matplotlib

I'm having some problems understanding the difference between pylab.xticks()
and pylab.yticks()
Consider the following:

> import pylab as P
> import numpy as N
>
> data = N.random.random((10, 10))
> P.matshow(data)
> P.xticks([0, 1, 2], ['1', '2', '3'])
> P.show()


Why does this work, but if I change P.xticks to P.yticks, it doesn't?

The error message that I get back doesn't give me any insight as to what
could cause the difference between xticks and yticks.

 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/figure.py",
line 612, in draw
    for a in self.axes: a.draw(renderer)
  File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axes.py",
line 1287, in draw
    self.transData.freeze()  # eval the lazy objects
ValueError: Domain error on eval_scalars in Transformation::freeze


 matplotlib.__version__
Out[2]: '0.90.1'

I am still in the learning phase, so any insight as to what's going on is
appreciated.

Best,
    Jan

Hello,

I just installed Matplotlib (and NumPy) on a windows XP machine, and
I'm getting the following traceback when I try to use the TkAgg
backend.

Python 2.5.1 (r251:54863, Apr 18 2007, 08:51:08) [MSC v.1310 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.use('TkAgg')
>>> from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_tkagg.py",
line 8, in <module>
    import tkagg                 # Paint image to Tk photo blitter extension
  File "C:\Python25\lib\site-packages\matplotlib\backends\tkagg.py",
line 1, in <module>
    import _tkagg
ImportError: DLL load failed: The specified module could not be found.
>>>

I found one old (2004) post
http://mail.python.org/pipermail/python-list/2004-April/258963.html
that seems to indicate that some sort version mismatch of the Tk/Tcl
libraries may be to blame.  But I don't know how to diagnose that or
what to do about it.

FWIW, I installed using matplotlib-0.90.1.win32-py2.5.exe and
numpy-1.0.3.1.win32-py2.5.exe.

Thanks in advance for any help you can give me.
Sincerely,
~Simon

This might help you it destroys the whole window:
pylab.get_current_fig_manager().destroy()
and then you open it again with show
Lee, Young-Jin wrote:
>
> Hi,
>
> I ’m writing a python program that draws figures one by one 
> interactively with the user’s input in dos mode. Basically, I give the 
> program a decision after each figure and then it draws the next one. 
> After the first figure, it got very much slowed down for the second 
> one and crashed for the third one. I feel like it has some memory 
> issues as I keep using ‘show’ after I close each. I used ‘clf()’ 
> before I draw a new one, but it doesn’t seem to help. Any idea? Thanks.
>
> Young Jin
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> ------------------------------------------------------------------------
>
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> Matplotlib-users mailing list
> Matplotlib-users@...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

It appears that IndexFormatter is no longer in ticker.py as the user guide
(Table 6.3, p.58) suggests.

Cheers,
    Jan

Dear  all,
thanks for your help. this is what I was looking for!
Dirk


2007/9/26, Eric Firing <efiring@...>:
>
> David Huard wrote:
> > Hi Dirk,
> >
> > If you haven't already done so, look at the numpy.ma <http://numpy.ma/>
> > module. It provides a masked array object that deals gracefully with
> > missing values. To the best of my knowledge, most matplotlib functions
> > understand masked arrays and deal with it accordingly, exception made of
> > those requiring a full matrix (such as contour). Take a look at
>
> contour handles masked arrays correctly, as far as I know; contourf has
> some bugs in its masked array handling, but depending on the type and
> distribution of voids, it may still be good enough.
>
> pcolor and image have no problems with masked arrays.
>
> Eric
>
> > examples/image_masked.py. Also, in the Basemap toolkit, there is at
> > least one example showing how to plot a masked array on a map.
> >
> > Cheers,
> >
> > David
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Matplotlib-users mailing list
> Matplotlib-users@...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hello.

I've been having trouble getting Unicode characters to render.  I just
get a box in the title of my figure, rather than the character I need.

Here is my code:
#!/usr/bin/env python
from pylab import *
plot([1,2,3,4])
title(u"\u0251")
savefig("test.eps")
savefig("test.png")
show()

That character is LATIN SMALL LETTER ALPHA.  It's used in the
International Phonetic Alphabet.

I'm on Linux and I'm using matplotlib 0.90.1-2 (debian package
version).  I have a few TTF fonts in my system that contain that
glyph.  One is 'Arial Unicode MS', which I copied from my windows
machine.

As you can see, I will need to generate an EPS that renders the
character...  That EPS file will be imported into MS Word on a Windows
PC and printed.

I will happily use any solution that allows me to use that character
in the final product... :)  It doesn't have to be unicode..

I believe that my fonts are configured correctly on this Linux
system--I can use the Arial Unicode MS font in Open Office.  However,
I'm not sure that MPL is finding them.

When I point the TTFPATH environment variable a directory that only
contains ARIALUNI.TTF, I get gibberish for all characters in my
figure.

When I use ~/.matplotlib/matplotlibrc to list Arial Unicode MS as the
only font in the san-serif family, I don't observe any change in the
text in the figure.

...I did successfully instantiate an FT2FONT object out of my
ARIALUNI.TTF file, but, I didn't know what to do with it at that
point.

Help?

Cheers,
--Dave Loyall
Omaha, Nebraska, USA

Looking back through the archives, I found this discussion of manipulating
ticklabels.


Jouni K. Sepp=C3=A4nen wrote:
>=20
> Eugen Wintersberger <eugen.wintersberger@...>
> writes:
>=20
>> The first line is the printing of the ticklabel list before the
>> pylab.show() command. The second after pylab.show(). Why the list
>> contains 1 entry before and 7 (as is should) after pylab.show()?
>=20
> I think matplotlib is deferring the creation of the tick labels because
> for all it knows, you might be going to plot something that will cause
> the axes to be rescaled and change the tick locations and labels.
>=20
>> I would like to access the labels before the final show command in a
>> script. But how is this possible with this behavior?=20
>=20
> You could set the tick positions and labels explicitly, or if you like
> the default tick locator, add the following before getting the ticklabel
> objects:
>=20
> a.xaxis.get_major_locator().refresh()
>=20

I am having the same problem as Eugen, and the suggested solution of using=
=20
a.xaxis.get_major_locator().refresh()
to force the creation of the full set of ticklabels doesn't seem to work fo=
r
me.

Sample script:

from pylab import *
#ion()
a =3Daxes([0.2,0.2,0.7,0.7])
t =3D arange(0.0, 2.0, 0.01)
s =3D sin(2*pi*t)
a.plot(t, s)
a.grid(True)
# matlab handle graphics style
a.xaxis.get_major_locator().refresh()
xticklabels =3D getp(a, 'xticklabels')
setp(xticklabels, 'color', 'r', fontsize=3D'medium')
setp(xticklabels, dashdirection=3D0, dashlength=3D10, dashrotation=3D90)
#savefig('axprops_demo')
show()

even with a.xaxis.get_major_locator().refresh(), only the first ticklabel
has its position adjusted.

replacing=20
setp(xticklabels, dashdirection=3D0, dashlength=3D10, dashrotation=3D90)
with code modifying the position
for i in range(len(xticklabels)):
   xtp =3D getp(xticklabels[i],'position')
   setp(xticklabels[i],position=3D(xtp[0],-0.05))

also only effects the first ticklabel.

changes to color and fontsize of the first ticklabel do carry over the full
set of ticklabels, but TextWithDash properties do not carry over.=20

Uncommenting ion() at the beginning of the script generates the desired
image with offset ticklabels, but requires using interactive mode.

Any help either getting=20
a.xaxis.get_major_locator().refresh()
to work properly, or to get TextWithDash properties to carry over from the
initial single ticklabel to the full set of ticklabels would be greatly
appreciated.=20

thanks,

Charles Seaton
Research Associate
STC-CMOP
 http://www.stccmop.org

--=20
View this message in context: http://www.nabble.com/Problem-with-tick-label=
s-in-scripts-tf4260235.html#a12932137
Sent from the matplotlib - users mailing list archive at Nabble.com.

On Friday 28 September 2007 07:36:23 am John Hunter wrote:
> On 9/27/07, Darren Dale <dd55@...> wrote:
> > Hi Eric, John,
> >
> > Have either of you been following this thread?
>
> I am now :-)
>
> As Eric suggests, None is overloaded vis-a-vis color handling, because
> for mpl properties it generally means do the default as defined by rc.
>  For colors people often want to use None for "no color" which is why
> we added support for the string "None".  Does this work in your use
> case Tom?

The above exchange was off-list, we're back on now. I think that would be what 
Tom is looking for, but it doesnt work:

In [1]: plot([1,2])
Out[1]: [<matplotlib.lines.Line2D instance at 0x710cb0>]

In [2]: savefig('dsd.png', facecolor='None', edgecolor='None')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/home/darren/<ipython console> in <module>()

/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py in savefig(*args, 
**kwargs)
    272 def savefig(*args, **kwargs):
    273     fig = gcf()
--> 274     return fig.savefig(*args, **kwargs)
    275 if Figure.savefig.__doc__ is not None:
    276     savefig.__doc__ = dedent(Figure.savefig.__doc__)

/usr/lib64/python2.5/site-packages/matplotlib/figure.py in savefig(self, 
*args, **kwargs)
    768                 kwargs[key] = rcParams['savefig.%s'%key]
    769
--> 770         self.canvas.print_figure(*args, **kwargs)
    771
    772     def colorbar(self, mappable, cax=None, **kw):

/usr/lib64/python2.5/site-packages/matplotlib/backends/backend_qt4agg.py in 
print_figure(self, *args, **kwargs)
    153         self.update(l, self.renderer.height-t, w, h)
    154
    155     def print_figure(self, *args, **kwargs):
--> 156         FigureCanvasAgg.print_figure(self, *args, **kwargs)
    157         self.draw()

/usr/lib64/python2.5/site-packages/matplotlib/backend_bases.py in 
print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, 
**kwargs)
   1194                 edgecolor=edgecolor,
   1195                 orientation=orientation,
-> 1196                 **kwargs)
   1197         finally:
   1198             self.figure.dpi.set(origDPI)

/usr/lib64/python2.5/site-packages/matplotlib/backends/backend_agg.py in 
print_png(self, filename, *args, **kwargs)
    415
    416     def print_png(self, filename, *args, **kwargs):
--> 417         self.draw()
    418         self.get_renderer()._renderer.write_png(str(filename))
    419

/usr/lib64/python2.5/site-packages/matplotlib/backends/backend_qt4agg.py in 
draw(self)
    140         if DEBUG: print "FigureCanvasQtAgg.draw", self
    141         self.replot = True
--> 142         FigureCanvasAgg.draw(self)
    143         self.update()
    144

/usr/lib64/python2.5/site-packages/matplotlib/backends/backend_agg.py in 
draw(self)
    377
    378         self.renderer = self.get_renderer()
--> 379         self.figure.draw(self.renderer)
    380
    381     def get_renderer(self):

/usr/lib64/python2.5/site-packages/matplotlib/figure.py in draw(self, 
renderer)
    586         self.transFigure.freeze()  # eval the lazy objects
    587
--> 588         if self.frameon: self.figurePatch.draw(renderer)
    589
    590         for p in self.patches: p.draw(renderer)

/usr/lib64/python2.5/site-packages/matplotlib/patches.py in draw(self, 
renderer)
    198         #renderer.open_group('patch')
    199         gc = renderer.new_gc()
--> 200         gc.set_foreground(self._edgecolor)
    201         gc.set_linewidth(self._linewidth)
    202         gc.set_alpha(self._alpha)

/usr/lib64/python2.5/site-packages/matplotlib/backend_bases.py in 
set_foreground(self, fg, isRGB)
    617             self._rgb = fg
    618         else:
--> 619             self._rgb = colors.colorConverter.to_rgb(fg)
    620
    621     def set_graylevel(self, frac):

/usr/lib64/python2.5/site-packages/matplotlib/colors.py in to_rgb(self, arg)
    277
    278         except (KeyError, ValueError, TypeError), exc:
--> 279             raise ValueError('to_rgb: Invalid rgb arg "%s"\n%s' % 
(str(arg), exc))
    280             # Error messages could be improved by handling TypeError
    281             # separately; but this should be rare and not too hard

ValueError: to_rgb: Invalid rgb arg "None"
invalid literal for float(): None

Alan Isaac wrote:
> Is there a standard function or practice for
> plotting the CDF of a series?  (I am aware
> of the output of hist.)

import numpy as np
from matplotlib import pylab

x = ... # whatever
n = len(x)
x2 = np.repeat(x, 2)
y2 = np.hstack([0.0, np.repeat(np.arange(1,n) / float(n), 2), 1.0])
pylab.plot(x2, y2)

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco

Thanks to Eric Firing and Christopher Barker for input on trying to
resolve the problem.  Christopher said:
%%%
You might try just:

easy_install numpy

easy_install matplotlib.
%%%


I did that and now the problem moved and I get:
===
>>> from pylab import *
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/matplotlib/pylab.py", line 222, in ?
    new_figure_manager, draw_if_interactive, show = pylab_setup()
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/matplotlib/backends/__init__.py", line 24, in pylab_setup
    globals(),locals(),[backend_name])
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/matplotlib/backends/backend_gtkagg.py", line 10, in ?
    from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK,
    FigureCanvasGTK,\
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/matplotlib/backends/backend_gtk.py", line 21, in ?
    from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
  File
  "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-linux-i686.egg/matplotlib/backends/backend_gdk.py", line 35, in ?
    from matplotlib.backends._ns_backend_gdk import pixbuf_get_pixels_array
ImportError: No module named _ns_backend_gdk
===

Googling around has indicated that the X11 stuff wasn't available when the
numpy and matplotlib were made. The gtk files and "-devel" seem to be there
when I do an "rpm -qa".  I went and got a new numpy from source and did
"python setup.py install".  It is interesting that when I get in to python
now, I can do:

>>> import gtk
>>> import numpy
>>> import matplotlib

and they all just return the prompt, indicating, I thought, that the
programs were installed ok.  

Here is the naive question ->  Is there something wrong, then with a
"from pylab import *"? The user is trying to do that. 

Thanks for any assistance that can be given.

Hal
=======================


> Hal Huntley wrote:

> > I'm a sys admin trying to install the matplotlib python package for
> > someone on our staff. I'm not overly familar with python.

> > We are trying to use matplotlib with pylab.  

> > uname -a
> > Linux andromeda 2.6.13-1.1532_FC4smp #1 SMP Thu Oct 20 01:51:51 EDT 2005
> > i686 i686 i386 GNU/Linux

> > The python version we have is the default that we got with the Fedora
> > Core 4 package.

> > python -V
> > Python 2.4.1

> > I've installed using /usr/bin/easy_install:
> > matplotlib-0.90.1-py2.4-win32.egg  numpy-1.0.3.1-py2.4-win32.egg
> 
> I've never understood eggs and easy_install, but it certainly doesn't 
> look right that you are installing things labelled "win32" on a Linux 
> box!  I'm surprised you got that far.
> 
> For linux, I like to install from source, since the distro packages for 
> numpy and mpl are usually too old.  If you get the tarballs, build and 
> install numpy first, then mpl.  You don't need or want Numeric or 
> numarray.  The build process may fail.  If it does, it is because you 
> need to install distro packages with headers for various libraries, and 
> you should be able to see from the failures which headers are missing.
> 
> Maybe someone else can provide more detailed instructions for Fedora C4.
> 
> Eric
> 
> 
> 
> > 
> > If we get in to python and give the command:
> >>>> from pylab import *
> > 
> > We get:
> > ==
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/pylab.py", line 1, in ?
> >     from matplotlib.pylab import *
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/matplotlib/pylab.py", line 201, in ?
> >     import mlab  #so I can override hist, psd, etc...
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/matplotlib/mlab.py", line 64, in ?
> >     import nxutils
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/matplotlib/nxutils.py", line 17, in ?
> >     from matplotlib._ns_nxutils import *
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/matplotlib/_ns_nxutils.py", line 7, in ?
> >     __bootstrap__()
> >   File
> >   "/usr/lib/python2.4/site-packages/matplotlib-0.90.1-py2.4-win32.egg/matplotlib/_ns_nxutils.py", line 5, in __bootstrap__
> >     del __bootstrap__, __loader__
> > NameError: global name '__loader__' is not defined
> > ==
> > 
> > I've read that numeric may need to be installed, so I got "Numeric-24.2"
> > and did:
> >     python setup.py build
> >     python setup.py install
> > 
> > That didn't help solve the issue.
> > 
> > Is there some other package that needs to be installed?  I checked the FAQ
> > and this issue does not seem to be there.
> > 
> > Regards,
> > 
> > Hal Huntley
> > SRI International

On Thursday 27 September 2007 01:28:46 am Tom Johnson wrote:
> On 9/26/07, Darren Dale <dd55@...> wrote:
> > I used your script to create the eps file, and created the attached
> > postscript
> > (you need an \end{document} in your latex code).
>
> Whoops!
>
>
> Do you see anything wrong
>
> > with the resulting postscript? It looks fine to me.
>
> Indeed.  I didn't realize this before, but the problem is actually with the
> pdf.  I have attached it.  Can you confirm that your pdf looks like mine?

No, it does not look like yours. See attached.

> Mine looks like this no matter which viewer I use (acrobat, evince, xpdf).
> This makes me wonder if it is 1) the eps file or 2) the compilation
> process.

It is probably a problem with either ghostscript or pdftops.

> Actually, the problem exists as early as the dvi file.

The dvi looks fine here, and so does my pdf. It is often the case that 
problems with usetex are solved by updating the external dependencies. I am 
using:

GPL Ghostscript 8.60
pdftops version 3.00
pdfeTeX 3.141592-1.30.5-2.2 (tetex-3.0_p1)

Andrew Straw wrote:
> I came across this piece by Adam Hupp on programming.reddit.com just 
> now. It looks interesting:
>
> http://hupp.org/adam/weblog/2007/09/03/etframes-applying-the-ideas-of-edward-tufte-to-matplotlib/ 
>
>   
This is indeed really interesting. Thanks for this link,

David