[Mne_analysis] python-MNE installation
Mainak Jas
mainakjas at gmail.com
Tue Sep 30 07:11:14 EDT 2014
Hi Tommi,
Can you verify that you are actually on bash and not on tcsh or some other
shell when you try the pip command? I think canopy works only on bash.
Mainak
On Tue, Sep 30, 2014 at 2:02 PM, Tommi Raij <raij at nmr.mgh.harvard.edu>
wrote:
> Hi Alex,
>
> Thank you, will try. However, as far as I could tell, Canopy does not
> include pip (following full Canopy installation, attempts to give pip
> commands just resulted in "command not found" errors until I used the yum
> command below). Then, the question becomes, how to properly install pip for
> Canopy?
>
> Best regards,
>
> Tommi
> ------------------------------
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Sent: 9/30/2014 2:13 AM
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Subject: Re: [Mne_analysis] python-MNE installation
>
> hi Tommi,
>
> the problem is that you have 2 python systems installed:
> - the system one that uses yum for installs + updates
> - canopy
>
> when you did "yum install -y python-pip" you installed pip
> for the system and not for canopy. I suspect canopy already
> comes with pip installed.
>
> I recommend you uninstall pip with yum and any other python
> packages you installed with yum and then make sure you use canopy.
>
> to check this use:
>
> which python
>
> it should point to the canopy folder. If it's the case do the same with pip
>
> which pip
>
> if it points to canopy then you can safely do:
>
> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>
> let us know how it goes.
>
> Alex
>
>
>
>
> On Mon, Sep 29, 2014 at 11:50 PM, <raij at nmr.mgh.harvard.edu> wrote:
> >
> > Hi,
> >
> > New python (and longtime MNE) user here, hello to all.
> >
> > I am having trouble installing MNE-python on a linux box outside Martinos
> > Center. The machine (Dell Precision T7500)) runs CentOS 6.5 and has
> > Freesurfer (5.3), MNE suite (developmental), and MATLAB installed - these
> > are running no prob.
> >
> > I am doing installation as root on a csh terminal.
> >
> > I have tried to follow the instructions at
> > http://martinos.org/mne/stable/getting_started.html as follows:
> >
> > 1. Install Canopy python. When launcing for the first time, I set up the
> > environment to point to /usr/pubsw/packages/python/, then make Canopy as
> > the default python. Version: canopy-1.4.1-full-rh5-64.sh
> >
> > 2. Install pip (this did not exist on my system):
> > yum install -y python-pip
> >
> > 3. Install developmental MNE-python suite
> > pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
> >
> > Then I open a new csh terminal as a regular user, and
> > 4. Add the following line to my user-level ~/.cshrc:
> > setenv PATH /usr/pubsw/packages/python/User/bin:${PATH}
> >
> > Next, I launch a fresh csh terminal, and launch ipython. This appears (?)
> > to work OK:
> >
> > tmsh:raij[55] ipython
> >
> > Python 2.7.6 | 64-bit | (default, Jun 4 2014, 16:32:15)
> > Type "copyright", "credits" or "license" for more information.
> >
> > IPython 2.1.0 -- An enhanced Interactive Python.
> > ? -> Introduction and overview of IPython's features.
> > %quickref -> Quick reference.
> > help -> Python's own help system.
> > object? -> Details about 'object', use 'object??' for extra details.
> >
> > In [1]:
> >
> >
> >
> >
> > However, trying to follow the instructions:
> >
> > ipython --pylab qt
> >
> > produces a long list of errors suggesting that matplotlib (that I did not
> > see mentioned in the MNE-python guide - is it needed and how is it best
> > installed to avoid breaking dependencies?) may not be installed.
> >
> > Moreover, regardless of if I launch ipython alone or with --pylab qt,
> > trying to "import mne" gives the error "No module named mne". See the end
> > of message for the full error list.
> >
> > Any suggestions would be much appreciated!
> >
> > Best regards,
> >
> > Tommi
> >
> >
> > ---
> > Tommi Raij, MD, PhD
> > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> > Bldg 149, 13th St
> > Charlestown, MA 02129
> > U.S.A.
> >
> >
> > ERROR OUTPUT FOR
> >
> > ipython --pylab qt (from a csh terminal)
> >
> > Python 2.7.6 | 64-bit | (default, Jun 4 2014, 16:32:15)
> > Type "copyright", "credits" or "license" for more information.
> >
> > IPython 2.1.0 -- An enhanced Interactive Python.
> > ? -> Introduction and overview of IPython's features.
> > %quickref -> Quick reference.
> > help -> Python's own help system.
> > object? -> Details about 'object', use 'object??' for extra details.
> > [TerminalIPythonApp] WARNING | Eventloop or matplotlib integration
> failed.
> > Is matplotlib installed?
> >
> ---------------------------------------------------------------------------
> > ImportError Traceback (most recent call
> last)
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/shellapp.pyc
> > in <lambda>(key)
> > 231 shell = self.shell
> > 232 if self.pylab:
> > --> 233 enable = lambda key: shell.enable_pylab(key,
> > import_all=self.pylab_import_all)
> > 234 key = self.pylab
> > 235 elif self.matplotlib:
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
> > in enable_pylab(self, gui, import_all, welcome_message)
> > 2980 from IPython.core.pylabtools import import_pylab
> > 2981
> > -> 2982 gui, backend = self.enable_matplotlib(gui)
> > 2983
> > 2984 # We want to prevent the loading of pylab to pollute the
> > user's
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
> > in enable_matplotlib(self, gui)
> > 2941 gui, backend =
> > pt.find_gui_and_backend(self.pylab_gui_select)
> > 2942
> > -> 2943 pt.activate_matplotlib(backend)
> > 2944 pt.configure_inline_support(self, backend)
> > 2945
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/pylabtools.pyc
> > in activate_matplotlib(backend)
> > 285 matplotlib.rcParams['backend'] = backend
> > 286
> > --> 287 import matplotlib.pyplot
> > 288 matplotlib.pyplot.switch_backend(backend)
> > 289
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/pyplot.py
> > in <module>()
> > 22
> > 23 import matplotlib
> > ---> 24 import matplotlib.colorbar
> > 25 from matplotlib import _pylab_helpers, interactive
> > 26 from matplotlib.cbook import dedent, silent_list, is_string_like,
> > is_numlike
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/colorbar.py
> > in <module>()
> > 27 import matplotlib.artist as martist
> > 28 import matplotlib.cbook as cbook
> > ---> 29 import matplotlib.collections as collections
> > 30 import matplotlib.colors as colors
> > 31 import matplotlib.contour as contour
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/collections.py
> > in <module>()
> > 21 import matplotlib.artist as artist
> > 22 from matplotlib.artist import allow_rasterization
> > ---> 23 import matplotlib.backend_bases as backend_bases
> > 24 import matplotlib.path as mpath
> > 25 from matplotlib import _path
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/backend_bases.py
> > in <module>()
> > 48
> > 49 import matplotlib.tight_bbox as tight_bbox
> > ---> 50 import matplotlib.textpath as textpath
> > 51 from matplotlib.path import Path
> > 52 from matplotlib.cbook import mplDeprecation
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/textpath.py
> > in <module>()
> > 9 from matplotlib.path import Path
> > 10 from matplotlib import rcParams
> > ---> 11 import matplotlib.font_manager as font_manager
> > 12 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT,
> > LOAD_NO_HINTING
> > 13 from matplotlib.ft2font import LOAD_TARGET_LIGHT
> >
> >
> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/font_manager.py
> > in <module>()
> > 51 import matplotlib
> > 52 from matplotlib import afm
> > ---> 53 from matplotlib import ft2font
> > 54 from matplotlib import rcParams, get_cachedir
> > 55 from matplotlib.cbook import is_string_like
> >
> > ImportError: libpng16.so.16: cannot open shared object file: No such file
> > or directory
> >
> >
> >
> > Inside python, the attempt to import MNE gives this error:
> >
> > In [1]: import mne
> >
> ---------------------------------------------------------------------------
> > ImportError Traceback (most recent call
> last)
> > <ipython-input-1-39fc8b1a8697> in <module>()
> > ----> 1 import mne
> >
> > ImportError: No module named mne
> >
> > In [2]:
> >
> >
> > _______________________________________________
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