning: invalid value > encountered in divide > > covar = (dat1*dat2).mean(0) / (dat1.std(0) * dat2.std(0)) > > /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 > > > > warnings.warn(x, RRuntimeWarning) > > Traceback (most recent call last): > > File "15subj_enet.py", line 68, in > > err_fds = cv_mc_corr_fds(fds) > > File > "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", > line 258, in __call__ > > return super(Learner, self).__call__(ds) > > File > "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", > line 136, in __call__ > > self._precall(ds) > > File > "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/measures/base.py", > line 120, in _precall > > self.__null_dist.fit(measure, ds) > > File > "/lustre/work/apps/anaconda/lib/python2.7/site-packages/mvpa2/clfs/stats.py", > line 427, in fit > > % (measure, skipped)) > > RuntimeError: Failed to obtain any value from . 1000 > measurements were skipped. Check above warnings, and your code/data > > > > > > I was wondering if someone could kindly explain what are those mean, and > how do I resolve this? > > > > Thank you very much! > > Carl > > > > ___ > Pkg-ExpPsy-PyMVPA mailing list > Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > ___ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
