matplotlib-users Mailing List for matplotlib (Page 5)

>>>>> "George" == George Nurser <ag...@no...> writes:

    George> I've had various versions of matplotlib from CVS installed
    George> on an Opteron (Red Hat LInux) here for a few weeks now. I
    George> had to modify setupext.py to look for various libraries in
    George> ../lib64 instead of /lib but matplotlib works very nicely
    George> most of the time, and I have started using it for real
    George> work.

    George> One cosmetic problem: the buttons at the bottom of the
    George> plot window have their graphics messed up. They just look
    George> like red crosses. The floating xml works, so I know what
    George> the buttons do, and it doesn't inconvenience me --- but it
    George> looks bad.

    George> Presumably some library is either out of date, incomplete,
    George> or not linked correctly. I am using the default TkAgg
    George> backend. Any thoughts on what I should look for would be
    George> appreciated.

We used to see something like this on OSX with the WX backend.  What
version of Tk are you using?  Could this be a byte order or byte size
problem?

The code that loads the buttons is in
matplotlib.backends.backend_tkagg

    def _Button(self, text, file, command):
        file = os.path.join(rcParams['datapath'], file)
        im = Tk.PhotoImage(master=self, file=file)
        b = Tk.Button(
            master=self, text=text, padx=2, pady=2, image=im, command=command)
        b._ntimage = im
        b.pack(side=Tk.LEFT)
        return b


you may want to read up on the tk PhotoImage and Button classes and
see if there is some option that makes this work.  I don't have access
to the opteron platform to test on.  The tk backend uses the ppm files
for the icons (eg home.ppm).  Do any of the other icon image formats
that ship with matplotlib (xpm, png, svg) work for you?  You can test
this by editing the _init_toolbar code in backend_tkagg.py

        self.bHome = self._Button( text="Home", file="home.ppm",
                                   command=self.home)

and trying different extensions.

Thanks,
JDH

On Wednesday 22 February 2006 7:32 am, Bruce wrote:
> Hi group,
>
> I wanted to try to usetex for my matplotlib plots, and thought that I
> had everything neccessary installed, but it doesn`t work. Perhaps
> someone in the group have some idea what is wrong here? Im using
> MikTex on xp and have the dvipng-miktex pakage installed. thx

Have you read the wiki? http://www.scipy.org/Wiki/Cookbook/Matplotlib/UsingTex

An intermediate dvi file is missing, probably because the latex executable is 
not on your path.

Darren

Hi group,

I wanted to try to usetex for my matplotlib plots, and thought that I
had everything neccessary installed, but it doesn`t work. Perhaps
someone in the group have some idea what is wrong here? Im using
MikTex on xp and have the dvipng-miktex pakage installed. thx

  File "C:\\Python23\\lib\\site-packages\\matplotlib\\text.py", line
334, in draw
    bbox, info =3D self._get_layout(renderer)
  File "C:\\Python23\\lib\\site-packages\\matplotlib\\text.py", line
179, in _get_layout
    w,h =3D renderer.get_text_width_height(
  File "C:\\Python23\\lib\\site-packages\\matplotlib\\backends\\backend_agg=
.py",
line 237, in get_text_width_height
    Z =3D self.texmanager.get_rgba(s, size, dpi, rgb)
  File "C:\\Python23\\lib\\site-packages\\matplotlib\\texmanager.py",
line 276, in get_rgba
    pngfile =3D self.make_png(tex, dpi, force=3DFalse)
  File "C:\\Python23\\lib\\site-packages\\matplotlib\\texmanager.py",
line 113, in make_png
    dvifile =3D self.make_dvi(tex)
  File "C:\\Python23\\lib\\site-packages\\matplotlib\\texmanager.py",
line 105, in make_dvi
    shutil.move(dvitmp, dvifile)
  File "C:\\Python23\\lib\\shutil.py", line 174, in move
    copy2(src,dst)
  File "C:\\Python23\\lib\\shutil.py", line 83, in copy2
    copyfile(src, dst)
  File "C:\\Python23\\lib\\shutil.py", line 38, in copyfile
    fsrc =3D open(src, 'rb')
IOError: [Errno 2] No such file or directory:
'a8cf192be8520ffec23612a6a3a0ee29.dvi
>>>

Christopher Barker wrote:
> John Hunter wrote:
> 
>> This is an annoyance that is caused by the fact that the GTK install
>> needs an X11 connection,
> 
> 
> Is it really necessary to import GTK when installing MPL? why? I think 
> getting rid of that requirement would be the best fix.
> 
>> Basically, you need to be able to
>> make sure you can launch an X11 app (eg xterm) in the environment that
>> you are running matplotlib install.
>>
>> Perhaps some UNIX guru can give the proper incantation.
> 
> 
> I've done it, but I'm not sure I remember how at the moment. But try 
> something like:
> 
> xhost +root
> 
> or even:
> 
> xhost +
> 
> which I think lets anyone have access to the Xserver.
> 
> -Chris
> 


I've replied to only to John, not the list. Here is the mail again:

================================================================================================

John Hunter wrote:

 >>>>>> "Steve" == Steve Schmerler <el...@gm...> writes:
 >
 >
 >
 >     Steve> 
------------------------------------------------------------------------
 >     Steve> elcorto@ramrod:~/Install/Matplotlib/matplotlib-0.86.2$ sudo
 >     Steve> python setup.py install installing data to
 >     Steve> lib/python2.3/site-packages/matplotlib/mpl-data pygtk
 >     Steve> present but import failed Using default library and include
 >     Steve> directories for Tcl and Tk because a Tk window failed to
 >     Steve> open.  You may need to define DISPLAY for Tk to work so
 >     Steve> that setup can determine where your libraries are located.
 >
 >     Steve> Gtk-WARNING **: cannot open display:
 >     Steve> 
------------------------------------------------------------------------
 >
 > This is an annoyance that is caused by the fact that the GTK install
 > needs an X11 connection, and in some setups when you install as root
 > the root user does not have access to your display.


Exactly this was the problem. I was logged in from machine A on machine 
B as user (ssh -X B) and wanted to install on B. So what I did on B was:

(as user):
user@B:<mpl_path>$ python setup.py build  # this works


(via sudo):
user@B:<mpl_path>$ sudo python setup.py install
python setup.py install installing data to
lib/python2.3/site-packages/matplotlib/mpl-data
pygtk present but import failed
Using default library and include directories for Tcl and Tk because a 
Tk window failed to open.  You may need to define DISPLAY for Tk to work 
so that setup can determine where your libraries are located.

Gtk-WARNING **: cannot open display:


(becoming su):
user@B:<mpl_path>$ su
user@B:<mpl_path># python setup.py install
X11 connection rejected because of wrong authentication.
The application 'setup.py' lost its connection to the display 
localhost:10.0;
most likely the X server was shut down or you killed/destroyed
the application.


 > I usually install
 > as suso: do you have sudo setup?  Basically, you need to be able to
 > make sure you can launch an X11 app (eg xterm) in the environment that
 > you are running matplotlib install.


Right, I can't open an X app on B via sudo or beeing su. Unfortunalelly 
I don't understand enough of the X-permission/xhost stuff to get this 
right :)

 > Perhaps some UNIX guru can give the proper incantation.


He did. Finally I logged in as root (ssh -X root@B) and then everthing
went fine.

================================================================================================


Additionally, if you want to install directly on A or B (not beeing 
logged in via ssh) just open a root terminal and install as usual. sudo 
and su won't do it.

cheers,
steve

-- 
Random number generation is the art of producing pure gibberish as 
quickly as possible.

Darren Dale wrote:
> Hi Steve,
> 
> On Tuesday 21 February 2006 13:00, Steve Schmerler wrote:
> 
>>1) Trying to export an .eps with using usetex = True:
>>
>>rcParams['text.usetex']=True; plot([1,2,3]); savefig("image.eps")
>>
>>I get an .eps where the axis numbers (are they called so?) are missing
>>(looks like a bounding box problem). Only the axes and what's inside the
>>plot box is there.
> 
> 
> What mpl version are you using, and have you tried setting 
> verbose=debug-annoying in your rc settings to see if any of the usetex 
> external dependencies are complaining about anything?
> 

I'm using 0.86.2 (from sourceforge).

This script

--------------------------------------
from pylab import *
from matplotlib import verbose, use

use('GTKAgg')
verbose.level = 'debug-annoying'

rcParams['text.usetex']=True
plot([1,2,3])
savefig("image.eps")
--------------------------------------

produces

---------------------------------------------------------------------------
schmerler@bach:~$ python test.py
FigureCanvasAgg.print_figure
FigureCanvasAgg.draw
RendererAgg.__init__
RendererAgg._get_agg_font
         findfont failed Lucida Grande
         findfont failed Verdana
         findfont failed Geneva
         findfont failed Lucida
         findfont found Bitstream Vera Sans, normal, normal 500, normal, 
12.0
findfont returning 
/usr/lib/python2.3/site-packages/matplotlib/mpl-data/Vera.ttf
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
matplotlib data path /usr/lib/python2.3/site-packages/matplotlib/mpl-data
latex -interaction=nonstopmode "/tmp/15f8552d172b5a41c557b4ad371e3782.tex"
This is e-TeX, Version 3.14159-2.1 (Web2C 7.4.5)
entering extended mode
(/tmp/15f8552d172b5a41c557b4ad371e3782.tex
LaTeX2e <2001/06/01>
Babel <v3.7h> and hyphenation patterns for american, french, german, 
ngerman, b
ahasa, basque, catalan, croatian, czech, danish, dutch, finnish, greek, 
iceland
ic, irish, italian, latin, magyar, norsk, norsk, portuges, romanian, 
russian, s
lovak, slovene, spanish, swedish, turkish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf/tex/latex/koma-script/scrartcl.cls
Document Class: scrartcl 2003/01/31 v2.9n LaTeX2e KOMA document class
(/usr/share/texmf/tex/latex/koma-script/scrlfile.sty
Package scrlfile, 2003/01/31 v2.9n LaTeX2e KOMA package
                   Copyright (C) Markus Kohm

) (/usr/share/texmf/tex/latex/base/size11.clo)
(/usr/share/texmf/tex/latex/koma-script/typearea.sty
Package typearea, 2003/01/31 v2.9n LaTeX2e KOMA package
                   Copyright (C) Frank Neukam, 1992-1994
                   Copyright (C) Markus Kohm, 1994-2002

)) (/usr/share/texmf/tex/latex/misc/type1cm.sty)
(/usr/share/texmf/tex/latex/misc/psfrag.sty
(/usr/share/texmf/tex/latex/graphics/graphics.sty
(/usr/share/texmf/tex/latex/graphics/trig.sty)
(/usr/share/texmf/tex/latex/config/graphics.cfg)
(/usr/share/texmf/tex/latex/graphics/dvips.def)))
(/usr/share/texmf/tex/latex/graphics/graphicx.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf/tex/latex/graphics/dvipsnam.def))
No file 15f8552d172b5a41c557b4ad371e3782.aux.
<15f8552d172b5a41c557b4ad371e3782.eps> [1]
(./15f8552d172b5a41c557b4ad371e3782.aux) )
Output written on 15f8552d172b5a41c557b4ad371e3782.dvi (1 page, 2352 bytes).
Transcript written on 15f8552d172b5a41c557b4ad371e3782.log.


dvips -R -T 12.750000in,18.030000in -o 
"/tmp/15f8552d172b5a41c557b4ad371e3782.ps" 
"/tmp/15f8552d172b5a41c557b4ad371e3782.dvi"

This is dvips(k) 5.92b Copyright 2002 Radical Eye Software 
(www.radicaleye.com)
' TeX output 2006.02.22:1254' -> /tmp/15f8552d172b5a41c557b4ad371e3782.ps
<texc.pro><psfrag.pro><f7b6d320.enc><texps.pro><special.pro><color.pro>.
<cmr10.pfb>[1<15f8552d172b5a41c557b4ad371e3782.eps>]

gs -dBATCH -dNOPAUSE -dSAFER -r6000 
-sDEVICE=epswrite -dLanguageLevel=2 -dEPSFitPage 
  -sOutputFile="/tmp/15f8552d172b5a41c557b4ad371e3782.eps" 
"/tmp/15f8552d172b5a41c557b4ad371e3782.ps"
GPL Ghostscript 8.01 (2004-01-30)
Copyright (C) 2004 artofcode LLC, Benicia, CA.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
---------------------------------------------------------------------------

It complains about not finding some Agg fonts, could this be it??

Trying to export an .ps rather than an .eps produces a .ps where 
everything is visible but the image is a whole A4 page.

>>2) Exporting .svg fails
> 
> 
> There is no svg support for the usetex option.

Oh too bad, would have been nice.

cheers,
steve

-- 
Random number generation is the art of producing pure gibberish as 
quickly as possible.

Ray,

You tripped over a bug in cm.py: when I added masked array support, I 
put the "x = ma.asarray(x)" too early in the to_rgba() method of 
ScalarMappable.  It is fixed now in CVS.  Thanks for finding the problem.

If you want to try the fix in your version, in place of your workaround, 
here is the revised method:

    def to_rgba(self, x, alpha=1.0):
         # assume normalized rgb, rgba
         if len(x.shape)>2: return x
         x = ma.asarray(x)
         x = self.norm(x)
         x = self.cmap(x, alpha)
         return x

Eric

Thouis (Ray) Jones wrote:
> Greetings,
> 
> I searched the mail archive for information on this question, and
> didn't find anything.  Hopefully this hasn't been addressed elsewhere.
> 
> I just spent a few hours tracking down a huge performance hit in
> imshow().  I'm loading some image data via numarray's fromfile(),
> stacking three imgaes to make an RGB, and showing it with imshow.
> 
> My image loading code looks like this:
> 
> def read_dib(filename):
>     f = open(filename, "rb")
>     fromfile(f, "UInt8", shape=(52, 1))
>     im = fromfile(f, "UInt16", shape=(512, 512))
>     if sys.byteorder == "big":
> 	im.byteswap()
>     return im.astype('Float') /  (2**12 - 1)
> 
> I load three images, and put them into a NxMx3 float numarray, and
> pass that to imshow.
> 
> The performance drop   is at this line in image.py:
>           im = _image.fromarray(x, 0)
> 
> in AxesImage.make_image()
> 
> I eventually tracked it down to x's type being <class
> 'numarray.ma.MA.MaskedArray'>, which gets passed off to numarray's
> NA_InputArray function, which chokes and calls setArrayFromSequence
> (i.e., it's not using the fact that the input data is a numarray, and
> is instead iterating over each element).  This is taking around 30
> seconds to convert a 512x512x3 image on a new Intel iMac.
> 
> I sped it up significantly by using this line instead:
> 
>                     im = _image.fromarray(numerix.ma.filled(x,0), 0)
> 
> Not that that's a good idea (but it works for me for now).
> 
> There is no invalid data in my image.  I'm not sure why it's ever
> being turned into a masked array.
> 
> I'm using matplotlib 0.86.2 and numarray-1.5.1, on OS X 10.3.5 on an Intel iMac.
> 
> Any advice would be appreciated.
> 
> Thanks,
> Ray Jones
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi Steve,

On Tuesday 21 February 2006 13:00, Steve Schmerler wrote:
> 1) Trying to export an .eps with using usetex = True:
>
> rcParams['text.usetex']=True; plot([1,2,3]); savefig("image.eps")
>
> I get an .eps where the axis numbers (are they called so?) are missing
> (looks like a bounding box problem). Only the axes and what's inside the
> plot box is there.

What mpl version are you using, and have you tried setting 
verbose=debug-annoying in your rc settings to see if any of the usetex 
external dependencies are complaining about anything?

> 2) Exporting .svg fails

There is no svg support for the usetex option.

Darren

Greetings,

I searched the mail archive for information on this question, and
didn't find anything.  Hopefully this hasn't been addressed elsewhere.

I just spent a few hours tracking down a huge performance hit in
imshow().  I'm loading some image data via numarray's fromfile(),
stacking three imgaes to make an RGB, and showing it with imshow.

My image loading code looks like this:

def read_dib(filename):
    f =3D open(filename, "rb")
    fromfile(f, "UInt8", shape=3D(52, 1))
    im =3D fromfile(f, "UInt16", shape=3D(512, 512))
    if sys.byteorder =3D=3D "big":
=09im.byteswap()
    return im.astype('Float') /  (2**12 - 1)

I load three images, and put them into a NxMx3 float numarray, and
pass that to imshow.

The performance drop   is at this line in image.py:
          im =3D _image.fromarray(x, 0)

in AxesImage.make_image()

I eventually tracked it down to x's type being <class
'numarray.ma.MA.MaskedArray'>, which gets passed off to numarray's
NA_InputArray function, which chokes and calls setArrayFromSequence
(i.e., it's not using the fact that the input data is a numarray, and
is instead iterating over each element).  This is taking around 30
seconds to convert a 512x512x3 image on a new Intel iMac.

I sped it up significantly by using this line instead:

                    im =3D _image.fromarray(numerix.ma.filled(x,0), 0)

Not that that's a good idea (but it works for me for now).

There is no invalid data in my image.  I'm not sure why it's ever
being turned into a masked array.

I'm using matplotlib 0.86.2 and numarray-1.5.1, on OS X 10.3.5 on an Intel =
iMac.

Any advice would be appreciated.

Thanks,
Ray Jones

The latest release of matplotlib was built against numpy 0.9.4.=20
Hopefully we will have a release soon to match up with the latest
numpy.

On 2/21/06, Gary <pa...@in...> wrote:
> John Hunter wrote:
>
> >
> >    Humufr> This morning I install the cvs version of matplotlib and
> >    Humufr> numpy and now I have a segfault when numpy is the
> >    Humufr> numerical package define in matplotlibrc. It's seems to
> >    Humufr> work fine with numarray.
> >
> >Make sure you have a clean install of both packages (rm -rf build
> >subdir in both and reinstall) and if you still get the segfault post a
> >minimum script run with --verbose-helpful ; this will give us the exact
> >version numbers of both the matplotlib and numpy packages.
> >
> >JDH
> >
> >
> >
>
> I just updated numpy to the latest version: 0.9.5, from the Windows
> binary installer.  I have MPL 0.86.2, also binary installer.
>
> import pylab crashes python
> import matplotlib is ok
> backing up to numpy 0.9.4 works ok.
> does this issue belong to a numpy list?
>
>
> How exactly does one run a script with --verbose-helpful ?  This does
> not seem to be a valid python switch.
>
> Here are the last lines prior to crash of
> python -v test.py
> where test.py contains one line:  import pylab
>
> import matplotlib.axes # precompiled from
> c:\python24\lib\site-packages\matplotl
> ib\axes.pyc
> # c:\python24\lib\site-packages\matplotlib\artist.pyc matches
> c:\python24\lib\si
> te-packages\matplotlib\artist.py
> import matplotlib.artist # precompiled from
> c:\python24\lib\site-packages\matplo
> tlib\artist.pyc
> # c:\python24\lib\site-packages\matplotlib\transforms.pyc matches
> c:\python24\li
> b\site-packages\matplotlib\transforms.py
> import matplotlib.transforms # precompiled from
> c:\python24\lib\site-packages\ma
> tplotlib\transforms.pyc
> # c:\python24\lib\site-packages\matplotlib\_transforms.pyc matches
> c:\python24\l
> ib\site-packages\matplotlib\_transforms.py
> import matplotlib._transforms # precompiled from
> c:\python24\lib\site-packages\m
> atplotlib\_transforms.pyc
>
>
> -gary
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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=3D121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

John Hunter wrote:
> This is an annoyance that is caused by the fact that the GTK install
> needs an X11 connection,

Is it really necessary to import GTK when installing MPL? why? I think 
getting rid of that requirement would be the best fix.

>Basically, you need to be able to
> make sure you can launch an X11 app (eg xterm) in the environment that
> you are running matplotlib install.
> 
> Perhaps some UNIX guru can give the proper incantation.

I've done it, but I'm not sure I remember how at the moment. But try 
something like:

xhost +root

or even:

xhost +

which I think lets anyone have access to the Xserver.

-Chris





-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
NOAA/OR&R/HAZMAT         (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

>>>>> "Jason" == Jason C Leach <jas...@gm...> writes:

    Jason> hi, I'm having trouble figuring out how to add a few more
    Jason> layers to a stacked bar graph.  What I have so far is:

    Jason>         p1 = axes.bar(ind, data['n'], width, color='r') p2
    Jason> = axes.bar(ind, data['l'], width, color='y',
    Jason> bottom=data['n']) p3 = axes.bar(ind, data['m'], width,
    Jason> color='b', bottom=data['l']) p4 = axes.bar(ind, data['h'],
    Jason> width, color='g', bottom=data['m'])

    Jason> But I don't think this is correct.  I only get two layers
    Jason> (red and green).  Does anyone know the proper method?

See examples/table_demo.py -- you need to keep a cumulative sum of the
bottom positions, eg

yoff = array([0.0] * len(colLabels)) # the bottom values for stacked bar chart
for row in xrange(rows):
    bar(ind, data[row], width, bottom=yoff, color=colours[row])
    yoff = yoff + data[row]
    cellText.append(['%1.1f' % (x/1000.0) for x in yoff])

JDH

hi,

I'm having trouble figuring out how to add a few more layers to a
stacked bar graph.
What I have so far is:

        p1 =3D axes.bar(ind, data['n'], width, color=3D'r')
        p2 =3D axes.bar(ind, data['l'], width, color=3D'y', bottom=3Ddata['=
n'])
        p3 =3D axes.bar(ind, data['m'], width, color=3D'b', bottom=3Ddata['=
l'])
        p4 =3D axes.bar(ind, data['h'], width, color=3D'g', bottom=3Ddata['=
m'])

But I don't think this is correct.  I only get two layers (red and
green).  Does anyone know the proper method?

Thanks,
Jason.



--
........................................
.... Jason C. Leach
.... PGP Key: 0x62DDDF75
.... Keyserver: gpg.mit.edu

John Hunter wrote:

>
>    Humufr> This morning I install the cvs version of matplotlib and
>    Humufr> numpy and now I have a segfault when numpy is the
>    Humufr> numerical package define in matplotlibrc. It's seems to
>    Humufr> work fine with numarray.
>
>Make sure you have a clean install of both packages (rm -rf build
>subdir in both and reinstall) and if you still get the segfault post a
>minimum script run with --verbose-helpful ; this will give us the exact
>version numbers of both the matplotlib and numpy packages.
>
>JDH
>
>  
>

I just updated numpy to the latest version: 0.9.5, from the Windows 
binary installer.  I have MPL 0.86.2, also binary installer.

import pylab crashes python
import matplotlib is ok
backing up to numpy 0.9.4 works ok.
does this issue belong to a numpy list?


How exactly does one run a script with --verbose-helpful ?  This does 
not seem to be a valid python switch.

Here are the last lines prior to crash of
python -v test.py
where test.py contains one line:  import pylab

import matplotlib.axes # precompiled from 
c:\python24\lib\site-packages\matplotl
ib\axes.pyc
# c:\python24\lib\site-packages\matplotlib\artist.pyc matches 
c:\python24\lib\si
te-packages\matplotlib\artist.py
import matplotlib.artist # precompiled from 
c:\python24\lib\site-packages\matplo
tlib\artist.pyc
# c:\python24\lib\site-packages\matplotlib\transforms.pyc matches 
c:\python24\li
b\site-packages\matplotlib\transforms.py
import matplotlib.transforms # precompiled from 
c:\python24\lib\site-packages\ma
tplotlib\transforms.pyc
# c:\python24\lib\site-packages\matplotlib\_transforms.pyc matches 
c:\python24\l
ib\site-packages\matplotlib\_transforms.py
import matplotlib._transforms # precompiled from 
c:\python24\lib\site-packages\m
atplotlib\_transforms.pyc


-gary

1) Trying to export an .eps with using usetex = True:

rcParams['text.usetex']=True; plot([1,2,3]); savefig("image.eps")

I get an .eps where the axis numbers (are they called so?) are missing 
(looks like a bounding box problem). Only the axes and what's inside the 
plot box is there.


2) Exporting .svg fails:

In [9]: rcParams['text.usetex']=True; plot([1,2,3]); savefig("image.svg")
Out[9]: [<matplotlib.lines.Line2D instance at 0xb61d202c>]
---------------------------------------------------------------------------
exceptions.NotImplementedError                       Traceback (most 
recent call last)

/home/schmerler/<console>

/usr/lib/python2.3/site-packages/matplotlib/pylab.py in savefig(*args, 
**kwargs)
     813 def savefig(*args, **kwargs):
     814     fig = gcf()
--> 815     return fig.savefig(*args, **kwargs)
     816 if Figure.savefig.__doc__ is not None:
     817     savefig.__doc__ = _shift_string(Figure.savefig.__doc__)

/usr/lib/python2.3/site-packages/matplotlib/figure.py in savefig(self, 
*args, **kwargs)
     647                 kwargs[key] = rcParams['savefig.%s'%key]
     648
--> 649         self.canvas.print_figure(*args, **kwargs)
     650
     651     def colorbar(self, mappable,  cax=None,

/usr/lib/python2.3/site-packages/matplotlib/backends/backend_gtkagg.py 
in print_figure(self, filename, dpi, facecolor, edgecolor, orientation)
     109             agg = self.switch_backends(FigureCanvasAgg)
     110             try:
--> 111                 agg.print_figure(filename, dpi, facecolor, 
edgecolor, orientation)
     112             except IOError, msg:
     113                 error_msg_gtk('Failed to save\nError message: 
%s'%(msg,), self)

/usr/lib/python2.3/site-packages/matplotlib/backends/backend_agg.py in 
print_figure(self, filename, dpi, facecolor, edgecolor, orientation)
     473                 from backend_svg import FigureCanvasSVG
     474                 svg = self.switch_backends(FigureCanvasSVG)
--> 475                 svg.print_figure(filename, dpi, facecolor, 
edgecolor, orientation)
     476             elif ext.find('ps')>=0 or ext.find('ep')>=0:
     477                 from backend_ps import FigureCanvasPS # lazy import

/usr/lib/python2.3/site-packages/matplotlib/backends/backend_svg.py in 
print_figure(self, filename, dpi, facecolor, edgecolor, orientation)
     282         svgwriter = codecs.open( filename, 'w', 'utf-8' )
     283         renderer = RendererSVG(w, h, svgwriter)
--> 284         self.figure.draw(renderer)
     285         renderer.finish()
     286

/usr/lib/python2.3/site-packages/matplotlib/figure.py in draw(self, 
renderer)
     522
     523         # render the axes
--> 524         for a in self.axes: a.draw(renderer)
     525
     526         # render the figure text

/usr/lib/python2.3/site-packages/matplotlib/axes.py in draw(self, 
renderer, inframe)
    1436         if not self._axisbelow:
    1437             if self.axison and not inframe:
-> 1438                 self.xaxis.draw(renderer)
    1439                 self.yaxis.draw(renderer)
    1440

/usr/lib/python2.3/site-packages/matplotlib/axis.py in draw(self, 
renderer, *args, **kwargs)
     560             tick.set_label1(label)
     561             tick.set_label2(label)
--> 562             tick.draw(renderer)
     563             if tick.label1On:
     564                 extent = tick.label1.get_window_extent(renderer)

/usr/lib/python2.3/site-packages/matplotlib/axis.py in draw(self, renderer)
     159             if self.tick2On: self.tick2line.draw(renderer)
     160
--> 161         if self.label1On: self.label1.draw(renderer)
     162         if self.label2On: self.label2.draw(renderer)
     163

/usr/lib/python2.3/site-packages/matplotlib/text.py in draw(self, renderer)
     856         if not self.get_visible(): return
     857         self.update_coords(renderer)
--> 858         self._mytext.draw(renderer)
     859         #bbox_artist(self._mytext, renderer, props={'pad':0}, 
fill=False)
     860         if self.get_dashlength() > 0.0:

/usr/lib/python2.3/site-packages/matplotlib/text.py in draw(self, renderer)
     346
     347                 renderer.draw_tex(gc, x, y, line,
--> 348                                   self._fontproperties, angle)
     349             return
     350

/usr/lib/python2.3/site-packages/matplotlib/backend_bases.py in 
draw_tex(self, gc, x, y, s, prop, angle, ismath)
     320
     321     def draw_tex(self, gc, x, y, s, prop, angle, ismath='TeX!'):
--> 322         raise NotImplementedError
     323
     324     def draw_text(self, gc, x, y, s, prop, angle, ismath=False):

NotImplementedError:

cheers,
steve

-- 
Random number generation is the art of producing pure gibberish as 
quickly as possible.

For the benefit of the list, below is a working script that makes a
simple plot with a patch element, outputs the plot to a png, and
outputs an html file that contains an image map so that the patch
element is clickable.

Thanks for all the help,

Julius

#!/usr/bin/env python

from pylab import *

dots =3D 150
fig =3D figure(num=3D1,figsize=3D(6,4),dpi=3Ddots,facecolor=3D'w')
ax =3D fig.add_subplot(111)
pl =3D ax.plot(range(0,10),range(0,10),'b-')
box =3D ax.axvspan(3,6,fc=3D'm',alpha=3D0.5)

fig.savefig('test.png',dpi=3Ddots)

img_height =3D fig.get_figheight() * dots

b_verts =3D box.get_verts()

#image maps use left-x,left-y,right-x,right-y
verts =3D [(b_verts[1][0],b_verts[1][1]),(b_verts[3][0],b_verts[3][1])]

tverts =3D box.get_transform().seq_xy_tups(verts)

#image maps have y=3D0 on top
tverts =3D (tverts[0][0],img_height-tverts[0][1],tverts[1][0],img_height-tv=
erts[1][1])

file =3D open('test.html','w')
file.write('''<HTML>
<HEAD>
  <TITLE>Image Map Test</TITLE>
</HEAD>
<BODY>
<map name=3D"map">
  <area shape=3D"rect" coords=3D"%d,%d,%d,%d" href=3D"http://www.google.com=
">
</map>
<img border=3D2 src=3D"./test.png" usemap=3D"#map">
</BODY>
</HTML> ''' % tverts )

file.close()

>>>>> "Humufr" == Humufr  <hu...@ya...> writes:

    Humufr> This morning I install the cvs version of matplotlib and
    Humufr> numpy and now I have a segfault when numpy is the
    Humufr> numerical package define in matplotlibrc. It's seems to
    Humufr> work fine with numarray.

Make sure you have a clean install of both packages (rm -rf build
subdir in both and reinstall) and if you still get the segfault post a
minimum script run with --verbose-helpful ; this will give us the exact
version numbers of both the matplotlib and numpy packages.

JDH

This morning I install the cvs version of matplotlib and numpy and now I 
have a segfault when numpy is the numerical package define in 
matplotlibrc. It's seems to work fine with numarray.

>>>>> "Julius" == Julius Lucks <jul...@gm...> writes:

    Julius> my question is what transform do I use to convert verts to
    Julius> pixel coordinates?  ax.get_transform() does not work.
    Julius> Should I use pl.get_transform?

"Does not work" is not very descriptive :-(

Yes, you should use the polygon transform

You might want to look at the "draw" method of the
matplotlib.patches.Polygon class to see how it gets the data into
pixel coords

        verts = self.get_verts()
        tverts = self._transform.seq_xy_tups(verts)

Thus all you need to do outside the class is 

  trans = pl.get_transform()
  verts = pl.get_verts()
  tverts = trans.seq_xy_tups(verts)
 
Should work...

The documentation for the matplotlib.transforms module is decent, if
you want to take a look

  http://matplotlib.sourceforge.net/matplotlib.transforms.html

JDH

>>>>> "Stephen" == Stephen English <st...@se...> writes:

    Stephen> All, I am trying to render a set of data/date points with
    Stephen> plot_date. How can I get matplotlib to only plot the y
    Stephen> axis of this graph? I can turn both off with axis("off"),
    Stephen> but I can't seem to find more detailed instructions
    Stephen> anywhere.  Also, although this is unimportant, it grates

You have to make the individual elements invisible.  Something like

for label in ax.get_xticklabels():
    label.set_visible(False)

For more refined control, for each tick there are a host of visibility
properties you can set

      gridOn     : a boolean which determines whether to draw the tickline
      tick1On    : a boolean which determines whether to draw the 1st tickline
      tick2On    : a boolean which determines whether to draw the 2nd tickline
      label1On   : a boolean which determines whether to draw tick label
      label2On   : a boolean which determines whether to draw tick label

for tick in ax.xaxis.get_major_ticks():
    tick.tick2On = False

and likewise for the minor ticks

    Stephen> somewhat to use matplotlib with the procedural (matlab
    Stephen> esque) instructions within my OO python code.  Are there
    Stephen> any tutorials or other docs on plotting graphs through
    Stephen> the more pythonic libraries?

As the code above illustrates, matplotlib is an OO library.  There is
no requirement to use it through the procedural pylab interface.  Most
of my personal use, except for quick scripts and interactive sessions,
is OO.

See this FAQ

  http://matplotlib.sourceforge.net/faq.html#OO

and this tutorial

  http://matplotlib.sourceforge.net/leftwich_tut.txt

A nice hybrid approach is to use a minimum of pylab for figure
management only, and do everything else through OO

  import matplotlib.numerix as nx
  from pylab import figure, close, show  # all you need
  
  x = nx.arange(0, 2.0, 0.01)
  y = nx.sin(2*nx.pi*x)
  fig1 = figure(1)
  fig2 = figure(2)
  
  ax1 = fig1.add_subplot(211)
  ax1.plot(x,y)
  ax1.set_xlabel('time (s)')
  ax1.set_ylabel('volts')
  ax1.set_title('a sinusoid')
  ax1.grid(True)
  
  # and more with fig2, etc....
  show()
  
Most of the action is in the Axes instance, and too a lesser extent
the Figure and Axis instances, so see the class documentation for the
figure, axes, and axis methods

  http://matplotlib.sourceforge.net/classdocs.html

Hope this helps,
JDH

>>>>> "Steve" == Steve Schmerler <el...@gm...> writes:

    Steve> ------------------------------------------------------------------------
    Steve> elcorto@ramrod:~/Install/Matplotlib/matplotlib-0.86.2$ sudo
    Steve> python setup.py install installing data to
    Steve> lib/python2.3/site-packages/matplotlib/mpl-data pygtk
    Steve> present but import failed Using default library and include
    Steve> directories for Tcl and Tk because a Tk window failed to
    Steve> open.  You may need to define DISPLAY for Tk to work so
    Steve> that setup can determine where your libraries are located.

    Steve> Gtk-WARNING **: cannot open display:
    Steve> ------------------------------------------------------------------------

This is an annoyance that is caused by the fact that the GTK install
needs an X11 connection, and in some setups when you install as root
the root user does not have access to your display.  I usually install
as suso: do you have sudo setup?  Basically, you need to be able to
make sure you can launch an X11 app (eg xterm) in the environment that
you are running matplotlib install.

Perhaps some UNIX guru can give the proper incantation.  In addition
to setting the DISPLAY as root, you may need to check your xhost
settings.

JDH

>>>>> "Tom" == Tom Denniston <tom...@al...> writes:

    Tom>  I am generating a few hundred graphs and doing so takes on
    Tom> the order of about 10-15 minutes.  Which seems to me rather
    Tom> slow.  When I profile my code it identifies the calls to
    Tom> get_yticklabels and get_xticklabels as taking over 90% of the
    Tom> time.  This seems strange but my calls to these functions are
    Tom> merely a sort round about way of setting the font size of the
    Tom> axis tick labels and suppressing the text for the
    Tom> xticklabels.  Is there a more efficient and cleaner way to do
    Tom> this?  artist.setp(axes.get_yticklabels(), visible=True,
    Tom> fontsize=7) artist.setp(axes.get_xticklabels(),
    Tom> visible=False)

This is a known performance bottleneck.  There are two reasons it is
slow.  Every tick label is handled as an independent object, when they
in most cases share most of their properties (font size, orientation)
and so could be better handled as a TextCollection, which does not
exist yet.  The second reason is that the text layout engine is doing
layout for newline separated strings with an arbitrary rotation for
every tick label, which is almost never used.  So some special case
optimizations to handle the no rotation, no newline text instances
(basically just bypass the layout machinery) would help a lot here.

Are you using matplotlib mathtext also, by chance?  This slows things
down a bit too, though is better in recent versions.

JDH

I've had various versions of matplotlib from CVS installed on an  
Opteron (Red Hat LInux) here for a few weeks now. I had to modify  
setupext.py to look for various libraries in ../lib64 instead of /lib  
but matplotlib works very nicely most of the time, and I have started  
using it for real work.

One cosmetic problem: the buttons at the bottom of the plot window  
have their graphics messed up. They just look like red crosses. The  
floating xml works, so I know what the buttons do, and it doesn't  
inconvenience me --- but it looks bad.

Presumably some library is either out of date, incomplete, or not  
linked correctly. I am using the default TkAgg backend. Any thoughts  
on what I should look for would be appreciated.


BTW the matplotlib users_guide_0.83.2.pdf seems to be unreadable from  
my Mac. It appears blank in (Tiger) Safari, and preview cannot open  
the file: it gives  'File error'.

Regards, George Nurser.

Hi thanks for the help. I have a related problem.  i had been  using py2exe with matplotlib and it was working well. upgraded to 0.86  and now it doesn't work. I know this is because the installation  directory is different now (no longer the share folder).  So I  thought I fixed it correctly but I get an error that indicates py2exe  "can't find lib/site-packages/matplotlib/backends or it is not a  regular file".  I am assuming that it doesn't like 'backends'  because it is a folder and not a file.  I changed my setup code to  this:
  
  data_files=[
              ("matplotlibdata",
                      glob.glob(os.path.join(distutils.sysconfig.PREFIX, 'lib',  'site-packages','matplotlib', "*")))]
  
  setup(
      options = options,
      # The lib directory contains everything except the executables and the python dll.
      windows = [app],
      data_files = data_files,
      # use out build_installer class as extended py2exe build command
      cmdclass = {"py2exe": build_installer},
      )
  
  how might I change this to get it working properly? thanks!!
  
  Jeff
  
Charlie Moad <cw...@gm...> wrote:  Recently the matplotlib data files have been moved into the matplotlib
module.  You should be able to safely remove share/matplotlib.

On 2/19/06, Jeff Peery  wrote:
> hello, I just upgraded from 0.84 to 0.86 on windows xp. I noticed that I
> have a couple different locations on my computere where it is installed.
> there is something in the python24/share and also
> python24/Lib/site-packages/
>
>  what do I gotta do to make sure I am using the newest version. can I just
> delete all the matplot lib folders and reinstall the newest version?
>
>  thakns!
>
>
>  ________________________________
>  Yahoo! Mail
>  Use Photomail to share photos without annoying attachments.
>
>


		
---------------------------------
 
 What are the most popular cars? Find out at Yahoo! Autos 

On 2/15/06, John Hunter <jdh...@ac...> wrote:
> >>>>> "Charlie" =3D=3D Charlie Moad <cw...@gm...> writes:
>
>     Charlie>      You could use html image maps to accomplish this.
>     Charlie> Obviously this would be in the context of a web page.  I
>     Charlie> think frontpage or dreamweaver has some nice tools for
>     Charlie> creating these.  Just google "html image maps" for more
>     Charlie> info.
>
> Andrew Dalke has a tutorial on creating html image maps with
> matplotlib
>
> http://www.dalkescientific.com/writings/diary/archive/2005/04/24/interact=
ive_html.html
>
> JDH
>

This tutorial was a start.  I want to do a similar thing, but use
rectangle objects for the image map, whose coordinates are derived
from matplotlib polygon objects.  I was wondering if anyone knew how
to do this, or could point me to some documentation.

Basically I have a simple figure:

>
from pylab import *

clf()
fig =3D figure(1,(4,4))
ax =3D axis()
pl =3D plot(range(0,10),range(0,10),'b-')
box =3D axvspan(3,5,fc=3D'm',alpha=3D0.5)

#get vertices [(ul.x,ul.y),(lr.x,lr.y)]
#ul =3D upper left
#lr =3D lower right
#have to multiply ul.y by the upper ylim since for axvspan, ul.y=3D1
spans the range
b_verts =3D box.get_verts()
verts =3D [(b_verts[1][0],b_verts[1][1]*ax.get_ylim()[1]),(b_verts[3][0],b_=
verts[3][1])]
>


my question is what transform do I use to convert verts to pixel coordinate=
s?
ax.get_transform() does not work.  Should I use pl.get_transform?

Thanks for your help!

Cheers,

Julius

All,
I am trying to render a set of data/date points with plot_date. How can I
get matplotlib to only plot the y axis of this graph? I can turn both off
with axis("off"), but I can't seem to find more detailed instructions
anywhere.
Also, although this is unimportant, it grates somewhat to use matplotlib
with the procedural (matlab esque) instructions within my OO python code.
Are there any tutorials or other docs on plotting graphs through the more
pythonic libraries?

Many thanks,

Stephen English