Re: [Matplotlib-users] Running matplotlib job with cron

[Eric Firing]

Paul Simon wrote:
I've written my first python script with matplotlib, which works fine at 
the command line but not with cron.  It's quite puzzling to me, and 
probably involves some path declaration that I don't know about.
 
#plot data from automate.csv
import matplotlib

Right here you should include:

matplotlib.use('Agg')

Without this, you are loading the interactive graphical backend, gtkagg. 
I don't know whether this is causing the problem with running under 
cron, but it is worth changing anyway.

I don't know why your debug output file is stopping after the first 
fontManager line.

What does your crontab file look like?  I think this is more a cron 
problem than an mpl problem.  Cron tends to run things in a very 
different environment than one has when running from the command line, 
and it is common--at least in my own experience--to have this sort of 
problem with things that work on the command line and not from cron.

Attached is a crontab file that we use in this manner.  Note that we set 
the shell to /bin/bash; otherwise cron will use the most minimal shell 
version.  Second, note that before executing the script, we execute a 
file that sets up the environment to be similar to what we have when 
logged in normally.  Third, the redirection of stdout and stderr to a 
log file facilitates debugging, allowing you to see the result of 
debugging print statements as well as any exceptions or other error 
messages.

Eric

import datetime
import numpy
from matplotlib import legend
from matplotlib.pyplot import figure, show, plot_date, setp, ylabel, 
savefig, xlabel
from matplotlib.dates import DayLocator, HourLocator, DateLocator, 
DateFormatter,drange, MinuteLocator, date2num, num2date
from matplotlib.mlab import csv2rec
from matplotlib.ticker import *
newr = csv2rec('/home/paulsimon/Documents/automate.csv')
x = date2num(newr.field(0))
fig = figure()
ax1 = fig.add_subplot(111)
line1, = ax1.plot_date(newr['dattim'], newr['bench_1'], '-r',label = 
'bench 1')
line2, = ax1.plot_date(newr['dattim'], newr['bench_2'], '-b', label = 
'bench 2')
line3, = ax1.plot_date(newr['dattim'], newr['eave'],'-k', label = 'eave')
line4, = ax1.plot_date(newr['dattim'], newr['outside'], '-g', label = 
'outside')
 
ylabel('temperature')
xlabel(r'time/date')
hours = HourLocator(range(0,26,4))
 
dateformatter = DateFormatter('%I:%M %p\n%m/%d/%y')
ax1.xaxis.set_major_formatter(dateformatter)
ax1.xaxis.set_major_locator(hours)
ax1.set_ylim(30,100)
# Rotate x labels
for label in ax1.xaxis.get_ticklabels():
    label.set_fontsize(8)
 
ax1.grid(True)
ax1.xaxis.grid(False)
yminorLocator = MultipleLocator(5)
ax1.yaxis.set_minor_locator(yminorLocator)
ax1.yaxis.grid(True,which='major', linestyle ='-')
ax1.yaxis.grid(True,which='minor',linestyle = ':')
leg = ax1.legend(('bench 1', 'bench 2', ' eave',  'outside'), 'lower 
right', shadow = True)
for t in leg.get_texts():
    t.set_fontsize('small')
   
savefig('/home/paulsimon/python_scripts/image.png', format = 'png')
 

Running with --debug option, here are the two different output files:
 
$HOME=/home/paulsimon
CONFIGDIR=/home/paulsimon/.matplotlib
matplotlib data path /usr/lib/python2.5/site-packages/matplotlib/mpl-data
loaded rc file 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 0.91.2
verbose.level debug
interactive is False
units is False
platform is linux2
loaded modules: ['_bisect', 'xml.sax.urlparse', 'distutils', 
'matplotlib.matplotlib', 'datetime', 'matplotlib.tempfile', 
'distutils.sysconfig', 'encodings.encodings', 'pytz.cStringIO', 'xml', 
'distutils.dep_util', 'struct', 'tempfile', 'xml.sax.urllib', 'imp', 
'_struct', 'pytz.os', 'zipimport', 'string', 'encodings.utf_8', 
'matplotlib.__future__', 'pytz.tzinfo', 'pytz.datetime', 'distutils.re', 
'bisect', 'signal', 'random', 'xml.sax.xmlreader', 'matplotlib.pytz', 
'distutils.log', 'pytz.tzfile', 'cStringIO', 'pkgutil', 'locale', 
'xml.sax.saxutils', 'encodings', 'dateutil', 'matplotlib.warnings', 
'matplotlib.string', 'pytz.pytz', 'urllib', 'matplotlib.sys', 're', 
'new', 'math', 'fcntl', 'UserDict', 'distutils.os', 'matplotlib', 
'codecs', 'md5', '_locale', 'matplotlib.sre_constants', 'matplotlib.os', 
'thread', 'pkg_resources', 'weakref', 'itertools', 'distutils.spawn', 
'distutils.sys', 'os', 'sre_parse', '__future__', 'matplotlib.copy', 
'xml.sax.types', '_sre', '__builtin__', 'matplotlib.re', 'operator', 
'distutils.util', 'distutils.string', 'matplotlib.datetime', 
'posixpath', 'errno', '_socket', 'binascii', 'sre_constants', 
'matplotlib.md5', 'types', 'pytz.sys', 'xml.sax.handler', 
'pytz.pkg_resources', 'xml.sax.os', 'matplotlib.xml', '_codecs', 'pytz', 
'matplotlib.pyparsing', 'copy', 'socket', '_types', 
'matplotlib.dateutil', 'hashlib', 'posix', 'encodings.aliases', 
'matplotlib.fontconfig_pattern', 'exceptions', 'xml.sax._exceptions', 
'pytz.bisect', 'distutils.distutils', 'copy_reg', 'sre_compile', 
'xml.sax', '_hashlib', '_random', 'pytz.struct', 'site', '__main__', 
'shutil', 'matplotlib.weakref', 'strop', 'encodings.codecs', 'gettext', 
'matplotlib.rcsetup', 'pytz.sets', 'xml.sax.codecs', 'stat', '_ssl', 
'warnings', 'encodings.types', 'sets', 'sys', 'xml.sax.sys', 'os.path', 
'pytz.gettext', 'matplotlib.distutils', '_weakref', 'distutils.errors', 
'urlparse', 'linecache', 'matplotlib.shutil', 'time']
Using fontManager instance from 
/home/paulsimon/.matplotlib/fontManager.cache
numerix numpy 1.0.4
backend GTKAgg version 2.12.1
 findfont found Bitstream Vera Sans, normal, normal 400, normal, 8.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
 findfont found Bitstream Vera Sans, normal, normal 400, normal, 8.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
 findfont found Bitstream Vera Sans, normal, normal 400, normal, 8.0
 
...
 

findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
 findfont found Bitstream Vera Sans, normal, normal 400, normal, 9.996
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
 
And this is the output file (complete) running under cron:
 
$HOME=/home/paulsimon
CONFIGDIR=/home/paulsimon/.matplotlib
matplotlib data path /usr/lib/python2.5/site-packages/matplotlib/mpl-data
loaded rc file 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 0.91.2
verbose.level debug
interactive is False
units is False
platform is linux2
loaded modules: ['_bisect', 'xml.sax.urlparse', 'distutils', 
'matplotlib.matplotlib', 'datetime', 'matplotlib.tempfile', 
'distutils.sysconfig', 'encodings.encodings', 'pytz.cStringIO', 'xml', 
'distutils.dep_util', 'struct', 'tempfile', 'xml.sax.urllib', 'imp', 
'_struct', 'pytz.os', 'zipimport', 'string', 'matplotlib.__future__', 
'pytz.tzinfo', 'pytz.datetime', 'distutils.re', 'bisect', 'signal', 
'random', 'xml.sax.xmlreader', 'matplotlib.pytz', 'distutils.log', 
'pytz.tzfile', 'cStringIO', 'pkgutil', 'locale', 'xml.sax.saxutils', 
'encodings', 'dateutil', 'matplotlib.warnings', 'matplotlib.string', 
'pytz.pytz', 'urllib', 'matplotlib.sys', 're', 'new', 'math', 'fcntl', 
'UserDict', 'distutils.os', 'matplotlib', 'codecs', 'md5', '_locale', 
'matplotlib.sre_constants', 'matplotlib.os', 'thread', 'pkg_resources', 
'weakref', 'itertools', 'distutils.spawn', 'distutils.sys', 'os', 
'sre_parse', '__future__', 'matplotlib.copy', 'xml.sax.types', '_sre', 
'__builtin__', 'matplotlib.re', 'operator', 'distutils.util', 
'distutils.string', 'matplotlib.datetime', 'posixpath', 'errno', 
'_socket', 'binascii', 'sre_constants', 'matplotlib.md5', 'types', 
'pytz.sys', 'xml.sax.handler', 'pytz.pkg_resources', 'xml.sax.os', 
'matplotlib.xml', '_codecs', 'pytz', 'matplotlib.pyparsing', 'copy', 
'socket', '_types', 'matplotlib.dateutil', 'hashlib', 'posix', 
'encodings.aliases', 'matplotlib.fontconfig_pattern', 'exceptions', 
'xml.sax._exceptions', 'pytz.bisect', 'distutils.distutils', 'copy_reg', 
'sre_compile', 'xml.sax', '_hashlib', '_random', 'pytz.struct', 'site', 
'__main__', 'shutil', 'matplotlib.weakref', 'strop', 'encodings.codecs', 
'gettext', 'matplotlib.rcsetup', 'pytz.sets', 'xml.sax.codecs', 'stat', 
'_ssl', 'warnings', 'encodings.types', 'encodings.ascii', 'sets', 'sys', 
'xml.sax.sys', 'os.path', 'pytz.gettext', 'matplotlib.distutils', 
'_weakref', 'distutils.errors', 'urlparse', 'linecache', 
'matplotlib.shutil', 'time']
numerix numpy 1.0.4
Using fontManager instance from 
/home/paulsimon/.matplotlib/fontManager.cache
 
The plot output took me a lot of time to work out, which I enjoyed, and 
the output is dazzling!
 
Paul Simon
 
 


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