matplotlib-users Mailing List for matplotlib (Page 7)

All,

John Hunter, lead author of matplotlib, has been awarded PSF's
Distinguished Service Award.

For details, see
http://pyfound.blogspot.co.uk/2012/09/announcing-2012-distinctive-service.html

Some of you may have already seen this. For those who haven't, it serves as
a poignant reminder to the immense effort of John and the matplotlib
developers over the past decade.

Best,
Damon


-- 
Damon McDougall
http://www.damon.is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Thanks for raising this. I have simplified and opened an issue for the bug (
https://github.com/matplotlib/matplotlib/issues/1246) and will be looking
at this asap.

All the best,

Phil

________________________________
 From: Jeff Whitaker <js...@fa...>
To: mat...@li... 
Cc: raw...@ya... 
Sent: Thursday, September 13, 2012 9:44 PM
Subject: Re: [Matplotlib-users] error installing basemap
 


Michael:  The NetCDFFile function was deprecated a few releases back, and recently removed.  If you have netcdf4-python installed you can do

from netCDF4 import Dataset as NetCDFFile

and the script should work as before.

Regarding the second error, you must open the file for write access
    (mode='w') if you want to add attributes to the data variables.

-Jeff



From: Michael Rawlins <raw...@ya...>
To: Jeff Whitaker <js...@fa...>; 
"mat...@li..." 
<mat...@li...> 
Sent: Thursday, September 13, 2012 10:28 PM
Subject: Re: [Matplotlib-users] error installing basemap

Making some progress. Following here:

http://code.google.com/p/netcdf4-python/wiki/UbuntuInstall

I've installed HDF5 after installing build-essential package. With just gcc installed I got an error.

The ./configure in netcdf4 directory failed, but completed with --disable-netcdf-4. I went ahead anyway hoping I don't need netCDF-4 formats or the additional netCDF-4 functions. Besides that issue, what's also not clear is where is setup.py file for the last step. It is not in the netcdf directory after the make install finished.  I assume netcdf-python package will not conflict with the python-netcdf and netcdf versions installed through package manager.  

Mike




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I get an error when trying to use axvline in a gridspec subplot when the Y axis is set to log scale in matplotlib 1.3.x (and I think recent 1.2.x versions) from github under python 2.7.3 and OS X 10.8.1.  This worked with matplotlib versions from github earlier this year.  Here is a simple code snippet to reproduce the problem, and the error that is generated.  The vertical line is drawn in the vsw sublot if I comment out the dens.axvline line.  The problem seems to be caused by the log scale in the dens subplot.

Any help is appreciated,
Scott

---------------------------------------------------------------------------
import matplotlib as mpl
import matplotlib.dates
import matplotlib.pyplot as plt
import numpy as np
import datetime as dt

starttime = dt.datetime(2012,9,12,20,15)
stoptime = starttime + dt.timedelta(hours=1)
fig = plt.figure(1,figsize=(480.0/72.0, 620.0/72.0), dpi=72)
gs = mpl.gridspec.GridSpec(4, 1, height_ratios=[1.,1.,1.,.67], top=.95, bottom=0.10, left=0.12, hspace=0.12)
vsw = plt.subplot(gs[0], label="vsw", autoscale_on=True, xlim=[starttime, stoptime])
vsw.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
dens = plt.subplot(gs[1], label="dens", autoscale_on=True, xlim=[starttime, stoptime], yscale='log')
dens.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
vsw.axvline(dt.datetime(2012,9,12,20,30))
dens.axvline(dt.datetime(2012,9,12,20,30))
plt.show()

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-36-781867aaf919> in <module>()
     15 dens.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
     16 vsw.axvline(dt.datetime(2012,9,12,20,30))
---> 17 dens.axvline(dt.datetime(2012,9,12,20,30))
     18 plt.show()

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in axvline(self, x, ymin, ymax, **kwargs)
   3571             self.transData, self.transAxes)
   3572         l = mlines.Line2D([x,x], [ymin,ymax] , transform=trans, **kwargs)
-> 3573         self.add_line(l)
   3574         self.autoscale_view(scalex=scalex, scaley=False)
   3575         return l

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in add_line(self, line)
   1504             line.set_clip_path(self.patch)
   1505 
-> 1506         self._update_line_limits(line)
   1507         if not line.get_label():
   1508             line.set_label('_line%d' % len(self.lines))

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in _update_line_limits(self, line)
   1525             # identify the transform to go from line's coordinates
   1526             # to data coordinates
-> 1527             trans_to_data = line_trans - self.transData
   1528 
   1529             # if transData is affine we can use the cached non-affine component

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/transforms.pyc in __sub__(self, other)
   1204             return self + other.inverted()
   1205         else:
-> 1206             raise ValueError('It is not possible to compute transA - transB '
   1207                              'since transB cannot be inverted and there is no '
   1208                              'shortcut possible.')

ValueError: It is not possible to compute transA - transB since transB cannot be inverted and there is no shortcut possible.

________________________________
 From: Jeff Whitaker <js...@fa...>
To: mat...@li... 
Cc: raw...@ya... 
Sent: Thursday, September 13, 2012 9:44 PM
Subject: Re: [Matplotlib-users] error installing basemap
 

On 9/13/12 2:34 PM, Michael Rawlins wrote:


>
>
>
>
>________________________________
> 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
>
>
Michael:  The NetCDFFile function was deprecated a few releases
    back, and recently removed.  If you have netcdf4-python installed
    you can do

from netCDF4 import Dataset as NetCDFFile

and the script should work as before.

Regarding the second error, you must open the file for write access
    (mode='w') if you want to add attributes to the data variables.

-Jeff


Jeff,

No I don't have netCDF4 installed. It's not in the package manager. Wasn't sure if there would be a conflict with python-netcdf that's installed. Guess that's the reverse interface. Now I'm having some trouble compiling netcdf4-python from sources following:

http://code.google.com/p/netcdf4-python/wiki/UbuntuInstall

The configure ended in error:

checking whether the C compiler works... no
configure: error: in `/home/rawlins/Downloads/netcdf-4.2.1.1':
configure: error: C compiler cannot create executables
  

Mike

On 9/13/12 2:34 PM, Michael Rawlins wrote:
>
>
> ------------------------------------------------------------------------
> *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... 
> <mailto: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 
> <http://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
>

Michael:  The NetCDFFile function was deprecated a few releases back, 
and recently removed.  If you have netcdf4-python installed you can do

from netCDF4 import Dataset as NetCDFFile

and the script should work as before.

Regarding the second error, you must open the file for write access 
(mode='w') if you want to add attributes to the data variables.

-Jeff

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 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

________________________________
 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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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/
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Hi Daniel,

2012/9/13 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 

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Mat...@li...
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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


2012/9/12 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
> >>
> >>
> >>
> >> 2012/9/5 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.

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

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?

OK, a little bit more of manual reading I got the "drag point"
working.  Now, even though it works, I would like the opinion of
someone with more experience on event handling to improve that.

Thanks, Filipe

On Wed, Sep 12, 2012 at 6:14 PM, Filipe Pires Alvarenga Fernandes
<oc...@gm...> wrote:
> After some modifications and manual reading I got "insert" point and
> "delete" point working, but I still cannot make the "drag" point
> work...
>
> -Filipe
>
>
> On Wed, Sep 12, 2012 at 4:04 PM, Filipe Pires Alvarenga Fernandes
> <oc...@gm...> wrote:
>> Hi all,
>>
>> I am trying to create a class to edit the points of a plot based on
>> the poly_editor.py example.  However, I have very little experience
>> with even handling and I need some help.
>>
>> Here is what I did so far, the "toggle" on/off works fine.  Also I
>> believe that actions "press", "release", "insert", "delete" are OK.
>> However, I am stuck at the drawing part of the problem.
>>
>> if anyone have an example of that to share or it you want to check
>> what I made so far:
>>
>> http://dl.dropbox.com/u/4411725/point_editor.py
>>
>> Thanks, Filipe.

After some modifications and manual reading I got "insert" point and
"delete" point working, but I still cannot make the "drag" point
work...

-Filipe


On Wed, Sep 12, 2012 at 4:04 PM, Filipe Pires Alvarenga Fernandes
<oc...@gm...> wrote:
> Hi all,
>
> I am trying to create a class to edit the points of a plot based on
> the poly_editor.py example.  However, I have very little experience
> with even handling and I need some help.
>
> Here is what I did so far, the "toggle" on/off works fine.  Also I
> believe that actions "press", "release", "insert", "delete" are OK.
> However, I am stuck at the drawing part of the problem.
>
> if anyone have an example of that to share or it you want to check
> what I made so far:
>
> http://dl.dropbox.com/u/4411725/point_editor.py
>
> Thanks, Filipe.

Hi all,

I am trying to create a class to edit the points of a plot based on
the poly_editor.py example.  However, I have very little experience
with even handling and I need some help.

Here is what I did so far, the "toggle" on/off works fine.  Also I
believe that actions "press", "release", "insert", "delete" are OK.
However, I am stuck at the drawing part of the problem.

if anyone have an example of that to share or it you want to check
what I made so far:

http://dl.dropbox.com/u/4411725/point_editor.py

Thanks, Filipe.

On Wed, Sep 12, 2012 at 5:57 PM, Aronne Merrelli
<aro...@gm...> wrote:
> On Tue, Sep 11, 2012 at 10:49 AM, Damon McDougall
> <dam...@gm...> wrote:
>> On Tue, Sep 11, 2012 at 3:34 PM, Neal Becker <ndb...@gm...> wrote:
>>> OK, I've attached my sanitized example
>>>
>>
>> ImportError: No module named pandas.
>>
>> Can you provide an example that doesn't depend on pandas?
>>
>
> I was playing with this example to remove the pandas stuff, and It
> looks a lot like the check for the best legend location is just not
> accounting correctly for the multiple legend entries in this case.
> Here is an even more minimal example, that I think reproduces the same
> problem as Neal's original example.
>
> colors = ['b','g','r']
> for n in range(3):
>     plt.scatter([n,],[n,],color=colors[n])
> plt.legend(['foo','foo','foo'],loc='best')
>
>
> Note that if you just put one legend name in there, the location is
> perfectly fine, it is just as it extends downward for the second and
> third names, that it covers over the point.
>
> FYI: Im using v1.1.0 mpl, in EPD 7.2.
>
> HTH,
> Aronne
>

Aronne, thanks for taking the time to produce a nice example. I can
now recreate the problem. I'm not sure how invasive it will be to fix
this, so it possibly won't make it in for version 1.2, but possibly a
bugfix release after the fact.

For anyone who's interested, here's the github issue:
https://github.com/matplotlib/matplotlib/issues/1235

-- 
Damon McDougall
http://www.damon.is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

On Tue, Sep 11, 2012 at 10:49 AM, Damon McDougall
<dam...@gm...> wrote:
> On Tue, Sep 11, 2012 at 3:34 PM, Neal Becker <ndb...@gm...> wrote:
>> OK, I've attached my sanitized example
>>
>
> ImportError: No module named pandas.
>
> Can you provide an example that doesn't depend on pandas?
>

I was playing with this example to remove the pandas stuff, and It
looks a lot like the check for the best legend location is just not
accounting correctly for the multiple legend entries in this case.
Here is an even more minimal example, that I think reproduces the same
problem as Neal's original example.

colors = ['b','g','r']
for n in range(3):
    plt.scatter([n,],[n,],color=colors[n])
plt.legend(['foo','foo','foo'],loc='best')


Note that if you just put one legend name in there, the location is
perfectly fine, it is just as it extends downward for the second and
third names, that it covers over the point.

FYI: Im using v1.1.0 mpl, in EPD 7.2.

HTH,
Aronne

 

Happiness - Upgrading numpy to v 1.6.2 - I had been using 1.6.0b - seems
to have fixed things - my app's memory usage is now flat.

 

Dominic

 

________________________________

From: Barraclough, Dominic (ext. 414) [mailto:dj...@qv...] 
Sent: Tuesday, September 11, 2012 4:28 PM
To: mat...@li...
Subject: [Matplotlib-users] a memory leak in matplotlib plot embedded
inwxpython

 

 

I'm using matplotlib plots embedded in a wxpython application to display
a stream of data. The application works effectively but I have noticed
that memory usage rises substantially over time (if left long enough the
process can go from 50MB to near 1GB of RAM). After some
experimentation, I have tracked the problem down to the canvas.draw()
call needed to refresh my matplotlib plos. Thinking that the problem may
be due to how I coded up my plots I looked to see if the problem was
present in the examples given at

 

http://matplotlib.sourceforge.net/examples/user_interfaces

 

and found that the problem seem to be present in some the examples
posted there if I added a timer to cause the canvas draw to be
repeatedly performed. 

 

 

The example below is based on  

 

http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_
wx2.html

 

and has been instrumented to report memory usage when running in
Windows. My tests indicate that working set memory rises by 11 to 12
Kbytes at each plot. 

 

Some what to my surprise, I found the same issue when I ran an even
simpler version on a linux mint virtual box running on my win7 system.
(I have not explored this much so somebody else might want to test
things on a non virtual linux box)  I assume this implies that python is
probably keeping something alive that was expected to be automatically
cleaned up at each draw. I have made some effort to localize the problem
further but right now I don't have the necessary  time to get heavily
into the inner workings of matplotlib or wxpython 

 

Has any body else seen this problem before, and if so, has any body a
work around that allows rapid replotting - I would guess that I could
periodically flush the figure and re build my plots but this would cause
periodic glitches in plotting? 

 

 

Dominic

 

 

System details

 

Win7 ultimate service pack1

Python 2.6.6 (but I've seen the problem with python2.5 and 2.7)

Matplotlib 1.1.1 (but also in earlier versions)

Wxpython 2.9.4.0 msw (classic) (put also on 2.8.12.0 unicode)

 

 

Example 

------------------------------------------------------------------------
-----------------------------------------------------------

import wxversion

wxversion.ensureMinimal('2.8')

 

from numpy import arange, sin, pi

 

import matplotlib

 

# uncomment the following to use wx rather than wxagg

#matplotlib.use('WX')

#from matplotlib.backends.backend_wx import FigureCanvasWx as
FigureCanvas

 

# comment out the following to use wx rather than wxagg

matplotlib.use('WXAgg')

from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as
FigureCanvas

 

from matplotlib.backends.backend_wx import NavigationToolbar2Wx

 

from matplotlib.figure import Figure

import win32process

import wx

 

class CanvasFrame(wx.Frame):

 

    def __init__(self):

        wx.Frame.__init__(self,None,-1,

                         'CanvasFrame',size=(550,350))

 

        #self.SetBackgroundColour(wx.NamedColor("WHITE")) # 2.9 does not
like

 

        self.figure = Figure()

        self.axes = self.figure.add_subplot(111)

        t = arange(0.0,3.0,0.01)

        s = sin(2*pi*t)

 

        self.axes.plot(t,s)

        self.canvas = FigureCanvas(self, -1, self.figure)

 

        self.sizer = wx.BoxSizer(wx.VERTICAL)

        self.sizer.Add(self.canvas, 1, wx.LEFT | wx.TOP | wx.GROW)

        self.SetSizer(self.sizer)

        self.Fit()

 

        self.add_toolbar()  # comment this out for no toolbar

        self.timer = wx.Timer(self, -1)

        

        self.Bind(wx.EVT_TIMER, self.OnUpdate)

        self.delay = 200

        self.timer.Start(self.delay, oneShot = False)

        self.proc_id = win32process.GetCurrentProcess()

        adict = win32process.GetProcessMemoryInfo(self.proc_id)

        self.memory_old = adict["WorkingSetSize"]

        self.i = 0

        

    def add_toolbar(self):

        self.toolbar = NavigationToolbar2Wx(self.canvas)

        self.toolbar.Realize()

        if wx.Platform == '__WXMAC__':

            # Mac platform (OSX 10.3, MacPython) does not seem to cope
with

            # having a toolbar in a sizer. This work-around gets the
buttons

            # back, but at the expense of having the toolbar at the top

            self.SetToolBar(self.toolbar)

        else:

            # On Windows platform, default window size is incorrect, so
set

            # toolbar width to figure width.

            tw, th = self.toolbar.GetSizeTuple()

            fw, fh = self.canvas.GetSizeTuple()

            # By adding toolbar in sizer, we are able to put it at the
bottom

            # of the frame - so appearance is closer to GTK version.

            # As noted above, doesn't work for Mac.

            self.toolbar.SetSize(wx.Size(fw, th))

            self.sizer.Add(self.toolbar, 0, wx.LEFT | wx.EXPAND)

        # update the axes menu on the toolbar

        self.toolbar.update()

 

 

    def OnUpdate(self, evt):

        self.OnPaint( evt)

        self.i +=1

        the_count =25

        if self.i %the_count ==0:            

            adict_now = win32process.GetProcessMemoryInfo(self.proc_id)

            memory_now = adict_now["WorkingSetSize"]

            delta = (memory_now - self.memory_old )/ (the_count *1024.0)
#convert to kbytes per update

            self.memory_old = memory_now

            print "memory now = %i delta = %f\n" %(memory_now, delta)

        

    def OnPaint(self, event):

        self.canvas.draw()

 

class App(wx.App):

 

    def OnInit(self):

        'Create the main window and insert the custom frame'

        frame = CanvasFrame()

        frame.Show(True)

 

        return True

 

app = App(0)

app.MainLoop()