matplotlib-users Mailing List for matplotlib (Page 13)

Hello,
does anybody have an idea how to set the x-axis scale to logarithmic on 
an errorbar plot? In other words, is there any way to plot data with 
error bars while having x-axis scale logarithmic?
Many thanks in advance for any useful suggestions.
Darius

>>>>> "Michael" == Michael J T O'Kelly <mo...@MI...> writes:
 Michael> I want to be able to specify the size of points in a
 Michael> scatter plot in data coordinates rather than points^2.
 Michael> The points should change in size at different zoom
 Michael> levels. Is there a built-in way to do this, or a good
 Michael> workaround for now?
You can't do this with the built-in scatter or RegularPolyCollection
(which scatter uses) because these assume a size in points. But you
can roll your own PolyCollection fairly easily
import matplotlib.cm as cm
import matplotlib.numerix as nx
from matplotlib.collections import PolyCollection
from pylab import figure, show
xs, ys, radii, colors = nx.mlab.rand(4,100)
radii *= 0.1
def poly(x,y,r,numsides):
 theta = 2*nx.pi/numsides*nx.arange(numsides) 
 return zip(x + r*nx.cos(theta), y + r*nx.sin(theta))
verts = [poly(x,y,r,6) for x,y,r in zip(xs, ys, radii)]
col = PolyCollection(verts)
col.set_array(colors)
col.set_cmap(cm.hot)
fig = figure()
ax = fig.add_subplot(111, xlim=(0,1), ylim=(0,1), aspect=1)
ax.add_collection(col)
show()

I want to be able to specify the size of points in a scatter plot in 
data coordinates rather than points^2. The points should change in size 
at different zoom levels. Is there a built-in way to do this, or a good 
workaround for now?
Thanks,
Michael

You're quite right. Thank you.
Charlie Moad wrote:
> Sounds like you need to upgrade numpy to 0.9.8.
> 
> - Charlie

Sounds like you need to upgrade numpy to 0.9.8.
- Charlie
On 7/3/06, Michael J.T. O'Kelly <mo...@mi...> wrote:
> I get a mysterious problem when I try to upgrade from 87.2 to 87.3.
>
> At first it complained of a bad configuration file. Once that was
> corrected, though, matplotlib still crashes Python as soon as "import
> pylab" or "import matplotlib" is called. No message of any kind is passed.
>
> The Windows error report says the exception was in multiarray.pyd. I
> can reinstall 87.2 and everything is fine. Any idea what the problem
> might be?
>
>
> Thanks!
>
> --Michael
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I get a mysterious problem when I try to upgrade from 87.2 to 87.3.
At first it complained of a bad configuration file. Once that was 
corrected, though, matplotlib still crashes Python as soon as "import 
pylab" or "import matplotlib" is called. No message of any kind is passed.
The Windows error report says the exception was in multiarray.pyd. I 
can reinstall 87.2 and everything is fine. Any idea what the problem 
might be?
Thanks!
--Michael

On Fri, 2006年06月30日 at 08:28 +0000, Christian Kristukat wrote:
> Hi,
> I'd love to have a backend which outputs skencil .sk files with text rendered
> through the skLaTeX plugin. For those who don't know it, skencil is a vector
> drawing program written in python. Its skLaTeX plugin allows to include LaTeX
> text in the drawing. Right now I'm creating eps files with matplotlib with the
> 'xpdf' distiller option and convert it to skencil file format with pstoedit
> which works but which is not very convenient.
you could try using the matplotlib SVG backend. Skencil can import SVG,
although skencil can only use the old X-style font system, so my plots
(which use Bitstream Vera fonts by default) didn't look too nice. You
could fix this by setting more compatible fonts in the matplotlibrc
presumably.
Alternatively, you could try Inkscape in place of Skencil for editing
SVG files. Inkscape can print to PS/EPS/AI for inclusion in a LateX or
skencil document (.ai). It can optionaly convert text to paths, avoiding
the font problems.
BC
> Has anybody already done something like that before? I don't know if I'll find
> the time to try it myself. In case not, please accept it as feature request.
> Christian
> 
> 
> 
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

 Hi all,
I tried to reproduce the Contour3D plot 
http://www.scipy.org/Cookbook/Matplotlib/mplot3D.
from numpy import *
import pylab as p
import mpl3d.mplot3d as p3
p.matplotlib.__version__
# in mplt3D change:
# levels, colls = self.contour(X, Y, Z, 20)
# to:
# C = self.contour(X, Y, Z, *args, **kwargs)
# levels, colls = (C.levels, C.collections)
delta = 0.025
x = arange(-3.0, 3.0, delta)
y = arange(-2.0, 2.0, 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)
# difference of Gaussians
Z = 10.0 * (Z2 - Z1)
fig=p.figure()
ax = p3.Axes3D(fig)
ax.contour3D(X,Y,Z)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
fig.add_axes(ax)
p.show()
python -i contour3.py --verbose-helpful
matplotlib data path /usr/lib64/python2.4/site-packages/matplotlib/mpl-data
$HOME=/home/nwagner
loaded rc file /home/nwagner/matplotlibrc
matplotlib version 0.87.3
verbose.level helpful
interactive is False
platform is linux2
numerix numpy 0.9.9.2726
font search path ['/usr/lib64/python2.4/site-packages/matplotlib/mpl-data']
CONFIGDIR=/home/nwagner/.matplotlib
loaded ttfcache file /home/nwagner/.matplotlib/ttffont.cache
backend GTKAgg version 2.8.0
Found dvipng version 1.5
Traceback (most recent call last):
 File 
"/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_gtk.py", 
line 284, in expose_event
 self._render_figure(self._pixmap, w, h)
 File 
"/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_gtkagg.py", 
line 73, in _render_figure
 FigureCanvasAgg.draw(self)
 File 
"/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_agg.py", 
line 391, in draw
 self.figure.draw(renderer)
 File "/usr/lib64/python2.4/site-packages/matplotlib/figure.py", line 
532, in draw
 for a in self.axes: a.draw(renderer)
 File "/usr/lib64/python2.4/site-packages/mpl3d/mplot3d.py", line 714, 
in draw
 self.w_xaxis.draw(renderer)
 File "/usr/lib64/python2.4/site-packages/mpl3d/mplot3d.py", line 613, 
in draw
 tick.draw(renderer)
 File "/usr/lib64/python2.4/site-packages/matplotlib/axis.py", line 
161, in draw
 if self.label1On: self.label1.draw(renderer)
 File "/usr/lib64/python2.4/site-packages/matplotlib/text.py", line 
1166, in draw
 self.update_coords(renderer)
 File "/usr/lib64/python2.4/site-packages/mpl3d/mplot3d.py", line 411, 
in update_coords
 return text_update_coords(self, renderer)
 File "/usr/lib64/python2.4/site-packages/mpl3d/mplot3d.py", line 102, 
in text_update_coords
 we = self._mytext.get_window_extent(renderer=renderer)
AttributeError: TextWithDash instance has no attribute '_mytext'
Nils

On 6/30/06, Belkind, Ronnen <Ron...@ci...> wrote:
>
>
>
> I downlaoded matplotlib-0.87.3.tar.gz from sourceforge and am attempting to
> compile/install it on a RedHat linux installation source. When I run setup
> I get the following error.
>
> $: python setup.py build
> Traceback (most recent call last):
> File "setup.py", line 63, in ?
> from setupext import build_agg, build_gtkagg, build_tkagg, build_wxagg,\
> File "setupext.py", line 118, in ?
> win32_compiler = get_win32_compiler()
> File "setupext.py", line 115, in get_win32_compiler
> if 'mingw32' in v:
> TypeError: 'in <string>' requires character as left operand
>
>
> I'm runing python 2.2.3. libpng, zlib, freetype, and Numeric are all
> installed.
> Any suggestions are greatly appreciated.
This error is 2.2 specific:
littlewood[~]> python
Python 2.2.2 (#1, Feb 24 2003, 19:13:11)
[GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 'ab' in 'abcde'
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
TypeError: 'in <string>' requires character as left operand
littlewood[~]> python2.3.5
Python 2.3.5 (#1, Jan 25 2006, 12:49:33)
[GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 'ab' in 'abcde'
True
I'm pretty sure that mpl requires python 2.3. At this point, python
2.2 is old enough that many packages just don't support it anymore.
Your only solutions would be to either update your python
installation, or run an older version of matplotlib that was still
2.2-compatible (but I don't know what that would be).
Regards,
f

Jules,
>
> ff = P.Figure(figsize=(5,4), dpi=100)
> ss = P.subplot(222)
> pp = ss.plot(x,y,'.-')
>
> # some program resets x,y limits
> P.show()
> #-----
> Is there any way to
> - find the axes objects that count "ff" as their parent?
The `figure` associated with a subplot object `ss` is `ss.figure`
The list of axes objects associated with a figure `ff` is ff.axes.
So, you should be able to access the subplots as 
ss.figure.axes
> - access the x,y points as "children" of the axes object ss?
Try something like
pp.get_xdata(), pp.get_ydata()
where pp is the output of ss.plot
IMHO, it'd be easier to go:
ff = P.figure()
ss = ff.add_subplot(222)
pp = ss.plot(x,y,'.-')
You can check that id(ff.axes[0])==id(ss)
Now, if you have several subplots in the same figure, with one line per 
subplot, you should consider creating a list where you'd store the output of 
subplot.plot. That way, you'd just have to parse the list to recvoer the 
xdata and ydata
For example
ff = P.figure()
plotlines = []
ss = ff.add_subplot(222)
plotlines.append(ss.plot(x,y))

Hello all
My specific question is this:
Suppose I have a figure, with an axes object, and an XY plot:
#-------
import matplotlib
import pylab as P
t = P.arange(0.0,1.0,0.02)
x = P.sin(2*P.pi*t)
y = P.exp(-t*3.)*P.cos(3*P.pi*t)
ff = P.Figure(figsize=(5,4), dpi=100)
ss = P.subplot(222)
pp = ss.plot(x,y,'.-')
# some program resets x,y limits
P.show()
#-----
(Sorry for my matlab-tainted language):
I would like to use ff.gca() to get the handle of the
active axes object (which should be ss) and then
determine the indices into the original data (x,y)
which reflect the points showing in the current
axis limits (whatever they have been set to)
Is there any way to
- find the axes objects that count "ff" as their parent?
- access the x,y points as "children" of the axes object ss?
I may be approaching my larger goal the wrong way,
but I am still interested in this question.
Thanks,
Jules

Hi,
 I have some confusion about ion/ioff, draw() and show(). After
drawing a figure I need to make it show up on the screen without
calling show() and entering the main loop. Here's the code that works:
ion()
l = plot(arange(10),2.*arange(10))
draw()
raw_input('pause')
However, if I remove ion() or place ion() after the plot() or draw()
commands, no figure is shown on the screen. This sucks because any
operation after ion() will be significantly slowed down before a call
to ioff(). I'm not sure if it's a bug that draw() does not update the
screen in ioff() mode.
Any tips?
Zhang Le

Hello.
I had a piece of code working perfectly fine with matplotlib 0.87.2.
Now I updated to 0.87.3 and it is about 100 times slower (!).
The code shows a PNG image using axes.imshow.
<code>
from pylab import *
from time import asctime, time
import Image
PNG_file='foo.png'
fh=figure()
ax = fh.add_subplot(111)
print 'Image intepolation = %s' % rcParams['image.interpolation']
print 'Image aspect = %s' % rcParams['image.aspect']
print 'Date/Time = %s' % asctime()
t1=time()
print "Starting Image.open"
image = Image.open(PNG_file)
print "Image.open terminated"
print "Starting imshow"
ax.imshow(image, origin='lower')
print "imshow terminated"
setp(ax.get_xticklabels(), visible=False)
setp(ax.get_yticklabels(), visible=False)
setp(ax.get_xticklines(), visible=False)
setp(ax.get_yticklines(), visible=False)
t2=time()
print 'Execution time [s] = %4.2f' % (t2-t1)
show()
</code>
I tried to create a patch but couldn't understand internal details of
matplotlib, so here are the directions:
1 - The offending part is imshow. (not PIL Image.open)
2 - 0.87.3 imshow has some new code:
<code>
 if vmin is not None or vmax is not None:
 im.set_clim(vmin, vmax)
 else:
 im.autoscale()
</code>
As I do not call imshow with vmax neither vmin this will always fall
into the else clause and call im.autoscale, that is the offending part
on axes.imshow.
Commenting im.autoscale() call makes it fast again, but i don't know
if this is right.
My image is 25K and 2400x1800 black and white PNG. I can send it...
I tried using aspect as 'normal', 'equal' and 'auto' but none had
performance as good as mpl 0.87.2.
Matplotlib 0.87.2 showed figure in less than 0.5 sec, 0.87.3 in about 45 sec.
Should I file a bug report?
--
Regards
Leandro Lameiro
Blog: http://lameiro.redirectme.net/blog