[Mne_analysis] python-MNE installation
raij at nmr.mgh.harvard.edu
raij at nmr.mgh.harvard.edu
Tue Sep 30 22:17:19 EDT 2014
Eric, thank you for the kind suggestion - this would seem to make sense as
some of the code I am seeing only works with Anaconda. The sole reason I
went with Canopy was because it is the only suggestion offered on the
MNE-python web pages
(http://martinos.org/mne/stable/getting_started.html).
Cheers, Tommi
> I personally have found Anaconda easier to work with than Canopy, too, if
> you want to try that.
>
> Eric
>
>
> On Tue, Sep 30, 2014 at 4:11 AM, Mainak Jas <mainakjas at gmail.com> wrote:
>
>> 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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>>
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