matplotlib-users Mailing List for matplotlib

On Tue, May 27, 2008 at 5:08 PM, John Hunter <jd...@gm...> wrote:
> On Tue, May 27, 2008 at 4:03 PM, C M <cmp...@gm...> wrote:
>
>> John, do you know why the times are coming out as 00:00:00 in your
>> example (and mine when I tried it), even though the actual times are
>> specified?
>
> Yes, these are the locations of the ticks, not the data points. The
> default tick locator tries to put the ticks on even days. If you want
> the ticks to be on the data points, you need to do:
>
> ax.set_xticks(dates)
>
> Also, please respons on list since you may not be the only one with
> the same question and I may not be the only one with the answer!
>
> JDH
Thank you, John, and I'm sorry, I thought I was replying on-list but I
guess I have my mail settings set up differently than I thought. I
always do intend to post to the list.

On Tue, May 27, 2008 at 4:03 PM, C M <cmp...@gm...> wrote:
> John, do you know why the times are coming out as 00:00:00 in your
> example (and mine when I tried it), even though the actual times are
> specified?
Yes, these are the locations of the ticks, not the data points. The
default tick locator tries to put the ticks on even days. If you want
the ticks to be on the data points, you need to do:
 ax.set_xticks(dates)
Also, please respons on list since you may not be the only one with
the same question and I may not be the only one with the answer!
JDH

Hi,
Here is what I get when using the verbose mode, since removing and 
installing over again Matplotlib didn't vhanged anything I suspect my 
LaTeX packages might be responsible,...
Thanks in advance for any help
$HOME=/home/fayette
CONFIGDIR=/home/fayette/.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', 'pylab', 
'datetime', 'matplotlib.tempfile', 'distutils.sysconfig', 
'encodings.encodings', '_numpy', 'xml', 'struct', 'tempfile', 
'xml.sax.urllib', 'pytz.os', 'matplotlib.matplotlib', 'string', 
'encodings.utf_8', 'matplotlib.__future__', 'pytz.tzinfo', 
'pytz.datetime', 'distutils.re', 'bisect', 'signal', 'Numeric', 'random', 
'xml.sax.xmlreader', 'matplotlib.pytz', 'ArrayPrinter', 'locale', 
'xml.sax.saxutils', 'encodings', 'umath', 'dateutil', 
'matplotlib.warnings', 'matplotlib.string', 'pytz.pytz', 'urllib', 
'matplotlib.sys', 're', 'new', 'math', 'numeric_version', 'fcntl', 
'UserDict', 'xml.sax.types', 'distutils.os', 'matplotlib', 'base', 
'codecs', 'paste', 'md5', '_locale', 'matplotlib.sre_constants', 
'matplotlib.os', 'thread', 'StringIO', 'weakref', 'itertools', 
'distutils.sys', 'os', 'marshal', '__future__', 'matplotlib.copy', 
'cStringIO', '_sre', '__builtin__', 'matplotlib.re', 'operator', 
'distutils.string', 'matplotlib.datetime', 'posixpath', 'errno', 
'_socket', 'binascii', 'Precision', 'sre_constants', 'matplotlib.md5', 
'types', 'pytz.sys', 'xml.sax.handler', 'xml.sax.os', 'matplotlib.xml', 
'multiarray', '_codecs', 'pytz', 'matplotlib.pyparsing', 'copy', 
'_struct', '_types', 'matplotlib.dateutil', 'hashlib', 'posix', 
'encodings.aliases', 'matplotlib.distutils', 'exceptions', 'sre_parse', 
'pytz.bisect', 'pickle', 'distutils.distutils', 'copy_reg', 'sre_compile', 
'xml.sax', '_hashlib', '_random', 'site', 'zipimport', '__main__', 
'shutil', 'matplotlib.weakref', 'strop', 'encodings.codecs', 'gettext', 
'matplotlib.rcsetup', 'pytz.sets', 'xml.sax._exceptions', 
'xml.sax.codecs', 'stat', '_ssl', 'warnings', 'encodings.types', 'sets', 
'sys', 'socket', 'xml.sax.sys', 'os.path', 'pytz.gettext', 
'matplotlib.fontconfig_pattern', '_weakref', 'distutils.errors', 
'urlparse', 'linecache', 'matplotlib.shutil', 'time']
numerix numpy 1.0.3.1
Using fontManager instance from 
/home/fayette/.matplotlib/fontManager.cache
backend GTKAgg version 2.12.0
==========================================================================================================
Matplotlib processing for : 
/home/fayette/LaTeX/ASCII_data_files/2008-04--Wp_vs_Wm_test12/SL4_64_200Mo_std/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.dat
 > Reading : 
/home/fayette/LaTeX/ASCII_data_files/2008-04--Wp_vs_Wm_test12/SL4_64_200Mo_std/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.dat
 > Drawing !
 > Saving : 
./eps_pdf/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.eps
Found dvipng version 1.5
 cd "/tmp" && latex -interaction=nonstopmode 
"/tmp/43f2d14607397712890028dfdf3f25ac.tex" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(/tmp/43f2d14607397712890028dfdf3f25ac.tex
LaTeX2e <2003年12月01日>
Babel <v3.8d> and hyphenation patterns for american, french, german, 
ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, 
esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, 
polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, 
swedish, tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/article.cls
Document Class: article 2004年02月16日 v1.4f Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
(/usr/share/texmf/tex/latex/type1cm/type1cm.sty)
(/usr/share/texmf/tex/latex/psnfss/helvet.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/psnfss/courier.sty)
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/geometry/geometry.sty
(/usr/share/texmf/tex/latex/geometry/geometry.cfg)
Package geometry Warning: Over-specification in `h'-direction.
 `width' (614.295pt) is ignored.
Package geometry Warning: Over-specification in `v'-direction.
 `height' (794.96999pt) is ignored.
) (/usr/share/texmf/tex/latex/psfrag/psfrag.sty
(/usr/share/texmf/tex/latex/graphics/graphics.sty
(/usr/share/texmf/tex/latex/graphics/trig.sty)
(/usr/share/texmf/tex/latex/graphics/graphics.cfg)
(/usr/share/texmf/tex/latex/graphics/dvips.def)))
(/usr/share/texmf/tex/latex/graphics/graphicx.sty)
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/graphics/color.cfg)
(/usr/share/texmf/tex/latex/graphics/dvipsnam.def))
No file 43f2d14607397712890028dfdf3f25ac.aux.
(/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/ot1pnc.fd)
<43f2d14607397712890028dfdf3f25ac.eps>
(/usr/share/texmf/tex/latex/psnfss/ot1phv.fd) [1]
(./43f2d14607397712890028dfdf3f25ac.aux) )
Output written on 43f2d14607397712890028dfdf3f25ac.dvi (1 page, 5996 
bytes).
Transcript written on 43f2d14607397712890028dfdf3f25ac.log.
 cd "/tmp" && dvips -q -R0 -o "43f2d14607397712890028dfdf3f25ac.ps" 
"43f2d14607397712890028dfdf3f25ac.dvi" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"
gs -dBATCH -dNOPAUSE -r6000 -sDEVICE=pswrite -sPAPERSIZE=letter 
-sOutputFile="/tmp/43f2d14607397712890028dfdf3f25ac.ps" 
"/tmp/43f2d14607397712890028dfdf3f25ac" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"
GPL Ghostscript 8.61 (2007年11月21日)
Copyright (C) 2007 Artifex Software, Inc. All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Loading NimbusSanL-Regu font from 
/usr/share/fonts/default/Type1/n019003l.pfb... 2703240 1112639 2569336 
1264022 1 done.
Loading CenturySchL-Roma font from 
/usr/share/fonts/default/Type1/c059013l.pfb... 2746924 1245014 2589432 
1296705 1 done.
gs -dBATCH -dNOPAUSE -sDEVICE=bbox "/tmp/43f2d14607397712890028dfdf3f25ac"
%%BoundingBox: 15 188 578 615
%%HiResBoundingBox: 15.986742 188.125799 577.219975 614.267981
	findfont found Bitstream Vera Sans, normal, normal 400, normal, 
15.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
	findfont found Bitstream Vera Sans, normal, normal 400, normal, 
20.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
On 2008年5月27日, John Hunter wrote:
> On Tue, May 27, 2008 at 2:50 AM, Florent Fayette <fa...@lp...> wrote:
> 
> > Maybe it comes from LaTeX, does Matplotlib rely on the LaTeX software or
> > does it own his own version someh text.usetex : Trueow hardcoded.
> 
> It does both. If text.usetex is False, we use our own fonts and
> text layout algorithms, which can look quite similar to latex because
> we ship some of the computer modern fonts. If text.usetex is True, we
> call out to latex and dvipng. If you post the output with the
> --verbose-debug flag set, we would know better what is going on on
> your system
> 
> > python simple_plot.py --verbose-debug > run.out
> 
> and post run.out.
> 
> JDH
> 
> 

On Tue, May 27, 2008 at 2:14 PM, Margherita Vittone wiersma
<vi...@fn...> wrote:
> id_list=[1,2,3,4,5,6]
> str_dates=['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
> '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']
>
> id_dates=datestr2num(str_dates)
>
> # It appears to ignore the formatting, it shows the month,day and year but not the time...
> formatter = DateFormatter('%m-%d-%y %H:%M:%S')
>
> ax = subplot(111)
> ax.plot_date(id_dates,id_list)
> ax.xaxis.set_major_formatter(dateFormatter)
"dateFormatter" is not defined -- I think you mean "formatter"
When I run this example with this change, I get tick labels with the
hour, minute and second as indicated...
Note recent versions of maptlotlib can takes dates explicitly (it will
handle the conversion for you). I would write this example as
(fig.autofmt_xdate will handle the ticklabel rotation for you)
import datetime
import dateutil.parser
import matplotlib.dates as mpldates
import matplotlib.pyplot as plt
ids = [1,2,3,4,5,6]
str_dates = ['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
 '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']
dates = [dateutil.parser.parse(s) for s in str_dates]
formatter = mpldates.DateFormatter('%m-%d-%y %H:%M:%S')
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(dates, ids, 'o')
ax.xaxis.set_major_formatter(formatter)
fig.autofmt_xdate()
ax.set_title("test dates")
plt.show()
JDH

Hi all,
I've been running into this one and tried compiling it a number of 
ways. Unfortunately the way it's fitting into our infrastructure, it's 
gotta be 64-bit. Here's the script:
#!/usr/bin/python/bin/python
from pylab import *
plot([1,2,3,4])
savefig('secondfig')
show()
I comment out the the "savefig" line and all works just fine.
The truss output I have is:
resolvepath("/usr/sfw/lib/libfreetype.so.6", 
"/usr/sfw/lib/libfreetype.so.6", 1023) = 29
open("/usr/sfw/lib/libfreetype.so.6", O_RDONLY) = 8
mmap(0xFFFFFFFF76500000, 32768, PROT_READ|PROT_EXEC, 
MAP_PRIVATE|MAP_FIXED, 8, 0) = 0xFFFFFFFF76500000
close(8) = 0
stat("/opt/SUNWspro/lib/rw7/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) 
Err#2 ENOENT
stat("/opt/SUNWspro/lib/sparcvis2/64/libfreetype.so.6", 
0xFFFFFFFF7FFF7A30) Err#2 ENOENT
stat("/opt/SUNWspro/lib/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
ENOENT
stat("/usr/ccs/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
ENOENT
stat("/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
stat("/usr/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
mmap(0x00000000, 8192, PROT_READ|PROT_WRITE|PROT_EXEC, 
MAP_PRIVATE|MAP_ANON, -1, 0) = 0xFFFFFFFF74700000
munmap(0xFFFFFFFF76500000, 32768) = 0
lseek(7, 0, SEEK_CUR) = 0
close(7) = 0
lseek(6, 0, SEEK_CUR) = 0
close(6) = 0
brk(0x101116C00) = 0
brk(0x10111AC00) = 0
brk(0x10111AC00) = 0
brk(0x10111EC00) = 0
Any ideas what my problem could be? I'm happy to provide any additional 
info as requested. Thanks
-Steve

Hello,
i am trying to plot information which will have on the x a timestamp imformation;
even if i specify the formatter i want(see code below) , it seems to be ingnored in the
labels, meaning, i don't see the time portion of it, just the date.
The code is very simple since i am just testing; thanks for suggestions in what 
i am doing wrong, best regards
Margherita
----------------------------------------------------------
from pylab import *
from pylab import figure, show, datestr2num, load
from matplotlib.dates import DateFormatter
import datetime
id_list=[1,2,3,4,5,6]
str_dates=['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
 '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']
id_dates=datestr2num(str_dates)
# It appears to ignore the formatting, it shows the month,day and year but not the time...
formatter = DateFormatter('%m-%d-%y %H:%M:%S')
ax = subplot(111)
ax.plot_date(id_dates,id_list)
ax.xaxis.set_major_formatter(dateFormatter)
labels = ax.get_xticklabels()
setp(labels, rotation=30, fontsize=8)
ax.set_title(" test dates")
show()
 
 

On Tue, May 27, 2008 at 2:50 AM, Florent Fayette <fa...@lp...> wrote:
> Maybe it comes from LaTeX, does Matplotlib rely on the LaTeX software or
> does it own his own version someh text.usetex : Trueow hardcoded.
It does both. If text.usetex is False, we use our own fonts and
text layout algorithms, which can look quite similar to latex because
we ship some of the computer modern fonts. If text.usetex is True, we
call out to latex and dvipng. If you post the output with the
--verbose-debug flag set, we would know better what is going on on
your system
> python simple_plot.py --verbose-debug > run.out
and post run.out.
JDH

I suspect this is another instance of this recently fixed bug:
http://sourceforge.net/tracker/index.php?func=detail&aid=1949982&group_id=80706&atid=560720
You can check out the SVN maintenance branch from here (which has this 
bugfix):
 svn co 
https://matplotlib.svn.sf.net/svnroot/matplotlib/branches/v0_91_maint 
matplotlib-0.91.x
Let us know how that works for you.
We should soon have a release fixing this bug.
Cheers,
Mike
telemeister wrote:
> Further to my original post...
> I forgot to note that I have specified Tkagg as the backend in the
> matplotlibrc file.
> I have Tkinter installed and it works OK in other apps independent of
> matplotlib.
>
>
> telemeister wrote:
> 
>> I've been using matplotlib successfully for some time on Win XP and think
>> it is great. I would like to use on my linux box (Slackware 12 +
>> python2.5)
>>
>> Either interactively, or in script, when the "show()" command is reached,
>> the plot seems to come up momentarily, but then vanishes and I get a
>> segmentation fault. This seems to be happen no matter what I am trying
>> to plot. It is always when it attempts to put the plot on the screen that
>> it fails.
>>
>> A possibly similar fault has been listed earlier in this forum:
>> http://www.nabble.com/segfault-with-TkAgg-and-any-GUI-in-2.5-td9700130.html#a9712842
>>
>> I have been working through some of the suggestions made in that case by
>> John Hunter:
>>
>> Firstly I did following:
>> rm -rf the site-packages/matplotlib and build subdirs and did a clean
>> install of matplotlib.
>>
>> I am upoading files with the outputs from the build and install. I can't
>> see any obvious errors in these but
>> perhaps someone can.
>>
>> http://www.nabble.com/file/p17470177/build.log build.log 
>> http://www.nabble.com/file/p17470177/install.log install.log 
>>
>> As suggested by John H. I Tried importing these packages individually,
>> with results as shown.
>>
>> import matplotlib._image (no problems)
>> import matplotlib._transforms (no problems)
>>
>> import matplotlib.backends._ns_backend_agg # for numpy (Failed: no
>> module named ns_backend_agg)
>>
>> (I'm using numpy)
>>
>> import matplotlib.backends._tkagg (no problems)
>> import matplotlib._agg (no problems)
>>
>>
>> Greatly appreciate any suggestions as to what I could try from here or
>> what other diagnostics I can provide.
>>
>> 
>
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

hello,
when histogramming a distribution in log scale, I have some empty bins, 
which drives the y axis to 1e-100 as a lower limit, completely squashing 
the histogram.... Bug or feature?
Johann
PS To be specific :
In [22]: entries, bins, patches = 
pl.hist(np.array(list1),bins=50,normed=1,log=True)
In [23]: entries
Out[23]:
array([ 1.18347753e+00, 4.10926113e-01, 2.53989507e-01,
 1.84039145e-01, 1.27510992e-01, 9.21486321e-02,
 7.45965117e-02, 5.08495253e-02, 4.23315845e-02,
 3.43298825e-02, 2.78768971e-02, 1.83264787e-02,
 1.62615233e-02, 1.23897320e-02, 1.26478515e-02,
 7.74358253e-03, 4.38803010e-03, 5.93674661e-03,
 3.61367185e-03, 4.38803010e-03, 2.58119418e-03,
 1.29059709e-03, 7.74358253e-04, 1.03247767e-03,
 1.54871651e-03, 2.32307476e-03, 5.16238835e-04,
 2.58119418e-04, 1.03247767e-03, 2.58119418e-04,
 5.16238835e-04, 0.00000000e+00, 2.58119418e-04,
 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
 2.58119418e-04, 2.58119418e-04, 2.58119418e-04,
 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
 0.00000000e+00, 2.58119418e-04])
In [24]: bins
Out[24]:
array([ 3.36150086e-09, 3.87417583e-01, 7.74835162e-01,
 1.16225274e+00, 1.54967032e+00, 1.93708790e+00,
 2.32450548e+00, 2.71192306e+00, 3.09934064e+00,
 3.48675822e+00, 3.87417580e+00, 4.26159338e+00,
 4.64901096e+00, 5.03642854e+00, 5.42384612e+00,
 5.81126370e+00, 6.19868128e+00, 6.58609885e+00,
 6.97351643e+00, 7.36093401e+00, 7.74835159e+00,
 8.13576917e+00, 8.52318675e+00, 8.91060433e+00,
 9.29802191e+00, 9.68543949e+00, 1.00728571e+01,
 1.04602746e+01, 1.08476922e+01, 1.12351098e+01,
 1.16225274e+01, 1.20099450e+01, 1.23973625e+01,
 1.27847801e+01, 1.31721977e+01, 1.35596153e+01,
 1.39470329e+01, 1.43344504e+01, 1.47218680e+01,
 1.51092856e+01, 1.54967032e+01, 1.58841208e+01,
 1.62715383e+01, 1.66589559e+01, 1.70463735e+01,
 1.74337911e+01, 1.78212087e+01, 1.82086262e+01,
 1.85960438e+01, 1.89834614e+01, 1.93708790e+01])

Hi,
Thanks for the help but I used the tricks you told me and it's not workign 
either, I removed matlpotlib and reinstalled it and I still have the same
different font. 
On the other hand on a different computer having the same distribution 
(fedora 8) BUT not up to date in the packages and things work just fine.
Maybe it comes from LaTeX, does Matplotlib rely on the LaTeX software or 
does it own his own version somehow hardcoded.
Thanks,
FF
On 2008年5月26日, John Hunter wrote:
> On Mon, May 26, 2008 at 8:32 AM, Florent Fayette <fa...@lp...> wrote:
> > Hello,
> >
> > I am using matplotlib under Fedora 8 and since an updaet I just realised
> > that the default font seems to be serif raher than the previously roman
> > font used in LaTeX, as some people observed it also ?
> >
> > How can I come back to the previous font using the simplest solution ?
> 
> I am not sure what font you used previously, but you can use the
> font.family setting in the matplotlibrc file (copy this file from
> site-packages/matplotlib/mpl-data/matplotlibrc you your home directory
> in the ~/.matplotlib directory and edit it. Eg.
> 
> font.family : sans-serif # for san serif
> 
> Since you mentioned latex, you can use latex to generate all the fonts
> in matplotlib by enabling usetex in matplotlibrc , provided you have
> latex and dvipng installed.
> 
> text.usetex : True
> 
> Finally, if you run your matplotlib test script with --verbose-debug
> you will get lots of extra information about what settings are used
> and what fonts are loaded.
> 
> JDH
> 
>