matplotlib-users Mailing List for matplotlib (Page 5)

>>>>> "Matt" == Matt Newville <new...@ca...> writes:

    >> > I've seen the matplotlib code, and have used a fair number of
    >> plotting >libraries in my day. The matplotlib results are
    >> wonderful, but the API is a bit goofy, don't you think? Does
    >> FigureCanvas->Figure->Axes make sense to you? I'd be OK with
    >> two of those, but I don't understand how three possibly 
    >> helps.
    >> 
    >> I don't think it's goofy at all.  You have FigureCanvas because
    >> seperating out the thing that "draws" the figure is the best
    >> way to implement backend neutrality.  You have Figure and Axes
    >> (rather than just Axes) because that's the best way to
    >> implement things like subplots, plotting overlapped axes, and
    >> figimage(), colorbars, and figure legends.

    Matt> I think we agree: the hierarchy is implementation driven,
    Matt> not use driven.

It depends on your perspective I guess.  Originally there was only a
Figure and Axes, and when we started supporting other backends than
GTK (eg WX) we needed to segregate the Figure from it's container to
provide a GUI independent way of representing the Figure.  In my view,
this was a use driven detail, since we wanted to use matplotlib with
other GUIs, but you may view it as an implementation driven, which it
is also.

If you are only using matplotlib in a single context, eg a WX App,
then yes, it is more overhead than you need.  But it is fairly useful
in a GUI neutral plotting library.

Because the GUI neutrality imposes some extra syntactic overhead when
working with OO matplotlib, I think it is a good idea to have GUI
specific OO wrappers to ease the common tasks, like you and Ken have
provided.


JDH

>>>>> "Graeme" == Graeme Lufkin <gra...@gm...> writes:
    Graeme> experience with matplotlib+PyGTK on platforms other than
    Graeme> Linux.  (Ahh, the joys of scientific programming: now
    Graeme> Windows.)  Perhaps wxWindows handles cross-platform apps
    Graeme> better, I'm not qualified to answer.  If other people are
    Graeme> interested, I could try writing up a Wiki page with one of
    Graeme> my small "matplotlib embedded in a GTK app" programs.  --

FYI, gtk was the first and only matplotlib backend for many releases,
then came PS and WX.  I use GTK/GTKAgg backends primarily for
application development with embedded matplotlib, and these apps run
on win32, OS X, linux and solaris.  So pygtk + matplotlib is a very
good combination for cross platform GUI developement, in my opinion.

JDH

On 12/9/05, Randewijk P-J <pjr...@su...> <pjr...@su...> wrote:
>
> Dear Paul,
>
>
> > It should depend on font.size in the rc file.
>
>
> That's what I thought.
>
> I changed the font.size to 5.
>
> Only my figtext's fontsize changed.  The legend's fontsize remained at
> (what appears to be) 12...
>
> I'm still running 0.84, can that be the problem ?


No.  This is a bug in the legend code.  The code initializes the text size
when the object is created, but does not update it at any later time.  This
should be fixed.

 -- Paul

--
Paul Barrett, PhD                   Johns Hopkins University
Assoc. Research Scientist     Dept of Physics and Astronomy
Phone: 410-516-5190            Baltimore, MD 21218

>>>>> "Michael" == Michael McKerns <mmc...@it...> writes:


    Michael> Matplotlib is currently too slow to render large
    Michael> datasets.  This needs improvement.  Is anyone working on
    Michael> this problem?  I believe this issue was also brought up
    Michael> at the last SciPy...


Hey Michael,

Performance questions are best addressed in the context of an example
script, with matplotlib version number and backend.  All of these can
have a big effect on the performance you are seeing.

Some commands (pcolor, scatter) are known to be too slow generally.
Others, like plotting markers, are highly optimized in recent version
of mpl for backend agg but not other backends.  imshow is about as
fast as we can make it for now...

So it would help to know in what context you are seeing performance
problems.  Sometimes it's as simple as improper use of mpl.  Eg

for line in some_big_data_set:
   plot(line)

will be an order of magnitude slower than using a line collection,
usually.

JDH

>>>>> "Charlie" == Charlie Moad <cw...@gm...> writes:

    Charlie> So I was fairly successful at performing the horrid act
    Charlie> known as building mpl for windows.  The problem I run
    Charlie> into (py24) is the "--install-script postinstall.py"
    Charlie> flag.  Where/what is this script?  The build works if I
    Charlie> omit this.

Historical detritus I think -- you can safely remove this from your
build and the mpl docs / setup code.

JDH

>>>>> ""Strauss" == "Strauss JM <jst...@su...>" <jst...@su...> writes:

    "Strauss> My problem however is that I am unable to change my font
    "Strauss> style (it seems to be Times New Roman or similar and I
    "Strauss> want it to be Arial) for the labels ext., even though I
    "Strauss> can change just about everything else there is to
    "Strauss> change, including font size, the coverage of the canvas
    "Strauss> by the figure and so forth.  This I do be merely
    "Strauss> changing the matplotlibrc file copied to my application
    "Strauss> directory.  Are there any suggestions or may be a
    "Strauss> request for more detail information regarding my
    "Strauss> problem?


Not sure -- maybe matplotlib is not finding your fonts.  Have you seen
http://matplotlib.sourceforge.net/fonts.html which gives some info
about setting font paths.  I suggest removing your matplotlib
generated font cache (~/.matplotlib/ttffont.cache) and then rerunning
your script with the --verbose-debug flag to see what fonts it's
looking for, finding and using.

JDH

>>>>> "Mike" == Mike Dewhirst <mi...@de...> writes:

    Mike> The entities are linked with named n:m relationships and I'd
    Mike> like to select one and display it in a box (with the entity
    Mike> name) and all related entities likewise in boxes linked to
    Mike> each other by lines representing the relationships tagged
    Mike> with the names of those relationships.

matplotlib may not be the best choice (someone already pointed you to
graphviz and pydot).  See also pyx.

But there is a graph drawing module for matplotlib -- see

  http://networkx.sf.net

JDH

>>>>> "Mark" == Mark Bakker <ma...@gm...> writes:

    Mark> Does anybody know a way to mix mathtext and regular text,
    Mark> for example in the axis label?

    Mark> Something like

    Mark> xlabel(r'$\rho^2$ along axis')

    Mark> doesn't work. I know this is mentioned in the manual.  Just
    Mark> wondering if somebody knows a workaround rather than using
    Mark> the full Latex option.

This isn't supported yet, but it would be nice to do this.  The two
things that have kept me from focusing more attention to mathtext are
the fact that the bakoma fonts we use are so bad noone wants to use
them (Nicholas recently submitted a patch for PS which allows
matplotlib mathtext to work with native PS AFM fonts)  and that there
is not TeX/LaTeX integration.  Nonetheless, it would be nice to
support this syntax.  

The current workaround is to use the roman fonts

    Mark> xlabel(r'$\rho^2$\ \rm{along\ axis}')

but since kerning is not supported in the bakoma fonts it doesn't look
that good, typically.

JDH

>>>>> "psong" == psong  <ps...@br...> writes:

    psong> Hi guys, I need to make a figure with custom axis
    psong> location. I would like to be able to put xaxis and yaxis at
    psong> arbitrary location (instead of the default location of top,
    psong> bottom, left, right). One such example would be the
    psong> symbolline example at
    psong> http://pyx.sourceforge.net/examples/graphs/index.html.  I
    psong> could not figure out how to do this with matplotlib after
    psong> reading the manual and going through the examples on
    psong> matplotlib website. I can draw the axis line myself (with
    psong> axhline and axvline) but it was very tedious and the result
    psong> does not look good. Can this be readily done with
    psong> matplotlib? Any suggestion will be appreciated.

There is no better way to do it current;y than they way you are doing
it.  It's a limitation and fixing it is on the goals list.  If you
want to take a crack at it, check out the code in axis.py....

JDH

>>>>> "Charlie" == Charlie Moad <cw...@gm...> writes:

    Charlie> Bump...... Anybody.........

You might want to look at Mark's work on axis equal and axis scaled.
It might help to place the radio widgets into an axes that has the
equal property set.

See Axes.set_aspect.

JDH

On Saturday 10 December 2005 10:25 am, Jiri Polcar wrote:
>     Hallo,
>
> when I use
>
>     rc('text', usetex=True)
>
> and then
>
>     savefig('main.eps')
>
> file 'main.eps' is very strange. BBox is bigger than plot and when I use
> 'ps2epsi' it's failed. Wihtout
>
>     rc('text', usetex=True)
>
> line works 'main.eps' normaly. What I must to do to get "correct" EPS
> file with TeX processing?

try updating to gnu-ghostscript-8.16

    Hallo,

when I use

    rc('text', usetex=True)

and then

    savefig('main.eps')

file 'main.eps' is very strange. BBox is bigger than plot and when I use
'ps2epsi' it's failed. Wihtout

    rc('text', usetex=True)

line works 'main.eps' normaly. What I must to do to get "correct" EPS
file with TeX processing?

--
JP

>/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_gtk.py
>      4 def fn_name(): return sys._getframe(1).f_code.co_name
>      5
>----> 6 import gobject
>      7 import gtk; gdk = gtk.gdk
>      8 import pango
>
>ImportError: No module named gobject
>
>
>If someone has seen this befor, please tell me how to solve the problem...
>
>  
>
looks like for me the gobject module is here:
/usr/lib/python2.3/site-packages/gtk-2.0/gobject.so

so probably you don't have the python gtk-2.0 bindings installed...

you don't mention which distro you use..  but say if it's debian based 
(or fedora/redhat with apt-get installed), do:

$> apt-cache search pygtk

then

$> apt-get install <pygtk2 package>

... might need pygtk2-devel  as well, if you're building matplotlib... 
can't remember.

cheers,
peter



-- 
Peter Groszkowski         Gemini Observatory
Tel: +1 808 9742509       670 N. A'ohoku Place
Fax: +1 808 9359235       Hilo, Hawai'i 96720, USA 

Hi to all,

I'm interessed in having an interactive plotting window where one of the
subplots would be for console output.
For example I would like to print in a subplot (similar to a console output=
)
the several computed values of a selecetd span from some other subplot.

Does anyone needed a similar feature?

Thanks in advance for your help.

Hugo Gamboa

Hi guys,
  I need to make a figure with custom axis location. I would like to be able
to put xaxis and yaxis at arbitrary location (instead of the default location
of top, bottom, left, right). One such example would be the symbolline
example at
http://pyx.sourceforge.net/examples/graphs/index.html.
I could not figure out how to do this with matplotlib after reading the manual
and going through the examples on matplotlib website. I can draw the axis
line myself (with axhline and axvline) but it was very tedious and the result
does not look good. Can this be readily done with matplotlib? Any suggestion
will be appreciated.

Best Wishes,

Simon

Dear Paul,


> It should depend on font.size in the rc file.


That's what I thought.

I changed the font.size to 5.

Only my figtext's fontsize changed.  The legend's fontsize remained at =
(what appears to be) 12...

I'm still running 0.84, can that be the problem ?

Regards,

Peter-Jan

Hi to all,

I'm interessed in having an interactive plotting window where one of the
subplots would be for console output.
For example I would like to print in a subplot (similar to a console output=
)
the several computed values of a selecetd span from some other subplot.

Does anyone needed a similar feature?

Thanks in advance for your help.

Hugo Gamboa

On 12/9/05, Randewijk P-J <pjr...@su...> <pjr...@su...> wrote:
>
>
> The font is defined as 'smaller', but 'smaller' than what...?


Smaller than the default font size, usually 12pt.  This option allows you t=
o
set the default font size for the entire plot and then just adjust the axis=
,
label, etc. font sizes relative to it. Therefore, if you decide that all th=
e
fonts of a plot are too small, then you only need to adjust the default fon=
t
size and the others will scale proportionaly.

It is not affected (imho) by either of the following settings in my
> 'matplotlibrc' file:
>
> "...
> font.size                 : 12


It should depend on font.size in the rc file.

...
> axes.labelsize    : 16
> ...
> tick.labelsize      : 10
> ..."
>

 -- Paul

--
Paul Barrett, PhD                   Johns Hopkins University
Assoc. Research Scientist     Dept of Physics and Astronomy
Phone: 410-516-5190            Baltimore, MD 21218

Dear All,

I want to change the fontsize used for my legends.

Analogues to the 'title', 'figtext', 'xlabel' and 'ylabel' commands, it
would have been nice to write:

legend(('...'),loc=3D'...',fontsize=3D10)

Unfortunately this is not (yet) implemented...

Time Out:
=3D=3D=3D=3D=3D=3D=3D=3D=3D
Can I make a RFC for this feature to be added...?
And the same for the 'axis' command, e.g. 'axis([...],fontsize=3D10)',
would also be a nice addition to mpl.
=3D=3D=3D=3D=3D=3D=3D=3D=3D

Back to the fontsize issue:

In 'legend.py':

"...
def __init__(self, parent, handles, labels, loc,
                 isaxes=3DTrue,
                 numpoints =3D 4,      # the number of points in the
legend line
                 prop =3D FontProperties(size=3D'smaller'),
                 pad =3D 0.2,          # the fractional whitespace =
inside
the legend border
                 markerscale =3D 0.6,    # the relative size of legend
markers vs. original
                 # the following dimensions are in axes coords
                 labelsep =3D 0.005,     # the vertical space between =
the
legend entries
                 handlelen =3D 0.05,     # the length of the legend =
lines
                 handletextsep =3D 0.02, # the space between the legend
line and legend text
                 axespad =3D 0.02,       # the border between the axes =
and
legend edge

                 shadow=3DFalse,
                 ):
..."

The font is defined as 'smaller', but 'smaller' than what...?

It is not affected (imho) by either of the following settings in my
'matplotlibrc' file:

"...
font.size		  : 12
...
axes.labelsize	  : 16
...
tick.labelsize      : 10
..."

Kind regards,

Peter-Jan

> --- Ursprüngliche Nachricht ---
> Von: "Carl Dr. Kleffner" <cmk...@gm...>
> An: mat...@li...
> Kopie: Darren Dale <dd...@co...>
> Betreff: Re: [Matplotlib-users] scatter with dots?
> Datum: Thu, 8 Dec 2005 16:36:09 +0100 (MET)
> 
> I will look into this. I'm very short on time, so this may take some....
> days. 
> Drawing markers with postscript procedures seems to me the favorite
> solution.
> If anyone is interested in that stuff: I found a wonderfull online book: 
> 'Mathematical Illustrations' from Bill Casselmann.
> http://www.math.ubc.ca/~cass/graphics/manual/
> It is a postscript book from the mathematical viewpoint.
> 
> Regards
> 
> Carl
> 

I'm now looking for another quick solution for postscript scatterplots:
is there an easy way to activate the markers '.' or ',' for 
scatterplots with postscript backends?

Carl

-- 
Telefonieren Sie schon oder sparen Sie noch?
NEU: GMX Phone_Flat http://www.gmx.net/de/go/telefonie

Hi,

I've been giving matplotlib (0.85) a spin, as a front end for 
'exploring' scientific simulation results. Now I've got the data in and 
had a play, there's been a few things which have confused me somewhat 
about the API/features:

* One of the most obvious obstacles at the moment is that I'm plotting 
surface plots, using contour[f] primarily, and haven't found an obvious 
way of removing 'previous' results from axes. Should this work with 
'gca().hold(False)' or equivalent? It doesn't seem to. As such I'm 
currently deleting and recreating the axes each time I change the data. 
  While this is not great, it is faster than not doing so, since 
otherwise the graph accumulates contours and increasingly takes long to 
redraw. I suppose I'm asking whether there is the equivalent of 
[axes].set_ydata(), but for contours :)

* Previously I've been using gnuplot to create pngs, which I can then 
form into a time series, mostly just plotting the data as a 'matrix'. 
While I take it for granted that python/matplotlib are loading/plotting 
the data in 'real-time' compared to just flicking between 
gnuplot-generated png's, pcolor is rather slow for me, and I'm unsure 
exactly what the other approaches (eg. imshow?) are targeted towards, or 
when they are appropriate compared to pcolor. However, not only is 
pcolor slow, but for some reason it defaults to automatically selecting 
a different (overly large) automatic axis-range than contour[f].

* For some reason my install leaves me with pylab windows which have no 
proper icons in the bottom button bar. I've set MATPLOTLIBDATA and 
PYTHONPATH, since I installed the modules into a subdir of my home 
directory.

* Closing the pylab windows using the window-manager results in the 
python process continuing - should this be calling some function to 
interrupt the show() function? (I'm running GTK/GTKAgg if its relevant)

Nevertheless, given these annoyances, I'm quite happy with the results 
so far - it is perhaps already simpler than the system I had been using 
previously, and has taken very little time to get to grips with :)
Having said that, I'm not entirely clear whether pylab is intended to be 
'the' interface to matplotlib, or just a simplified front-end - it seems 
quite confusing from reading some of the online documents.

Thanks for matplotlib, (I'll think of other things to ask, in time!)

		Hello,

I did probably something not good but it seems for me that the legend() 
function is not working properly (at least with errorbar)

x = arange(0,1.0,0.01)
p1 = errorbar(x,x,x,fmt='o') # or errorbar(x,x,x,fmt='o')
legend()

it seems to put in the legend all the points and lines.

I tried to do a

legend((p1),('p1'))

but it's not working, you have to do:

legend((p1,),('p1',))

to obtain the legend. Perhaps that must be indicate in the documentation 
that a you need a tuple and the method to have a legend with errorbar.


Thanks,

N.

			Hi,

I saw a small problem with the color.

setp(line,markerfacecolor=(48,48,48,))
setp(line,markerfacecolor='#303030')


don't give the same result but if I understand correctly this page 
http://www.w3schools.com/html/html_colorsfull.asp
that must be the same color.

Regards,

N.

Currently in matplotlib 0.85 we have this to support py2exe starting at
line 392 in __init__.py (Revision: 1.83):

    if sys.platform=='win32' and sys.frozen:
        path = os.path.join(os.path.split(sys.path[0])[0],
'matplotlibdata')
        if os.path.isdir(path):  return path
        else:
            # Try again assuming sys.path[0] is a dir not a exe
            path = os.path.join(sys.path[0], 'matplotlibdata')
            if os.path.isdir(path): return path

Wheras modifying line 392 to include darwin as well as win32 we can
allow py2app on OS X to work with matplotlib in the same way that py2exe
does:

    if sys.platform in ('win32','darwin') and sys.frozen: 
        path = os.path.join(os.path.split(sys.path[0])[0],
'matplotlibdata') 
        if os.path.isdir(path):  return path 
        else:
            # Try again assuming sys.path[0] is a dir not a exe 
            path = os.path.join(sys.path[0], 'matplotlibdata') 
            if os.path.isdir(path): return path


I have found this modification useful in making distributable py2app
applications for systems without matplotlib installed.


Richard Bolt
Texmate, Inc.

Hi again list,

Sorry to insist but this problem stuck me a lot.

I'm working in matplotlib OO mode.

I first create an instance of Subplot(): a = Subplot(f,111) with f an 
existing figure.
I plot some basic data using a.plot([1,2,3])
Then i add this subplot to the figure with the method f2.add_subplot(a).
The subplot is well displayed in the figure.

But my problem is i can't zoom on the figure. Xlabel and YLabel are 
redrawn but no the subplot.

Can anybody give me a solution please?
I need to create separately the figure and the subplot.

Thanks a lot,
Philippe Collet