matplotlib-users Mailing List for matplotlib

matploblib communication problem, graphics question
==========================================

i've had a hard time today to drill down on some infos
about matplotlib of http://matplotlib.sourceforge.net/.
this is an sf.net-managed project, its mailing lists are
managed by <shudder/> gnu mailman in a pre-1994 version.

still there is a sf.net standard forum interface, which
however denies me to post. i've set up an account on
sourceforge---not an experience i need; boarding an
intercontinental flight is swift in comparison.

but having an account on sf.net is not enough to post to
a mailing list there, so i filled out a second longish
form to subscribe to the list thru the <horrors/>
mailman interface. i had to re-enter my email address.

now what is left to me is to try writing directly to
mat...@li... and then scoop
it up on 
http://sourceforge.net/mailarchive/forum.php?forum_name=matplotlib-users

as it is so incredibly hard to make oneself heard on
the matplotlib list, i realized that questions from
outsiders are maybe not welcome, so i do a cross-post
to reach more audience.

i need to do some raster-image scaling and i've been
hunting hi and lo for a python library that can do that.
so far choices are (in order of perceived aptness)::

imagemagick of old,

pythonware.com/products/pil,

antigrain.com,

matplotlib,

cairo of cairographics.org.

Cairo is definitely may favorite here. i know with
certainty that cairo is good at scaling images, as
firefox3 is using it to achieve a smoothness and
readability in scaled images that rivals the quality
of safari’s.

but i have been unable to uncover any information
about raster-image scaling in cairo---can’t be, right?
an open source project that becomes part of firefox3
and i can’t find out how to use their flagship
functionality?

so i went to matplotlib. i now have these methods to
open image files with matplotlib::

def get_image_jpg():
import Image
from pylab import *
import numpy
print dir( numpy )
from numpy import int8, uint8
# these lines are incredible -- just open that damn jpg. can be as 
simple as `load(route)` -- ALL the pertinent
# information well be in time derived from the route and the routed 
resource structure (the router, and the
# routee). pls someone giveme a `MATPLOBLIB.read()`, a 
`MATPLOBLIB.load()`, or a `MATPLOBLIB.get()` already.
image = Image.open( image_locator )
rgb = fromstring( image.tostring(), uint8 ).astype( float ) / 255.0
# rgb = resize( rgb,( image.size[ 1 ], image.size[ 0 ], 3 ) )
rgb = resize( rgb,( 100, 150, 3 ) )
imshow( rgb, interpolation = 'nearest' )
axis( 'off' ) # don’tdisplaytheimageaxis
show()

def get_image_png( image_locator ):
from pylab import imread as _read_png
from pylab import imshow as _show_image
from pylab import gray
from pylab import mean
a = imread( image_locator )
#generates a RGB image, so do
aa=mean(a,2) # to get a 2-D array
imshow(aa)
gray()

quite incredible, right? it can somehow be done, but
chances are you drown in an avalanche of boiler plate.
and sorry for the shoddy code, i copied it from their
website.

so they use pil to open an image file. pil’s image
scaling is 1994, and the package is hardly maintained
and not open. yuck. whenever you have a question
about imaging in python people say ‘pill’ like they
have swallowed one.

let’s face it, pil is a bad choice to do graphics.
here i did install pil, because matplotlib seemed to
be basically handling raster-images and image
transformations.

the matplotlib people have the nerve to put a short
doc to their root namespace items, as are, `axhspan`,
`cla`, `gcf`, and such more. this interface is
hardly usable. it shouldn’t be that hard to open an
image file in an image manipulation library. nobody
wants to maintain that kind of sphpaghetti.

i haven’t been succesful so far to find out how to
scale an image in cairo or matlotlib, or an other
alternative. please don’t sugggest doing it with
pil or imagemagick, i won’t answer.

is there any coherent python imaging interest group
out there? can i do it with pyglet maybe?

cheers & ~flow

On Friday 23 May 2008 12:25:39 pm Friedrich Hagedorn wrote:
> On Fri, May 23, 2008 at 05:30:02PM +0200, Friedrich Hagedorn wrote:
> > The next problem is that the standard size of the mpl graphic (8, 6)
> > inches is too big for my latex document (0.5\linewidth). Therefore I must
> > scale the mpl graphic (\includegraphics[width=0.5\linewidth]{...}). But
> > with this scaling the font in the mpl graphic are also scaled and I have
> > no chance adapeting the two fonts (mpl, latex) without manual iterations.
> >
> > Ok, I could adjust the figsize but the last time I did it (long time ago)
> > there were other misplaced objects in the mpl graphic (I dont remember
> > exactly, sorry).
>
> I tried this now with (width = 7cm = 2.67in)
>
> In [1]: figure(figsize=(2.67,2))
> Out[1]: <matplotlib.figure.Figure object at 0x8c3b36c>
>
> In [2]: subplot(111)
> Out[2]: <matplotlib.axes.AxesSubplot object at 0x8c3b3ec>
>
> and the problem is that the remaining (abolute) space of the margin
> ist too small for the whole labeling (ticks and axis). But I dont
> want to adjust all the default values every time a what a plot in
> my latex document.
>
> On Fri, May 23, 2008 at 12:00:03PM -0400, Darren Dale wrote:
> > Wouldn't this cause some problems with how the text is layed out on
> > the canvas? The way it works now, a title can be centered over the axes
> > because the extents of the text are known. If you allow the fonts and
> > font sizes to be dictated by the latex document, they will end up being
> > positioned incorrectly.
>
> Shortly: Yes this is a problem but pgf could solve it.
>
> I dont know it exactly but if you do all the graphic stuff with pgf in
> latex so you can adjust the text boxes in a various way in respect to
> different points. E.g. baseline -left, -right, -center and so on. This is
> explaind in the pgfmanual in section 53.3.3.
>
> If I fly over the pgfmanual I get the impression that I could do
> everything with it :-) But to do this its a hard work (for beginners).
>
> Therefore I like to have the convinient pylab-interface to create pretty
> standard plots for latex.

I'll keep it in mind, but I have just committed myself to another mpl-related 
project for the summer, so I dont think I will have time to look into this 
for a while. But we love code submissions...

On Fri, May 23, 2008 at 05:30:02PM +0200, Friedrich Hagedorn wrote:
>
> The next problem is that the standard size of the mpl graphic (8, 6) inches
> is too big for my latex document (0.5\linewidth). Therefore I must scale
> the mpl graphic (\includegraphics[width=0.5\linewidth]{...}). But with this
> scaling the font in the mpl graphic are also scaled and I have no chance
> adapeting the two fonts (mpl, latex) without manual iterations.
> 
> Ok, I could adjust the figsize but the last time I did it (long time ago)
> there were other misplaced objects in the mpl graphic (I dont remember
> exactly, sorry).

I tried this now with (width = 7cm = 2.67in)

In [1]: figure(figsize=(2.67,2))
Out[1]: <matplotlib.figure.Figure object at 0x8c3b36c>

In [2]: subplot(111)
Out[2]: <matplotlib.axes.AxesSubplot object at 0x8c3b3ec>

and the problem is that the remaining (abolute) space of the margin
ist too small for the whole labeling (ticks and axis). But I dont
want to adjust all the default values every time a what a plot in
my latex document.

On Fri, May 23, 2008 at 12:00:03PM -0400, Darren Dale wrote:
>
> Wouldn't this cause some problems with how the text is layed out on
> the canvas? The way it works now, a title can be centered over the axes 
> because the extents of the text are known. If you allow the fonts and 
> font sizes to be dictated by the latex document, they will end up being 
> positioned incorrectly.

Shortly: Yes this is a problem but pgf could solve it.

I dont know it exactly but if you do all the graphic stuff with pgf in
latex so you can adjust the text boxes in a various way in respect to
different points. E.g. baseline -left, -right, -center and so on. This is
explaind in the pgfmanual in section 53.3.3.

If I fly over the pgfmanual I get the impression that I could do 
everything with it :-) But to do this its a hard work (for beginners).

Therefore I like to have the convinient pylab-interface to create pretty
standard plots for latex.


By,  Friedrich

Neil Crighton wrote:
> I'd like to plot values where the area of a marker is proportional to
> some value.  How is the size value given in, say:
> 
> scatter(x,y,'o',s=10)
> 
> used to generate the markers?  By eye it looks like the size value is
> proportional to the area (i.e. proportional to the radius squared for
> circle markers), but it would be nice to know for sure.

Hi Neil,

good eyes ;-) Have a look at the scatter documentation:

"s is a size in points^2.  It is a scalar
or an array of the same length as x and y."

Manuel

> Thanks,
> Neil
> 
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On Friday 23 May 2008 11:30:03 am Friedrich Hagedorn wrote:
> On Fri, May 23, 2008 at 10:51:05AM -0400, Darren Dale wrote:
> > On Friday 23 May 2008 10:35:14 am Friedrich Hagedorn wrote:
> > > Hello,
> > >
> > > are there plan to implement a new backend for the latex proper use
> > > which create the drawing comand in the pgf language? With this kind
> > > of graphic creation I could overcome all the (font-) scaleing problems
> > > I have when I want to include a mpl graphic in my latex document.
> >
> > I'm not familiar with pgf, could you provide some more information?
>
> pgf is a tex-based graphic language similar to ps-tricks but also
> for pdftex. There are very nice graphics:
>
>   http://www.ctan.org/get/graphics/pgf/base/doc/generic/pgf/pgfmanual.pdf
>
> The basic drawing is like this (a cross)
>
> \begin{tikzpicture}
>   \draw (-1.5,0) -- (1.5,0); % horizontal line
>   \draw (0,-1.5) -- (0,1.5); % vertical line
>   \draw (1,1) node{$y=x^2$}; % text label
> \end{tikzpicture}
>
> There also exsits makro pakages for (more ore less convinent) data plots
> but then you dont have the nice python interface.
>
> > What problems do you have with font scaling, and what additional
> > capabilities do you think such an approach would offer?
>
> I want that fonts in the mpl graphics have the same (or otherwise related)
> proerties as the main-font in my latex document.

I understand this desire. John Hunter came up with the idea of the current 
latex support around the time that I was writing my dissertation. Like you 
note below, we sometimes have to iterate to get just what we want, but I 
think that is unavoidable. More below...

> So, therefore I have to know all the font properties from my latex
> document (\normalfont): type, family, size.
>
> The next problem is that the standard size of the mpl graphic (8, 6) inches
> is too big for my latex document (0.5\linewidth). Therefore I must scale
> the mpl graphic (\includegraphics[width=0.5\linewidth]{...}). But with this
> scaling the font in the mpl graphic are also scaled and I have no chance
> adapeting the two fonts (mpl, latex) without manual iterations.
>
> Ok, I could adjust the figsize but the last time I did it (long time ago)
> there were other misplaced objects in the mpl graphic (I dont remember
> exactly, sorry).
>
> But if I had the whole mpl graphic as pgf commands there would be no
> problem with the font stuff, scaleing and line widths. And may be you
> could extend the mpl graphic with some tricky (and eye candy) pgf
> extensions (ok I am also a beginner with the pgf language but its
> realy powerfull).

Wouldn't this cause some problems with how the text is layed out on the 
canvas? The way it works now, a title can be centered over the axes because 
the extents of the text are known. If you allow the fonts and font sizes to 
be dictated by the latex document, they will end up being positioned 
incorrectly.

P.S. please be careful that your responses go to the userlist

On Fri, May 23, 2008 at 10:51:05AM -0400, Darren Dale wrote:
> On Friday 23 May 2008 10:35:14 am Friedrich Hagedorn wrote:
> > Hello,
> >
> > are there plan to implement a new backend for the latex proper use
> > which create the drawing comand in the pgf language? With this kind
> > of graphic creation I could overcome all the (font-) scaleing problems
> > I have when I want to include a mpl graphic in my latex document.
> 
> I'm not familiar with pgf, could you provide some more information? 

pgf is a tex-based graphic language similar to ps-tricks but also
for pdftex. There are very nice graphics:

  http://www.ctan.org/get/graphics/pgf/base/doc/generic/pgf/pgfmanual.pdf

The basic drawing is like this (a cross)

\begin{tikzpicture}
  \draw (-1.5,0) -- (1.5,0); % horizontal line
  \draw (0,-1.5) -- (0,1.5); % vertical line
  \draw (1,1) node{$y=x^2$}; % text label
\end{tikzpicture}

There also exsits makro pakages for (more ore less convinent) data plots 
but then you dont have the nice python interface.

> What problems do you have with font scaling, and what additional 
> capabilities do you think such an approach would offer?

I want that fonts in the mpl graphics have the same (or otherwise related)
proerties as the main-font in my latex document.

So, therefore I have to know all the font properties from my latex 
document (\normalfont): type, family, size.

The next problem is that the standard size of the mpl graphic (8, 6) inches
is too big for my latex document (0.5\linewidth). Therefore I must scale
the mpl graphic (\includegraphics[width=0.5\linewidth]{...}). But with this
scaling the font in the mpl graphic are also scaled and I have no chance
adapeting the two fonts (mpl, latex) without manual iterations.

Ok, I could adjust the figsize but the last time I did it (long time ago)
there were other misplaced objects in the mpl graphic (I dont remember
exactly, sorry).

But if I had the whole mpl graphic as pgf commands there would be no
problem with the font stuff, scaleing and line widths. And may be you
could extend the mpl graphic with some tricky (and eye candy) pgf 
extensions (ok I am also a beginner with the pgf language but its
realy powerfull).

BTW. In the same way I can create very nice ciruit schematic with 
CircuitMacros

  www.ece.uwaterloo.ca/~aplevich/Circuit_macros/html/examples.pdf
  
I hope you could understand what I mean :-)


By,  Friedrich

> On Friday 23 May 2008 10:35:14 am Friedrich Hagedorn wrote:
>> are there plan to implement a new backend for the latex proper use 
>> which create the drawing comand in the pgf language? With this kind 
>> of graphic creation I could overcome all the (font-) scaleing problems 
>> I have when I want to include a mpl graphic in my latex document. 

On Fri, 23 May 2008, Darren Dale wrote:
> I'm not familiar with pgf, could you provide some more information? What 
> problems do you have with font scaling, and what additional capabilities do 
> you think such an approach would offer? 

PGF is the LaTeX portable graphics format, which can be used 
both with PDF production and DVI->PS production.  It is 
a very nice innovation for LaTeX users, especially via its 
TikZ interface.

PGF users get the full power of LaTeX for typesetting on 
their diagrams. This is great.  For this reason, I often 
write PGF/TikZ code by hand when my graphs are simple.

A PGF backend would be wonderful for LaTeX users who are 
producing documents for final distribution.

All that said, I suspect the payoff to me personally would 
be modest, as I am almost always producting documents for 
later publication, at which point I generally need to 
provide EPS or PDF figures.

If you are still interested, you may find the following to 
be useful:
<URL:http://www.tug.org/pracjourn/2007-1/mertz/>

hth,
Alan Isaac

I'd like to plot values where the area of a marker is proportional to
some value.  How is the size value given in, say:

scatter(x,y,'o',s=10)

used to generate the markers?  By eye it looks like the size value is
proportional to the area (i.e. proportional to the radius squared for
circle markers), but it would be nice to know for sure.

Thanks,
Neil

On Friday 23 May 2008 10:35:14 am Friedrich Hagedorn wrote:
> Hello,
>
> are there plan to implement a new backend for the latex proper use
> which create the drawing comand in the pgf language? With this kind
> of graphic creation I could overcome all the (font-) scaleing problems
> I have when I want to include a mpl graphic in my latex document.

I'm not familiar with pgf, could you provide some more information? What 
problems do you have with font scaling, and what additional capabilities do 
you think such an approach would offer?

Darren

Hello,

are there plan to implement a new backend for the latex proper use
which create the drawing comand in the pgf language? With this kind
of graphic creation I could overcome all the (font-) scaleing problems 
I have when I want to include a mpl graphic in my latex document.

Even gnuplot has such an backend but I dont want to use it anymore :-)


By,  Friedrich

Robert Garrett schrieb:
> Hi,
> I'd like to use Python to plot data in real-time.  I've created a GUI 
> using wxPython and have embedded a Matplotlib graph into a pane.  My 
> problem is that I don't know the best way to update the graph.  What's 
> the recommended method for this?
First use the set_data (or set_xdata, set_ydata) methods of the artists
which you might have created with the plot command. Then redraw the
figure on screen using a .canvas.draw() call of your figure object.

> The data comes from a peripheral device connected to the PC, so I also 
> need a way of regularly polling the hardware.  I've managed this using 
> a separate thread, but this doesn't work for updating the graph (Xlib 
> complained).
In wxPython changing the GUI should only happen from the main thread.
Use wx.PostEvent with some user defined event object to send the newly
aquired data from the acquisition thread to the main thread. In the
event handling routine update the graph as described above. See the
threading demo of the wxPython demo how to implement this.

Gregor

Hi,
I'd like to use Python to plot data in real-time.  I've created a GUI using
wxPython and have embedded a Matplotlib graph into a pane.  My problem is
that I don't know the best way to update the graph.  What's the recommended
method for this?  The data comes from a peripheral device connected to the
PC, so I also need a way of regularly polling the hardware.  I've managed
this using a separate thread, but this doesn't work for updating the graph
(Xlib complained).

I'm sure this must be something that people have done many times before, but
I've been unable to find a simple explanation on how to achieve it!  Any
help or suggestions would be much appreciated.

Thanks,
Rob

On Thu, May 22, 2008 at 03:25:41PM -0700, Christopher Brown wrote:
> Hi Users,
> 
> What is the best way to add a subscript to a tick label using the 
> default font?

Hm, could you give a short example of what you want? I do subscripts
with this code:

In [1]: subplot(111)
Out[1]: <matplotlib.axes.AxesSubplot object at 0x8cbbf2c>

In [2]: xticks((0, 0.5, 1), (r'$t_0$', r'$t_1$', r'$t_2$'), fontsize=18)
Out[2]: 
([<matplotlib.axis.XTick object at 0x8cd028c>,
  <matplotlib.axis.XTick object at 0x8ffb0ac>,
  <matplotlib.axis.XTick object at 0x8ffb0cc>],
 <a list of 3 Text xticklabel objects>)


But sure this is not the best way to do it :-)


By,  Friedrich