Re: Import matplotlib in relax -- October 21, 2013

Hi Edward.

The errors I get is written below:

I don't know if it is a packaging error, or if it is related to relax?

But it seems weird, and I would just like to hear if you have the same error. :-)

Best

Troels

relax> import matplotlib.pyplot as plt

Traceback (most recent call last):

File "<console>", line 1, in <module>

File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 6, in <module>

from matplotlib.figure import Figure, figaspect

File "/usr/lib64/python2.6/site-packages/matplotlib/figure.py", line 18, in <module>

from axes import Axes, SubplotBase, subplot_class_factory

File "/usr/lib64/python2.6/site-packages/matplotlib/axes.py", line 17, in <module>

import matplotlib.dates as mdates

File "/usr/lib64/python2.6/site-packages/matplotlib/dates.py", line 104, in <module>

from dateutil.rrule import rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY, \

File "/usr/lib/python2.6/site-packages/dateutil/rrule.py", line 26, in <module>

MDAY366MASK = tuple(M31+M29+M31+M30+M31+M30+M31+M31+M30+M31+M30+M31+M31[:7])

TypeError: unsupported operand type(s) for +: 'xrange' and 'xrange'

relax>

########################3

[tlinnet@haddock ~]$ relax_disp -i

relax repository checkout rNone

None

Molecular dynamics by NMR data analysis

This is free software which you are welcome to modify and redistribute under the conditions of the

GNU General Public License (GPL). This program, including all modules, is licensed under the GPL

and comes with absolutely no warranty. For details type 'GPL' within the relax prompt.

Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within

the prompt.

Processor fabric: Uni-processor.

Hardware information:

Machine: x86_64

Processor: x86_64

Endianness: little

Total RAM size: 24013 Mb

Total swap size: 26191 Mb

Operating system information:

System: Linux

Release: 2.6.32-358.18.1.el6.x86_64

Version: #1 SMP Fri Aug 2 17:04:38 EDT 2013

GNU/Linux version: Red Hat Enterprise Linux Server 6.4 Santiago

Distribution: redhat 6.4 Santiago

Full platform string: Linux-2.6.32-358.18.1.el6.x86_64-x86_64-with-redhat-6.4-Santiago

Python information:

Architecture: 64bit ELF

Python version: 2.6.6

Python branch: tags/r266

Python build: r266:84292, May 27 2013 05:35:12

Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-3)

Libc version: glibc 2.2.5

Python implementation: CPython

Python revision: 84292

Python executable: /usr/bin/python

Python flags: sys.flags(debug=0, py3k_warning=0, division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)

Python float info: sys.floatinfo(max=1.7976931348623157e+308, max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16, radix=2, rounds=1)

Python module path: ['/sbinlab2/software/NMR-relax/relax_disp', '/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python', '/sbinlab2/tlinnet', '/sbinlab2/software/x64/haddock2.1', '/sbinlab2/software/x64/lib64/python2.6/site-packages', '/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/python', '/usr/lib64/python26.zip', '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages', '/usr/lib64/python2.6/site-packages/gst-0.10', '/usr/lib64/python2.6/site-packages/gtk-2.0', '/usr/lib64/python2.6/site-packages/webkit-1.0', '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode', '/usr/lib/python2.6/site-packages', '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info']

Python packages and modules (most are optional):

Name Installed Version Path

minfx True 1.0.5 /usr/lib/python2.6/site-packages/minfx

bmrblib True 1.0.3 /usr/lib/python2.6/site-packages/bmrblib

numpy True 1.4.1 /usr/lib64/python2.6/site-packages/numpy

scipy True 0.7.2 /usr/lib64/python2.6/site-packages/scipy

wxPython True 2.8.12.0 (gtk2-unicode) /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx

mpi4py True 1.3.1 /usr/lib64/python2.6/site-packages/mpi4py

epydoc False

optparse True 1.5.3 /usr/lib64/python2.6/optparse.pyc

readline True /usr/lib64/python2.6/lib-dynload/readline.so

profile True /usr/lib64/python2.6/profile.pyc

bz2 True /usr/lib64/python2.6/lib-dynload/bz2.so

gzip True /usr/lib64/python2.6/gzip.pyc

io True /usr/lib64/python2.6/io.pyc

xml True 0.8.4 (PyXML) /usr/lib64/python2.6/site-packages/_xmlplus/__init__.pyc

xml.dom.minidom True /usr/lib64/python2.6/site-packages/_xmlplus/dom/minidom.pyc

relax information:

Version: repository checkout

Processor fabric: Uni-processor.

relax C modules:

Module Compiled File type Path

target_functions.relax_fit True ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, not stripped /sbinlab2/software/NMR-relax/relax_disp/target_functions/relax_fit.so

##########################################

2013/10/18 Edward d'Auvergne <edward@xxxxxxxxxxxxx>

Hi Troels,

It should be possible to get your matplotlib plotting code into the
relax library, just as the Grace plotting code is. The Grace code is
at lib/software/grace.py. Maybe I should create a new package called
lib.plotting and shift the Grace module there? Then all the plotting
modules - grace, opendx, matplotlib, gnuplot, etc. - can sit together.
New user functions can be created by copying user_functions.grace and
pipe_control.grace to user_functions.matplotlib and
pipe_control.matplotlib. The pipe_control.matplotlib module simply
assembles the data from the relax data store and passes it into
lib.software.matplotlib for plotting.

As for the import error, could you copy and paste the full message?
This is not normal and it could have something to do with different
Python versions being used by relax and when you type 'python'. Could
you run 'relax -i' and check that the Python binaries are identical?
Cheers. It should be possible to have this running!

Regards,

Edward

On 18 October 2013 09:25, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi Edward.
>
> I am trying to plot some custom made graphs via matplotlib in relax.
>
> Basically, I extract the r2 values for each spin, and plot them.
>
> But I get a package error when I do
>
> import matplotlib.pyplot as plt
>
> It is a dateutil error? And I am not able to pinpoint the error.
>
> I have checked that I can do the import in my normal python installation.
>
> My current solution is to extract the wanted values from relax into a
> dictionary, and dump the dictionary in json format.
>
> Then make a normal python script, that reads the json dictionary, and plot
> the values.
>
> I would be interested to hear if you have the same problem importing
> matplotlib in relax, or if it is only my setup?
>
> Can this be fixed?
>
> Another solution could be to open a dumped relax saved state in a python
> section and run through the data.
> Is it possible to do this?
>
> Best
> Troels
>
>

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Re: Import matplotlib in relax

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