matplotlib-users Mailing List for matplotlib

Daniel,
I found that I came across this often, so I created three functions (one for sharing x, one for y, and one for both). In looking over them right now, there may be some inconsistencies between their style, but the idea is there. I am pasting them below in case they are useful to someone else. The original ideas came from figure.autofmt_xdate.
-Sterling
def autofmt_sharexy(fig=None):
 if fig==None:
 fig = gcf()
 for a in fig.axes:
 if a.is_first_col():
 if not a.is_first_row():
 a.get_yticklabels()[-1].set_visible(False)
 else:
 for yl in a.get_yticklabels():
 yl.set_visible(False)
 a.set_ylabel('')
 if not a.is_last_row():
 for xl in a.get_xticklabels():
 xl.set_visible(False)
 a.set_xlabel('')
 else:
 if not a.is_last_col():
 a.get_xticklabels()[-1].set_visible(False)
 subplots_adjust(hspace=0,wspace=0)
def autofmt_sharey(trim_xlabel=True,fig=None):
 if fig==None:
 fig = gcf()
 from matplotlib.ticker import MaxNLocator
 for a in fig.axes:
 if a.is_first_col():
 if not a.is_first_row():
 a.get_yticklabels()[-1].set_visible(False)
 else:
 for yl in a.get_yticklabels():
 yl.set_visible(False)
 a.set_ylabel('')
 if trim_xlabel:
 a.get_xticklabels()[0].set_visible(False)
 if not trim_xlabel:
 a.xaxis.set_major_locator(MaxNLocator(6))
 xtl = a.get_xticklabels()
 setp(xtl[0::2],visible=False)
 subplots_adjust(wspace=0)
def autofmt_sharex(fig=None):
 if fig==None:
 fig = gcf()
 nax=len(fig.get_axes())
 if nax==0: return
 try:
 nr=fig.axes[0].numRows
 nc=fig.axes[0].numCols
 except:
 print 'Unable to determine numRows,numCols'
 return
 def is_last_row(n):
 if n>nax-nc-1:
 return True
 else:
 return False
 for i,ax in enumerate(fig.axes):
 if not is_last_row(i):
 for xt in ax.get_xticklabels(): xt.set_visible(False)
 ax.set_xlabel('')
-Sterling
On Sep 13, 2012, at 1:23PM, Daniel Welling wrote:
> Greetings, all.
> 
> I have an issue: I have several axes stacked in a column with a common time vector on each x-axis. Each plot is a contour, so overplotting is not an option. In a perfect world, I want the following:
> 1) The subplots are tightly spaced such that with ax.grid() activated, the grid lines appear continuous. This makes comparing simultaneous characteristics between subplots very easy.
> 2) The subplots are linked via the "sharex" keyword so I can move them all in unison.
> 3) Only the bottommost subplot has x tick labels; on other plots, the long time-formatted labels stick out of the left and right of the plots.
> 
> Items 2 and 3 are contradictory: if I turn off tick labels (e.g. ax.set_xticklabels('')) on one axes, the others turn off as well, including the bottom axes. That is bad.
> Does anyone know of a good workaround for this?
> 
> Thanks for your help.
> 
> -dw
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
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________________________________
 From: Michael Droettboom <md...@st...>
To: mat...@li... 
Sent: Thursday, September 13, 2012 2:09 PM
Subject: Re: [Matplotlib-users] error installing basemap
 
You need to also install the python development package (python-dev), which contains the headers. 
Mike
________________________________
 From: Michael Rawlins <raw...@ya...>
To: Michael Droettboom <md...@st...>; 
"mat...@li..." 
<mat...@li...> 
Sent: Thursday, September 13, 2012 3:11 PM
Subject: Re: [Matplotlib-users] error installing basemap
ailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users
OK basemap installed. Thanks. But I'm getting an error running a script that worked with previous installation(s) of python, matplotlib, and basemap. The error:
user@comsys:~>python map2_TempDiff_4panels.py
Traceback (most recent call last):
 File "map2_TempDiff_4panels.py", line 27, in <module>
  from mpl_toolkits.basemap import NetCDFFile
ImportError: cannot import name NetCDFFile
I installed python-mpltoolkits.basemap from package manager, before testing my script.
MR
An update: My test script, which works with previously, now gets past the header initializations. Here they are:
import sys,getopt
from mpl_toolkits.basemap import Basemap, shiftgrid, cm 
#from mpl_toolkits.basemap import NetCDFFile
from Scientific.IO.NetCDF import NetCDFFile
from pylab import *
import matplotlib.pyplot as plt
Notr clear why the first import NetCDFFile statement does not work. Farther down the script, the code stops on this statement:
data.missing_value=-9.99
There error to standard output:
Traceback (most recent call last):
 File "map2_TempDiff_4panels.py", line 266, in <module>
  data.missing_value=-9.99
IOError: netcdf: write access to read-only file
 
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Hi Daniel,
2012年9月13日 Daniel Welling <dan...@gm...>
>
> Greetings, all.
>
> I have an issue: I have several axes stacked in a column with a common time vector on each x-axis. Each plot is a contour, so overplotting is not an option. In a perfect world, I want the following:
> 1) The subplots are tightly spaced such that with ax.grid() activated, the grid lines appear continuous. This makes comparing simultaneous characteristics between subplots very easy.
> 2) The subplots are linked via the "sharex" keyword so I can move them all in unison.
> 3) Only the bottommost subplot has x tick labels; on other plots, the long time-formatted labels stick out of the left and right of the plots.
>
> Items 2 and 3 are contradictory: if I turn off tick labels (e.g. ax.set_xticklabels('')) on one axes, the others turn off as well, including the bottom axes. That is bad.
> Does anyone know of a good workaround for this?
To obtain what you want you have to set the tick labels invisible is
the axes where you don't want them to show up.
>From http://matplotlib.org/examples/pylab_examples/shared_axis_demo.html:
setp( ax.get_xticklabels(), visible=False)
As the axis are shared, the ticklabels are also shared, so setting
them to "", erase them from all the axes.
I hope that this helps.
Cheers,
Francesco
>
> Thanks for your help.
>
> -dw
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Greetings, all.
I have an issue: I have several axes stacked in a column with a common time
vector on each x-axis. Each plot is a contour, so overplotting is not an
option. In a perfect world, I want the following:
1) The subplots are tightly spaced such that with ax.grid() activated, the
grid lines appear continuous. This makes comparing simultaneous
characteristics between subplots very easy.
2) The subplots are linked via the "sharex" keyword so I can move them all
in unison.
3) Only the bottommost subplot has x tick labels; on other plots, the long
time-formatted labels stick out of the left and right of the plots.
Items 2 and 3 are contradictory: if I turn off tick labels (e.g.
ax.set_xticklabels('')) on one axes, the others turn off as well, including
the bottom axes. That is bad.
Does anyone know of a good workaround for this?
Thanks for your help.
-dw

________________________________
 From: Michael Droettboom <md...@st...>
To: mat...@li... 
Sent: Thursday, September 13, 2012 2:09 PM
Subject: Re: [Matplotlib-users] error installing basemap
 
You need to also install the python development package (python-dev), which contains the headers. 
Mike
OK basemap installed. Thanks. But I'm getting an error running a script that worked with previous installation(s) of python, matplotlib, and basemap. The error:
user@comsys:~>python map2_TempDiff_4panels.py
Traceback (most recent call last):
 File "map2_TempDiff_4panels.py", line 27, in <module>
  from mpl_toolkits.basemap import NetCDFFile
ImportError: cannot import name NetCDFFile
I installed python-mpltoolkits.basemap from package manager, before testing my script.
MR
>
>
>------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>_______________________________________________
Matplotlib-users mailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users 
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users 

You need to also install the python development package (python-dev), 
which contains the headers.
Mike
On 09/13/2012 02:06 PM, Michael Rawlins wrote:
>
> Following instructions here:
>
> http://matplotlib.org/basemap/users/installing.html
>
> Got this error and termination after issuing python setup.py install 
> from the basemap directory.
>
> src/_proj.c:4:20: fatal error: Python.h: No such file or directory
> compilation terminated.
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv 
> -O2 -Wall -Wstrict-prototypes -fPIC -Isrc 
> -I/usr/lib/python2.7/dist-packages/numpy/core/include 
> -I/usr/include/python2.7 -c src/_proj.c -o 
> build/temp.linux-i686-2.7/src/_proj.o" failed with exit status 1
>
>
> I'm running a new installation of Ubuntu 12.04. I installed Python and 
> Matplotlib through package manager. Several examples tested fine. I 
> see no Python.h file on my system. Thanks in advance for suggestions.
>
> MR
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Following instructions here:
http://matplotlib.org/basemap/users/installing.html
Got this error and termination after issuing python setup.py install from the basemap directory.
src/_proj.c:4:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Isrc -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/_proj.c -o build/temp.linux-i686-2.7/src/_proj.o" failed with exit status 1
I'm running a new installation of Ubuntu 12.04. I installed Python and Matplotlib through package manager. Several examples tested fine. I see no Python.h file on my system. Thanks in advance for suggestions.
MR

Have you tried setting pdf.fonttype to "42", which will include the font 
verbatim rather than trying to subset it? That may help with 
illustrator. You may also have better luck importing an SVG into 
Illustrator.
Mike
On 09/13/2012 02:46 AM, florisvb wrote:
> I'm trying to get my pdf outputs from matplotlib to work properly in
> illustrator, but keep having the issue that illustrator does not recognize
> the computer modern fonts (eg. CMR10 etc). Everything else seems to work
> perfectly.
>
> I'm running matplotlib (1.1.1) in ubuntu precise, and illustrator (CS3) on
> my mac. I installed the fonts-cmu package on my ubuntu machine, and I have
> the cm fonts installed in illustrator (eg. cmr10 etc. as well as CMU Serif
> etc). I've been using the following options in matplotlib for pdf rendering,
> and haven't been able to make the fonts work in illustrator:
>
> backend: Agg (also tried pdf)
> usedistiller: xpdf
> font.family: serif
> font.serif: CMU Serif
> text.usetex: True
> text.latex.unicode: True (also tried the default)
>
> After some searching it seemed like I should try the Pgf backend project,
> which supports xelatex:
> https://github.com/pwuertz
>
> But after importing that pgf backend with:
>
> import matplotlib as mpl
> mpl.use("module://backend_pgf")
>
> then importing matplotlib.pyplot yields this error:
>
> from matplotlib.cbook import check_output
> ImportError: cannot import name check_output
>
> All I could find after search was that I needed python 2.7+... but I am
> using python 2.7.3.
>
> Any suggestions for how to get my matplotlib/pdf fonts to work properly in
> Illustrator would be much appreciated... via whatever method is easiest!
>
> Thanks,
>
> - Floris
>
>
>
>
>
>
>
> --
> View this message in context: http://matplotlib.1069221.n5.nabble.com/Font-compatibility-issue-with-Adobe-Illustrator-and-MPL-PDF-s-tp38904.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Can we use the markers as alternatives for linestyles?
Consider the following in sage:
Suppose I have defined f(x) for a range already, say by the following:
x = np.arange(0,1,0.001)
import matplotlib.pyplot as plt
plt.plot(x,f(x), color='magenta', linestyle='--', linewidth=4,
label="$f(x)$")
I want to know the equivalent syntax for '++' marker for the same plot of
f(x) against (x).
On Thu, Sep 13, 2012 at 1:02 AM, Damon McDougall
<dam...@gm...>wrote:
> On Wed, Sep 12, 2012 at 11:31 PM, Goutam Paul <gou...@ie...>
> wrote:
> > It seems that there are only five line-styles:
> >
> > "-" (solid) – default
> > "--" (dashed)
> > "-." (dash dot)
> > ":" (dotted)
> > "None" or " " or "" (nothing)
> >
> > What if I want to have more linestyles? Say, ++, **, xx, ~~, etc. Is it
> > possible to have user-defined linestyles? How?
> >
>
> User-defined line styles is difficult. There is an open github issue
> on this topic: https://github.com/matplotlib/matplotlib/issues/346
>
> Though, porting some of the existing markers over as linestyles would
> be a nice addition, I think.
>
> --
> Damon McDougall
> http://www.damon.is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>

Exactly, changing (0.5, 0.5) to something like (0.6, 0.5) has no effect in
my side.
My python version is: 2.7.2
and matplotlib: 1.1.0
So maybe is a version problem, but it's the work computer so I can't update
easily anything. I will try other computer.
Thank you all for your help,
Illa
2012年9月12日 Dale Chayes <dal...@he...>
> [replying only to the list -Dale]
>
> On Sep 12, 2012, at 07:02 , Jae-Joon Lee wrote:
>
> > Your code works as expected in my side.
>
> I wasn't quite sure what to expect, but based on Jae-Joon's note:
>
> > So, changing (0.5, 0.5) to something like (0.6, 0.5) has no effect in
> > your side?
>
> It seems to work on my installation. I actually changed to (0.3,0.5) which
> made a nice view.
>
> > Hmm, what is you matplotlib version?
>
> OS X 10.7.4 using python and tools from fink:
> i python27 1:2.7.3-1
> i python27-shlibs 1:2.7.3-1
> i matplotlib-basemap-py27 1.0.2-1
> i matplotlib-py27 1.1.1-1
> i numpy-py27 1.6.1-1
>
> Thanks to the folks who make this work,
> -Dale
>
>
> > Maybe this is a bug in old version of matplotlib.
> >
> > Regards,
> >
> > -JJ
> >
> >
> > On Wed, Sep 12, 2012 at 6:16 PM, darkside <in....@gm...>
> wrote:
> >> Thank you for your help.
> >>
> >> A simple example that doesn't work for me is:
> >> ----------------------------------------
> >> import pylab as p
> >> import numpy as np
> >> from mpl_toolkits.axes_grid.inset_locator import zoomed_inset_axes
> >> from mpl_toolkits.axes_grid.inset_locator import mark_inset
> >> from mpl_toolkits.axes_grid.anchored_artists import AnchoredSizeBar
> >> from matplotlib.ticker import MaxNLocator
> >>
> >> fig = p.figure(figsize=(12,8))
> >> ax = p.subplot(111)
> >>
> >> z = p.arange(0,1.415,0.01)
> >> d = z**2+np.random.random(len(z))
> >>
> >> ax.plot(z,d,'ro',label='text')
> >>
> >> p.xlabel('z',fontsize=18)
> >> p.ylabel('Luminosity distance',fontsize=18)
> >> p.grid(True)
> >>
> >> axins = zoomed_inset_axes(ax,
> >> 3,bbox_to_anchor=(0.5,0.5),bbox_transform=ax.figure.transFigure, loc=2)
> >>
> >>
> >> axins.plot(z,d,'r.')
> >>
> >> ax.legend(loc=2,bbox_to_anchor=(1,1))
> >>
> >> x,y = (0.86,1.3)
> >> x2,y2 = (1,1.7)
> >> axins.set_xlim(x,x2)
> >> axins.set_ylim(y,y2)
> >> axins.tick_params(axis='both',labelsize=12)
> >> axins.xaxis.set_major_locator(MaxNLocator(2))
> >> axins.yaxis.set_major_locator(MaxNLocator(3))
> >>
> >> mark_inset(ax,axins,loc1=1,loc2=3, fc="none", ec="0.5")
> >>
> >> p.draw()
> >> p.show()
> >> -----------------------------------------------------------
> >> The "bbox_to_anchor" label is supposed to move the zoomed axis, but it
> does
> >> nothing, no matter what two numbers I place there.
> >> I guess that I miss something, but I can't figure out what. I really
> >> appreciate your help.
> >>
> >> Best regards,
> >> Illa
> >>
> >>
> >>
> >> 2012年9月5日 Jae-Joon Lee <lee...@gm...>
> >>>
> >>> On Mon, Aug 20, 2012 at 10:50 PM, darkside <in....@gm...>
> >>> wrote:
> >>>> I am using zoomed_inset_axes, but the default position overlaps the
> >>>> yticks
> >>>> and the parent axe ticks, so I am trying:
> >>>> axins = zoomed_inset_axes(ax,
> >>>> 3,bbox_to_anchor(0.5,1),bbox_transform=ax.figure.transFigure, loc=2)
> >>>
> >>> This is supposed to work, and my quick test did work. Can you post a
> >>> complete but simple exampl?
> >>>
> >>> Regards,
> >>>
> >>> -JJ
> >>
> >>
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I'm trying to get my pdf outputs from matplotlib to work properly in
illustrator, but keep having the issue that illustrator does not recognize
the computer modern fonts (eg. CMR10 etc). Everything else seems to work
perfectly.
I'm running matplotlib (1.1.1) in ubuntu precise, and illustrator (CS3) on
my mac. I installed the fonts-cmu package on my ubuntu machine, and I have
the cm fonts installed in illustrator (eg. cmr10 etc. as well as CMU Serif
etc). I've been using the following options in matplotlib for pdf rendering,
and haven't been able to make the fonts work in illustrator:
backend: Agg (also tried pdf)
usedistiller: xpdf
font.family: serif
font.serif: CMU Serif
text.usetex: True
text.latex.unicode: True (also tried the default)
After some searching it seemed like I should try the Pgf backend project,
which supports xelatex:
https://github.com/pwuertz
But after importing that pgf backend with:
import matplotlib as mpl
mpl.use("module://backend_pgf")
then importing matplotlib.pyplot yields this error:
from matplotlib.cbook import check_output
ImportError: cannot import name check_output
All I could find after search was that I needed python 2.7+... but I am
using python 2.7.3.
Any suggestions for how to get my matplotlib/pdf fonts to work properly in
Illustrator would be much appreciated... via whatever method is easiest!
Thanks,
- Floris
--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Font-compatibility-issue-with-Adobe-Illustrator-and-MPL-PDF-s-tp38904.html
Sent from the matplotlib - users mailing list archive at Nabble.com.