matplotlib-users Mailing List for matplotlib (Page 13)

Hi John,

On Sat, 3 Sep 2005, John Hunter wrote:

> >>>>> "arnd" == arnd baecker <arn...@we...> writes:
>     arnd> the y-axis has a different font (italic) than the x-axis
>     arnd> (sans-serif).  Looking at the code, this is because it is
>     arnd> set as math text ($ ...$).  Is there a trick to ensure a
>     arnd> sans-serif font for the y-axis?  (I would like to use
>     arnd> matplotlib plots in a presentation and sans-serif fonts are
>     arnd> better suited for this.)
>
> What version of mpl are you using?  I thought in a previous post you
> said you were using cvs (could be mistaken).

You remember the version I am running better than I do ;-).
In [1]: import matplotlib
In [2]: matplotlib.__version__
Out[2]: '0.84.cvs.2'

> I wrote an extension to
> text.py to special case exponential formatting specifically to solve
> the mismatched fonts problem.  So make sure you are using a current
> problem of matplotlib and if you still have the problem check your
> input against the regex in matplotlib.text.Text
>
>     # special case superscripting to speedup logplots
>     _rgxsuper = re.compile('\$([\-+0-9]+)\^\{(-?[0-9]+)\}\$')
>
> If you can fix up this expression to include your case that would be
> most helpful.

I think the expression is alright:
I looked at matplotlib/text.py - class Text. It seems that
for this example the routine does not pass by the
first use of self._rgxsuper:


	print "Arriving here1"
        if angle==0:
	    print "Arriving here2"
            if ismath!='TeX':            # <==== change to "==" here?
		print "Arriving here3"
 		m = None
            else:
                m = self._rgxsuper.match(self._text)
		print "passing by here..."
	    print "Arriving here4"
            if m is not None and not rcParams['text.usetex']:
		print "Arriving here5"
                bbox, info = self._get_layout_super(self._renderer, m)
                base, xt, yt = info[0]
                renderer.draw_text(gc, xt, yt, base,
                                   self._fontproperties, angle,
                                   ismath=False)

                exponent, xt, yt, fp = info[1]
                renderer.draw_text(gc, xt, yt, exponent,
                                   fp, angle,
                                   ismath=False)
                return

However, changing ismath!='TeX' to ismath=='TeX'
seems to work (for this particular example): I.e. I get
the non-math fonts on the vertical axis.
Can you confirm that this change is the correct solution?

Best,

Arnd

P.S.: BTW: splattering the prints around seems like poor-mans
debugging ;-) Are there better solutions available?

>>>>> "arnd" == arnd baecker <arn...@we...> writes:
    arnd> the y-axis has a different font (italic) than the x-axis
    arnd> (sans-serif).  Looking at the code, this is because it is
    arnd> set as math text ($ ...$).  Is there a trick to ensure a
    arnd> sans-serif font for the y-axis?  (I would like to use
    arnd> matplotlib plots in a presentation and sans-serif fonts are
    arnd> better suited for this.)

What version of mpl are you using?  I thought in a previous post you
said you were using cvs (could be mistaken).  I wrote an extension to
text.py to special case exponential formatting specifically to solve
the mismatched fonts problem.  So make sure you are using a current
problem of matplotlib and if you still have the problem check your
input against the regex in matplotlib.text.Text

    # special case superscripting to speedup logplots
    _rgxsuper = re.compile('\$([\-+0-9]+)\^\{(-?[0-9]+)\}\$')

If you can fix up this expression to include your case that would be
most helpful.

Thanks,
JDH

Hi,

for this example

  from pylab import *
  x=arange(10)
  semilogy(x,1+x)

the y-axis has a different font (italic) than the x-axis (sans-serif).
Looking at the code, this is because it is set as math text ($ ...$).
Is there a trick to ensure a sans-serif font for the y-axis?
(I would like to use matplotlib plots in a presentation
and sans-serif fonts are better suited for this.)

Best,

Arnd

On Saturday 03 September 2005 1:14 am, Alan G Isaac wrote:
> On Fri, 2 Sep 2005, Darren Dale apparently wrote:
> > are you using a mac?
>
> No. I'm on a PC.  And although I in general understand
> John's request for a script, I think the EPS file I provided
> will be more helpful in pinning this down.  It took me
> a while to see it, but finally I got it.
>
> If you look at the bounding box, it is outside all standard
> paper sizes.  Now it turns out that pdfwrite assumes a paper
> size and clips outside that size.  Thus my figure did not
> show because it was clipped.  This does not happen when one
> uses dvips because the EPS file is handled *as* an EPS
> *before* creation of the PDF file.
>
> Lesson (I think): matplotlib should create its EPS files so
> that they have bounding boxes inside a4 width and letter
> paper height boundaries, or people will have trouble with
> their standard configurations of some standard tools.

I have wondered why the origin of the bbox was shifted in eps files, but it 
shouldn't matter. Seeing as how dvips, ps2pdf, and epstopdf all work as 
expected, it sounds like a dvipdfm bug to me. 

I don't think its a good idea to limit the size of eps figures. At some point, 
I will make eps files that are larger than A4 for use in posters.

Darren

> Thanks Sascha,
>
> The point of my reply was that others can benefit from what you've
> learned.  Even if you feel like you are a newbie, trust me, others
> will be glad to benefit from what you've learned.  So please send the
> information to the list.  I've forwarded your response.

It's been a pleasure. I actually intended to send my reply to the list and 
did not look at who I was really sending it to. Sorry again.

Sascha 

On Fri, 2 Sep 2005, Darren Dale apparently wrote: 
> are you using a mac? 

No. I'm on a PC.  And although I in general understand 
John's request for a script, I think the EPS file I provided 
will be more helpful in pinning this down.  It took me 
a while to see it, but finally I got it.

If you look at the bounding box, it is outside all standard 
paper sizes.  Now it turns out that pdfwrite assumes a paper 
size and clips outside that size.  Thus my figure did not 
show because it was clipped.  This does not happen when one
uses dvips because the EPS file is handled *as* an EPS 
*before* creation of the PDF file.

Lesson (I think): matplotlib should create its EPS files so 
that they have bounding boxes inside a4 width and letter 
paper height boundaries, or people will have trouble with 
their standard configurations of some standard tools.

Alan Isaac

PS I belive the matplotlib EPS files are written with 
a superfluous gsave (just search for 'gsave' and you'll find 
it in the file where it should not be), but this is not the 
source of my problem.

>  I could guess at what you are trying to do, but  =20
> it would help a lot if  you posted an example =20
> that we could run, with  comments about what you  =20
> want to happen versus what is happening.

thanks... attached is an image of roughly what i =20
want.  a program is below.

#!/usr/bin/python
from pylab import *
N=3D20
def xycs():
  x,y=3Dresize(rand(2*N),(2,N))
  x[:N/2]*=3D2;y[:N/2]/=3D2;
  c=3Darray([0]*(N/2)+[1]*(N/2))
  s=3Darray(([400]+[30]*(N/2-1))*2)
  print zip(c,s)
  p=3Dscatter(x,y,c=3Dc,s=3Ds,faceted=3D0)
  grid(True)
  setp(p, 'alpha', 0.75)
  savefig('scat_lgnd.png')
  show()
  return 0
if __name__=3D=3D'__main__':
  xycs()

I will be out of the office until September 26.  I will respond to your message as soon as I return.

Thank you,

Eli

>>>>> "Alan" == Alan Isaac <ai...@am...> writes:

    Alan> On Fri, 02 Sep 2005, John Hunter wrote:
    >> If you could send a docstring patch, that would be great.

    Alan> I was going to but I looked in pylab.py and found a note
    Alan> that the plot function def and docs were automatically
    Alan> generated, so I did not know what file to patch.  (Sorry;
    Alan> I'm new to this kind of thing.)

No problem.

pylab.py is for the most part a thin wrapper of functionality of
axes.py.  Eg, pylab.plot calls ax.plot and pylab.imshow calls
ax.imshow.  So if you find a problem with a pylab docstring, you can
usually find the original function in axes.py and fix that.

If you are on a win32 platform, which I think wyou are, you can install
ming32 and run a diff command like the one suggested by Charles Moad
at

  http://sourceforge.net/mailarchive/message.php?msg_id=12793726

If you are not comfortable with cvs/patch/diff, that's fine.  Just
edit the files in question and send them to me as an attachment and I
can deal with them.  

Thanks,
JDH

On Friday 02 September 2005 10:00 pm, John Hunter wrote:
> >>>>> "Alan" == Alan G Isaac <ai...@am...> writes:
>
>     Alan> My lovely matplotlib EPS graphics are missing in my PDF
>     Alan> files if I use dvipdfm.  It looks (?) like they are included
>     Alan> but then are blanked out afterwards.  Any idea why?  I have
>     Alan> never had trouble with other EPS files.
>
> We've seen a number of reports of problems in converting matplotlib
> eps files -> pdf.  To help us narrow the potential causes of the
> problem, could you provide the results of --verbose-helpful with an
> example script and rc file, as well as platform and version info for
> latex, gs, and otherwise.  Just give us as much information as you
> can, what sequence of commands you are issuing and what versions of
> each you are using.  Nonstandard rc settings (usetex?) and so on.
>
> matplotlib can be used in a lot of ways.  If you submit a script and
> an rc file (if it is different in any way than the default) and the
> commands you are typing and some extra version info, then it helps
> pare down the list of potential explanations for the problems you are
> seeing.

Alan, are you using a mac? If so, I wonder if this is related to embedding the 
native mac fonts. One user a while back reported having to change his font 
settings in matplotlibrc to load the bitstream fonts instead of the apple 
fonts. 

-- 
Darren S. Dale

Bard Hall
Department of Materials Science and Engineering
Cornell University
Ithaca, NY. 14850

dd...@co...
http://people.ccmr.cornell.edu/~dd55/

>>>>> "Jack" == Jack Andrews <ef...@iv...> writes:

    Jack> hi, i've been having lots of fun with scatter plots and
    Jack> coloured circles.  i want to provide a legend.

    Jack> i'm using colour to define discrete elements rather than
    Jack> continuous values (so colorbar() isn't much help to me -- i
    Jack> think...)

    Jack> basically: (red) chevrolet (orange) mazda (yellow) honda ...

    Jack> any tips?

I could guess at what you are trying to do, but it would help a lot if
you posted an example that we could run, with comments about what you
want to happen versus what is happening.

Have you seen examples/legend_demo2.py, which illustrates how to make
legends for a subset of objects in the plot?

JDH

>>>>> "Alan" == Alan G Isaac <ai...@am...> writes:

    Alan> My lovely matplotlib EPS graphics are missing in my PDF
    Alan> files if I use dvipdfm.  It looks (?) like they are included
    Alan> but then are blanked out afterwards.  Any idea why?  I have
    Alan> never had trouble with other EPS files.

We've seen a number of reports of problems in converting matplotlib
eps files -> pdf.  To help us narrow the potential causes of the
problem, could you provide the results of --verbose-helpful with an
example script and rc file, as well as platform and version info for
latex, gs, and otherwise.  Just give us as much information as you
can, what sequence of commands you are issuing and what versions of
each you are using.  Nonstandard rc settings (usetex?) and so on.

matplotlib can be used in a lot of ways.  If you submit a script and
an rc file (if it is different in any way than the default) and the
commands you are typing and some extra version info, then it helps
pare down the list of potential explanations for the problems you are
seeing.

Thanks,
JDH

My lovely matplotlib EPS graphics are missing in my PDF 
files if I use dvipdfm.  It looks (?) like they are included   
but then are blanked out afterwards.  Any idea why?  I have never had
trouble with other EPS files.

I tried cutting out all the page size stuff in the EPS file 
(what is that about?) but it did not help.

Using dvips and ps2pdf gives a fine result.
The EPS files appear to be valid, but must be doing
something that upsets dvipdfm.

Thanks,
Alan Isaac

PS Here is a "stripped down" example file.

%%%%%%%%%%%  temp.tex %%%%%%%%%%%%%%%%%%%
\documentclass[10pt]{book}
\usepackage{graphicx}
\begin{document}
\begin{figure}[htp]
\centering
\includegraphics[width=\textwidth]{temp.eps}
\end{figure}
\end{document}


%%%%%%%%%%%  temp.eps %%%%%%%%%%%%%%%%%%%
%!PS-Adobe-3.0 EPSF-3.0
%%BoundingBox: 188 781 765 1214
%%LanguageLevel: 2
%%EndComments
%%BeginProlog
% This copyright applies to everything between here and the %%EndProlog:
% Copyright (C) 2005 artofcode LLC, Benicia, CA.  All rights reserved.
%%BeginResource: procset GS_epswrite_2_0_1001
/GS_epswrite_2_0_1001 80 dict dup begin
/!{bind def}bind def/#{load def}!/N/counttomark #
/rG{3{3 -1 roll 255 div}repeat setrgbcolor}!/G{255 div setgray}!/K{0 G}!
/r6{dup 3 -1 roll rG}!/r5{dup 3 1 roll rG}!/r3{dup rG}!
/w/setlinewidth #/J/setlinecap #
/j/setlinejoin #/M/setmiterlimit #/d/setdash #/i/setflat #
/m/moveto #/l/lineto #/c/rcurveto #
/p{N 2 idiv{N -2 roll rlineto}repeat}!
/P{N 0 gt{N -2 roll moveto p}if}!
/h{p closepath}!/H{P closepath}!
/lx{0 rlineto}!/ly{0 exch rlineto}!/v{0 0 6 2 roll c}!/y{2 copy c}!
/re{4 -2 roll m exch dup lx exch ly neg lx h}!
/f{P fill}!/f*{P eofill}!/s{H stroke}!/S{P stroke}!
end def
%%EndResource
/pagesave null def
%%EndProlog
%%Page: 1 1
%%BeginPageSetup
GS_epswrite_2_0_1001 begin
/pagesave save store
0.012 0.012 scale
%%EndPageSetup
mark
15690 65160 48000 36000 re
255 G
15690 65160 48000 36000 re
f
83.3333 w
2 J
15690 65160 48000 36000 re
S
21690 68760 37200 28800 re
f
K
21690 68760 37200 28800 re
S
cleartomark end pagesave restore
 showpage
%%PageTrailer
%%Trailer
%%Pages: 1

>>>>> "Sascha" == Sascha  <sas...@gm...> writes:

    >> Using the agg backend you can obtain an RGBA buffer or RGB
    >> string which can then be loaded as a PIL Image for processing.
    >> I've adapted a the examples/agg_oo.py to demonstrate.

    Sascha> Thanks a lot, Nicolas! Excellent... no more temp file! It
    Sascha> took me some time to figure out how to get the PNG image
    Sascha> data from PIL, but it worked out quite well.


Could you post a complete example so that others won't have to spend
that extra time figuring out how to put all the pieces together?

Thanks,
JDH

> I posted this to the list a few days ago:
>
> Using the agg backend you can obtain an RGBA buffer or RGB string which
> can then be loaded as a PIL Image for processing.  I've adapted a the
> examples/agg_oo.py to demonstrate.

Thanks a lot, Nicolas! Excellent... no more temp file! It took me some time 
to figure out how to get the PNG image data from PIL, but it worked out 
quite well.

Sascha 

John Porter wrote:
> Hi,
> I have written some code which generates 3D plots, this was inspired by
> the 3D axes code posted recently.  The basic idea is that 2D Artist
> elements have their 'draw' method subverted to generate the projected 3D
> coordinates. The plot is interactive and allows panning and tilting of
> the graph by pressing and holding mouse-2.
> 
> I am new to this list, and was wondering where I should post the code
> (it consists of two modules).

Very cool!  I can report that it works under ipython -pylab with the TkAgg 
backend as well, using stock mpl 0.83.2.

Excellent work!

Cheers,

f

Hi John,

>I will, but it's very much work in progress....
>There are 
hardly any comments, but there are a few tests at the bottom 
>of 
mplot3d.

Very nice work, the script are working nice... mhm, I didn't 
understand the problem about WXAgg, I just commented out the lines 
involving self.toolbar.something, changed the default backend, and it's 
working also with WXAgg. But probably I did not understood correctly 
your email.

Thanks for the nice job.

Andrea.

I will be out of the office until September 26.  I will respond to your message as soon as I return.

Thank you,

Eli

John Hunter wrote:

>>>>>>"John" == John Porter <jp...@ca...> writes:
>>>>>>            
>>>>>>
>
>    John>      fig = p.figure() ax = mplot3d.Axes3D(fig)
>
>Very nice screenshot!! -- did you intend to the mplot3d module so we
>could test ourselves?
>
>JDH
>
>
>  
>
I will, but it's very much work in progress....
There are hardly any comments, but there are a few tests at the bottom 
of mplot3d.

John

I will be out of the office until September 26.  I will respond to your message as soon as I return.

Thank you,

Eli

I think (hope) what Martin (nice email address btw) means is that when you=
=20
use the history button it reverts back to the old axis limits, but not to=
=20
the old position.
The history function needs to be updated to both keep track of axes limits=
=20
and axes positions.
This is also important for the new axis('equal') command that was submitted=
=20
as a patch and will hopefully appear in the next release.
I guess this shouldn't be too difficult.
Mark

Date: Fri, 2 Sep 2005 16:11:45 +0200 (MEST)
From: "Martin Richter" <law...@gm...>
To: mat...@li...=20
>=20
> orge.net <http://orge.net>
> Subject: [Matplotlib-users]=20
> =3D?ISO-8859-1?Q?zoomhistory,_zoom_to_rectangle?=3D
>=20
> Hello,
>=20
> one of Matplotlib's greatest advantage (besides the great graphics of
> course) is the ability to zoom in into plotted curves. The zoomhistory is
> thereby a very good and useful tool.
> I figured out two things:
>=20
> 1) Unfortunetly this history seems not to work properly in some cases. I
> was able to track down this error on the call of the subplot-command (see
> example below).
> Is this a little bug or am I using those commands in a way they are not
> supposed to be used?

>>>>> "John" == John Porter <jp...@ca...> writes:

    John>      fig = p.figure() ax = mplot3d.Axes3D(fig)

Very nice screenshot!! -- did you intend to the mplot3d module so we
could test ourselves?

JDH

Hi,
I have written some code which generates 3D plots, this was inspired by
the 3D axes code posted recently.  The basic idea is that 2D Artist
elements have their 'draw' method subverted to generate the projected 3D
coordinates. The plot is interactive and allows panning and tilting of
the graph by pressing and holding mouse-2.

I am new to this list, and was wondering where I should post the code
(it consists of two modules).

This example code here generates the attached png:

def run1():
     delta = 0.025
     x = y = p.arange(-3.0, 3.0, delta)
     X, Y = p.meshgrid(x,y)

     Z1 = p.bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0)
     Z2 = p.bivariate_normal(X, Y, 1.5, 0.5, 1, 1)
     Z = Z2-Z1

     X = X * 10
     Y = Y * 10
     Z = Z * 500

     fig = p.figure()
     ax = mplot3d.Axes3D(fig)
     ax.plot_surface(X,Y,Z, div=10)

     ax.set_xlabel('X')
     ax.set_ylabel('Y')
     ax.set_zlabel('Z')

     fig.add_axes(ax)
     p.savefig("surface.png", dpi=40)
     p.show()

matplotlib's __init__.py is apparently looking
at os.environ['HOME'], but the default XP setting
for that is '%USERPROFILE%', which then gets passed
(*without* expansion) on by get_home even though it's
expansion is needed.  So import pylab does not work.

I don't have time to look at this now.
This is a common problem on Windows.
I'll post a solution I've found when I'm back home.

Cheers,
Alan Isaac

I have converted many eps files generated with matplotlib to pdf. This work=
s=20
well (for me) with both Acrobat 6 and GSview 4.0.
Mark