matplotlib-users Mailing List for matplotlib

That is what I was assuming, but it still seems a little odd that 
matplotlib generates
that large of a memory footprint. Loading the fits file into the 
program using pyfits,
with the code only uses 19MB of real memory and 600MB of virtual 
memory (strangly
adding the line img = hdu[1].data, increases this to 208MB/800MB).
Displaying images of various sizes I get these
numbers from Activity Monitor
Size Real Mem Virtual
3k x 3k 0.68GB 1.57GB
4k x 4k		0.92GB 1.80GB
5k x 5k		1.20GB	 2.10GB
5.5k x 5.5k 1.38GB 2.28GB
And the limit seems to be somewhere just above 5.5k by 5.5k (darn :( )
Cheers
 Tommy
On Jun 30, 2009, at 7:27 PM, Perry Greenfield wrote:
> Because the image is so large, and matplotlib carries out various 
> operations on the image (scaling, resampling, etc), it uses a lot of 
> memory. This is one area where a specialized display program will be 
> more efficient. If you need to use matplotlib, decide whether you 
> really only want to display a subsection, or only need a lower 
> resolution version (e.g., boxcar smooth and subsample) before 
> displaying. I've found that image sizes well over 1kx1k can take 
> some time to display, and those that are much larger can cause you 
> to run out of memory. At least, that's what I think is happening.
>
> Perry
>
> On Jun 30, 2009, at 7:20 PM, Tommy Grav wrote:
>
>> I am trying to use imshow to plot some semi-large fits images.
>> Here is the code:
>>
>> from math import *
>> import numpy as np
>> from matplotlib import pyplot as plt
>> from matplotlib import cm as cm
>> import pyfits
>>
>> cat = "/Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/"
>> fname = "o4985g0263o.warp.MD09.skycell.092"
>>
>> hdu = pyfits.open(cat+fname+".fits")
>> print hdu.info()
>> img = hdu[1].data.astype("int")
>>
>> plt.figure(figsize=[12,12])
>> plt.imshow(img,cmap=cm.cool)
>> plt.savefig("test.png")
>>
>> Which gives the result:
>>
>> Filename: /Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/
>> o4985g0263o.warp.MD09.skycell.092.fits
>> No. Name Type Cards Dimensions Format
>> 0 PRIMARY PrimaryHDU 6 () int16
>> 1 CompImageHDU 101 (6000, 6000) float32
>> None
>> Python(23117,0xa04f2720) malloc: *** mmap(size=1152000000) failed
>> (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> Traceback (most recent call last):
>> File "quick_look.py", line 16, in <module>
>> plt.savefig("test.png")
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/pyplot.py", line 345, in savefig
>> return fig.savefig(*args, **kwargs)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/figure.py", line 990, in savefig
>> self.canvas.print_figure(*args, **kwargs)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/backend_bases.py", line 1419, in
>> print_figure
>> **kwargs)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 
>> 323,
>> in print_png
>> FigureCanvasAgg.draw(self)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 
>> 279,
>> in draw
>> self.figure.draw(self.renderer)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/figure.py", line 772, in draw
>> for a in self.axes: a.draw(renderer)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/axes.py", line 1545, in draw
>> im.draw(renderer)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/image.py", line 233, in draw
>> im = self.make_image(renderer.get_image_magnification())
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/image.py", line 180, in make_image
>> x = self.to_rgba(self._A, self._alpha)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/cm.py", line 79, in to_rgba
>> x = self.cmap(x, alpha=alpha, bytes=bytes)
>> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/matplotlib/colors.py", line 501, in __call__
>> rgba = np.empty(shape=xa.shape+(4,), dtype=lut.dtype)
>> MemoryError
>>
>> I found the earlier thread of http://www.mail-archive.com/mat...@li.../msg11216.html
>> but that didn't seem to produce any fixes or good explanations.
>>
>> I am on a Mac Pro Intel machine running 10.5.7 and
>> [Heimdall:tgrav ~/Work/myCode/Python/pyPS1SC]> python
>> ActivePython 2.5.4.3 (ActiveState Software Inc.) based on
>> Python 2.5.4 (r254:67916, Jan 20 2009, 14:11:42)
>> [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
>> Type "help", "copyright", "credits" or "license" for more 
>> information.
>>>>> import numpy
>>>>> numpy.__version__
>> '1.3.0rc2'
>>>>> import pyfits
>>>>> pyfits.__version__
>> '2.1.1dev462'
>>>>> import matplotlib
>>>>> matplotlib.__version__
>> '0.98.5.2'
>>>>>
>>
>> Cheers
>> Tommy
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Because the image is so large, and matplotlib carries out various 
operations on the image (scaling, resampling, etc), it uses a lot of 
memory. This is one area where a specialized display program will be 
more efficient. If you need to use matplotlib, decide whether you 
really only want to display a subsection, or only need a lower 
resolution version (e.g., boxcar smooth and subsample) before 
displaying. I've found that image sizes well over 1kx1k can take some 
time to display, and those that are much larger can cause you to run 
out of memory. At least, that's what I think is happening.
Perry
On Jun 30, 2009, at 7:20 PM, Tommy Grav wrote:
> I am trying to use imshow to plot some semi-large fits images.
> Here is the code:
>
> from math import *
> import numpy as np
> from matplotlib import pyplot as plt
> from matplotlib import cm as cm
> import pyfits
>
> cat = "/Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/"
> fname = "o4985g0263o.warp.MD09.skycell.092"
>
> hdu = pyfits.open(cat+fname+".fits")
> print hdu.info()
> img = hdu[1].data.astype("int")
>
> plt.figure(figsize=[12,12])
> plt.imshow(img,cmap=cm.cool)
> plt.savefig("test.png")
>
> Which gives the result:
>
> Filename: /Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/
> o4985g0263o.warp.MD09.skycell.092.fits
> No. Name Type Cards Dimensions Format
> 0 PRIMARY PrimaryHDU 6 () int16
> 1 CompImageHDU 101 (6000, 6000) float32
> None
> Python(23117,0xa04f2720) malloc: *** mmap(size=1152000000) failed
> (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Traceback (most recent call last):
> File "quick_look.py", line 16, in <module>
> plt.savefig("test.png")
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/pyplot.py", line 345, in savefig
> return fig.savefig(*args, **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/figure.py", line 990, in savefig
> self.canvas.print_figure(*args, **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backend_bases.py", line 1419, in
> print_figure
> **kwargs)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 323,
> in print_png
> FigureCanvasAgg.draw(self)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/backends/backend_agg.py", line 279,
> in draw
> self.figure.draw(self.renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/figure.py", line 772, in draw
> for a in self.axes: a.draw(renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/axes.py", line 1545, in draw
> im.draw(renderer)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/image.py", line 233, in draw
> im = self.make_image(renderer.get_image_magnification())
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/image.py", line 180, in make_image
> x = self.to_rgba(self._A, self._alpha)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/cm.py", line 79, in to_rgba
> x = self.cmap(x, alpha=alpha, bytes=bytes)
> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/colors.py", line 501, in __call__
> rgba = np.empty(shape=xa.shape+(4,), dtype=lut.dtype)
> MemoryError
>
> I found the earlier thread of http://www.mail-archive.com/mat...@li.../msg11216.html
> but that didn't seem to produce any fixes or good explanations.
>
> I am on a Mac Pro Intel machine running 10.5.7 and
> [Heimdall:tgrav ~/Work/myCode/Python/pyPS1SC]> python
> ActivePython 2.5.4.3 (ActiveState Software Inc.) based on
> Python 2.5.4 (r254:67916, Jan 20 2009, 14:11:42)
> [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import numpy
>>>> numpy.__version__
> '1.3.0rc2'
>>>> import pyfits
>>>> pyfits.__version__
> '2.1.1dev462'
>>>> import matplotlib
>>>> matplotlib.__version__
> '0.98.5.2'
>>>>
>
> Cheers
> Tommy
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

I am trying to use imshow to plot some semi-large fits images.
Here is the code:
from math import *
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import cm as cm
import pyfits
cat = "/Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/"
fname = "o4985g0263o.warp.MD09.skycell.092"
hdu = pyfits.open(cat+fname+".fits")
print hdu.info()
img = hdu[1].data.astype("int")
plt.figure(figsize=[12,12])
plt.imshow(img,cmap=cm.cool)
plt.savefig("test.png")
Which gives the result:
Filename: /Volumes/Sweden/PS1SC/Data/PS20090603-3/MD09/skycell.092/ 
o4985g0263o.warp.MD09.skycell.092.fits
No. Name Type Cards Dimensions Format
0 PRIMARY PrimaryHDU 6 () int16
1 CompImageHDU 101 (6000, 6000) float32
None
Python(23117,0xa04f2720) malloc: *** mmap(size=1152000000) failed 
(error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Traceback (most recent call last):
 File "quick_look.py", line 16, in <module>
 plt.savefig("test.png")
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/pyplot.py", line 345, in savefig
 return fig.savefig(*args, **kwargs)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/figure.py", line 990, in savefig
 self.canvas.print_figure(*args, **kwargs)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/backend_bases.py", line 1419, in 
print_figure
 **kwargs)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/backends/backend_agg.py", line 323, 
in print_png
 FigureCanvasAgg.draw(self)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/backends/backend_agg.py", line 279, 
in draw
 self.figure.draw(self.renderer)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/figure.py", line 772, in draw
 for a in self.axes: a.draw(renderer)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/axes.py", line 1545, in draw
 im.draw(renderer)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/image.py", line 233, in draw
 im = self.make_image(renderer.get_image_magnification())
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/image.py", line 180, in make_image
 x = self.to_rgba(self._A, self._alpha)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/cm.py", line 79, in to_rgba
 x = self.cmap(x, alpha=alpha, bytes=bytes)
 File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/colors.py", line 501, in __call__
 rgba = np.empty(shape=xa.shape+(4,), dtype=lut.dtype)
MemoryError
I found the earlier thread of http://www.mail-archive.com/mat...@li.../msg11216.html
but that didn't seem to produce any fixes or good explanations.
I am on a Mac Pro Intel machine running 10.5.7 and
[Heimdall:tgrav ~/Work/myCode/Python/pyPS1SC]> python
ActivePython 2.5.4.3 (ActiveState Software Inc.) based on
Python 2.5.4 (r254:67916, Jan 20 2009, 14:11:42)
[GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> numpy.__version__
'1.3.0rc2'
 >>> import pyfits
 >>> pyfits.__version__
'2.1.1dev462'
 >>> import matplotlib
 >>> matplotlib.__version__
'0.98.5.2'
 >>>
Cheers
Tommy

On 6/30/2009 5:42 PM ms apparently wrote:
> I am writing a script that uses pyplot.show() to show a plot, on which
> the user has to ponder and decide a course of action (telling the script
> what to do on a raw_input).
This is not how `show` is used. But
you could save the plot as a temporary file
and open it in a viewer. Or build a GUI
for the user to interact with:
http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_tk.html
Alan Isaac

Hi,
I am writing a script that uses pyplot.show() to show a plot, on which
the user has to ponder and decide a course of action (telling the script
what to do on a raw_input).
I would be happy if the pyplot window does not "freeze" python below,
i.e. if the window can somehow exist while the python script continues
to work. Now if I want the script to continue, I have to close the
window. I didn't find examples on how to manage this. Any hint on where
to read?
Thanks,
Massimo

I have a working system now. Here's what I did to fix it.
1. Installed libpng from source
2. Installed freetype2 from source
3. Installed pkg-config from source
4. Installed a new version of the Xcode developer tools for the mac.
During the build I still saw a few 'incompatible architecture' errors flash
by, but I guess they weren't serious enough for the build to stop.
On Tue, Jun 30, 2009 at 9:51 AM, Rick Muller <rpm...@gm...> wrote:
>
>
> On Tue, Jun 30, 2009 at 9:14 AM, Michael Droettboom <md...@st...>wrote:
>
>> What does
>>
>> pkg-config libpng --modversion --libs --cflags
>>
>> give?
>>
>> The pkg-config error may actually be a red herring, since matplotlib will
>> look in /usr/local even if pkg-config fails, and it obviously found the
>> headers or it wouldn't have gotten to the linking stage. As the author of
>> the pkg-config support I would like to rule that out as the problem though.
>>
>> I think it's more likely that the libpng isn't being built correctly to
>> match the kind of binary matplotlib is building. I'm afraid that's where I
>> hit the end of my knowledge as a non-Mac user, but I'm sure another Mac
>> developer will chime in.
>>
>
> Okay, I just installed pkg-config, and it now finds the proper libpng...
>
> libpng: 1.2.37
>
> However, I still get exactly the same compile problem:
>
> g++ -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
> -bundle -u
> ndefined dynamic_lookup build/temp.macosx-10.3-fat-2.6/src/ft2font.o
> build/temp.
> macosx-10.3-fat-2.6/src/mplutils.o
> build/temp.macosx-10.3-fat-2.6/CXX/cxx_extens
> ions.o build/temp.macosx-10.3-fat-2.6/CXX/cxxsupport.o
> build/temp.macosx-10.3-fa
> t-2.6/CXX/IndirectPythonInterface.o
> build/temp.macosx-10.3-fat-2.6/CXX/cxxextens
> ions.o -L/usr/local/lib -L/usr/lib -L/usr/X11R6/lib -lfreetype -lz -lstdc++
> -lm
> -o build/lib.macosx-10.3-fat-2.6/matplotlib/ft2font.so
> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libPng.dylib, file is
> not o
> f required architecture for architecture ppc
> collect2: ld returned 1 exit status
> lipo: can't open input file:
> /var/folders/tu/tuLdYMqlEm00c5EVXrMQ+U+++TQ/-Tmp-//
> ccU5pNn1.out (No such file or directory)
> error: command 'g++' failed with exit status 1
>
> --
> Rick Muller
> rpm...@gm...
>
-- 
Rick Muller
rpm...@gm...

Hi,
this must have been answered many times already, but I searched the
archives, online docs, but couldn't find anything.
If I do:
$ python
Python 2.6.2 (release26-maint, Apr 19 2009, 01:58:18)
[GCC 4.3.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pylab
>>> pylab.plot([1, 3, 3])
[<matplotlib.lines.Line2D object at 0x2154350>]
>>> pylab.show()
>>> pylab.show()
>>>
the first pylab.show() shows the plot and stays hanging (this is ok)
and then if I close it, to get back to the shell, the second call to
show() does nothing.
One fix is to use:
ipython --pylab
but if I just want to call regular python, or from my own script ---
how do I plot for the second time?
Ondrej

Hi All,
my program lets slow down my cpu. This only appears if i plot to much
points. I am not sure how many point i need to get this, normally i plot
3*14e6 + 8e3, that is round about 50million points. My system is a
dual core 2GHz cpu with 2Gbyte Ram.
Here is my method to plot,
 def drawtransientall(self,min):
 self.subplot = self.figure.add_subplot(111)
 self.subplot.grid(True)
 list_t1,list_peaks,t2,list_samples =
self.computetransientall(min,min+self.maxitems)
 offset = 0
 color = ['green','red','blue','magenta','cyan']
 markerPeaks = ['v','<','1','3','s']
 markerSamples = ['^','>','2','4','p']
 self.plots=[[],[]]
 for i in range(len(self.showBands)):
 self.plots[0] +=
self.subplot.plot(list_t1[i],list_peaks[i],color=color[i],marker=markerPeaks[i],
 linestyle='None')
 self.plots[1] +=
self.subplot.plot(t2,list_samples[i]+offset,color=color[i],
marker=markerSamples[i],linestyle='None')
 offset +=1
self.subplot.set_xlim(t2[0]-np.abs(t2[-1]-t2[0])/100,t2[-1]+np.abs(t2[-1]-t2[0])/100)
 ymax = np.amax(list_samples)
 ymin = np.amin(list_samples)
 self.subplot.set_ylim([ymin-np.abs(ymin)*0.1, ymax*1.2 + 2])
 self.subplot.set_ylabel("abs(Sample(t)) und
abs(Peak(t)+Offset)-->",fontsize = 12)
 self.subplot.set_xlabel("Zeit in Sek. -->",fontsize = 12)
Any ideas how to avoid the slow down of my cpu ?
regards Markus

Hi Fabrice,
Good to hear that you were able to get it work.
Here is some tweak on transforms.
This way, the plot is shown correctly even if you change the y-limits of axes.
 trans0 = blended_transform_factory(ax0.transData, ax0.transAxes)
 trans1 = blended_transform_factory(ax1.transData, ax1.transAxes)
 bbox = Bbox.from_extents(xmin, 0, xmax, 1)
 mybbox1 = TransformedBbox(bbox, trans0)
 mybbox2 = TransformedBbox(bbox, trans1)
I think the code is worth to be included as an mpl example.
I'll push this into the svn if you don't mind.
Regards,
-JJ
On Tue, Jun 30, 2009 at 8:12 AM, Fabrice Silva<si...@lm...> wrote:
> Le lundi 29 juin 2009 à 16:11 -0400, Jae-Joon Lee a écrit :
>> I think the issue here is to connect points in two different axes,
>> which is possible but can be a bit difficult.
> That was my problem
>
>> In the svn version of matplotlib, there are some helper classes to
>> ease this job a bit.
> Thanks for your pointer. Sadly the mpl.toolkits.axes_grid is not shipped
> by debian package, and downloading it requires other stuff. So I adapted
> from the inset_locator.py the attached file.
>
> Finally I can "zoom" with the mere script :
>    import matplotlib.pyplot as plt
>    from mpl_axes_grid_inset_locator import zoom_effect
>    S1 = plt.subplot(211)
>    S1.plot(... # xlim (0.,1.2)
>    S2 = plt.subplot(223)
>    S2.plot(... # xlim (0.0095,.012)
>    S3 = plt.subplot(224)
>    S3.plot(... # xlim (0.84,1.)
>    # Labels stuff
>    # [...]
>
>    patch_props=dict(ec="r", alpha=0.5, fc="r")
>    zoom_effect(S1,S2, 0.01, 0.011, **patch_props)
>    zoom_effect(S1,S3, 0.90, 0.95, **patch_props)
>
> It produces two zoom subplots with the wanted patch.
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Try calling legend() again once you've changed the lines; in ipython - 
pylab, this
x = linspace(-10, 10, 101)
sub = subplot(111)
plot(x, x**2, label="x^2")
plot(x, x**3, label="x^3")
legend() #Two lines, two legend entries
sub.lines[0].remove() #One line, two legend entries
sub.get_lines()
legend() #One line, one legend entry
works for me.
&C
On Jun 30, 2009, at 2:39 AM, Magnus Benjes wrote:
> Hello,
>
> I know how to remove a line from an axes. But a I also want to 
> remove the label of the line from the legend of the axes.
>
> In the sample code you can see two labels in the legend, while there 
> is only one line in the axes left.
>
>
> import numpy as N
> from matplotlib.pyplot import *
>
> x = N.linspace(-10,10,201)
> ax = figure().add_subplot(111)
> ax.plot(x, x**2, label="$x^2$")
> ax.plot(x, x**3, label="$x^3$")
> ax.legend()
> ax.lines[0].remove()
> show()
>
>
> Regards
> Magnus
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Chloe Lewis
Graduate student, Amundson Lab
Division of Ecosystem Sciences, ESPM
University of California, Berkeley
137 Mulford Hall - #3114
Berkeley, CA 94720-3114
ch...@na...

Thanks Reinier,
 For posterity ended up just doing the following:
matplotlib.interactive(True)
...
s = ax.scatter(data1, data2, data3)
draw()
s.remove()
s = ax.scatter(data4, data5, data6)
draw()
>Hi Ryan,
>
>This is currently not supported. Since also the 2D PatchCollection does not support it I >don't see how to easily add it either...
>
>Cheers,
>Reinier

Hello,
I've been struggling with this for a while now and have effectively two
issues. One, how can I define the range over which hexbin ... bins? And two,
how do I change the background color of a plot? The latter I thought would
be trivial, but nothing I've tried has worked. Let's take the example:
import numpy as np
import matplotlib.cm as cm
import matplotlib.pyplot as plt
n = 100000
x = np.random.standard_normal(n)
y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)
#xmin = x.min()
#xmax = x.max()
#ymin = y.min()
#ymax = y.max()
xmin = 0
xmax = 10
ymin = 0
ymax = 30
plt.hexbin(x,y, cmap=cm.jet)
#plt.hexbin(x,y, cmap=cm.jet, extent=[xmin, xmax, ymin, ymax])
plt.axis([xmin, xmax, ymin, ymax])
plt.title("Hexagon binning")
cb = plt.colorbar()
cb.set_label('counts')
plt.show()
Let's say i'm only interested in the positive quadrant of the data, so I
only want to bin data in the range of 0-10 in x and 0-30 in y. The first
thing I tried was to use the extent option to only bin the specified range
of data, but that gives these errors:
[tesla:~/NMR/500-Tupp/IM7][349] HexBin.py
Traceback (most recent call last):
 File "HexBin.py", line 28, in <module>
 plt.hexbin(x,y, cmap=cm.jet, extent=[xmin, xmax, ymin, ymax])
 File "/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py", line 1920,
in hexbin
 ret = gca().hexbin(*args, **kwargs)
 File "/usr/lib64/python2.5/site-packages/matplotlib/axes.py", line 5447,
in hexbin
 collection.update(kwargs)
 File "/usr/lib64/python2.5/site-packages/matplotlib/artist.py", line 548,
in update
 raise AttributeError('Unknown property %s'%k)
AttributeError: Unknown property extent
After that, I just set the plt.axis range to what I'm interested in.
However, the range not binned by hexbin shows up as white, instead of the
0-count blue. I've tried adding facecolor, edgecolor, axisbg, and who knows
what else as part of plt.hexbin, plt.axis, and plt.savefig, But most have no
consequence on the plot. plt.savefig(myname, facecolor='blue') successfully
changed everything blue except the white region within the plot.
So, where am I going wrong? I'm finding myself out of options and would
ideally not like to trim or add false points to my data just to get the axis
and colors correct.
Best,
Alex

On Tue, Jun 30, 2009 at 9:14 AM, Michael Droettboom <md...@st...> wrote:
> What does
>
> pkg-config libpng --modversion --libs --cflags
>
> give?
>
> The pkg-config error may actually be a red herring, since matplotlib will
> look in /usr/local even if pkg-config fails, and it obviously found the
> headers or it wouldn't have gotten to the linking stage. As the author of
> the pkg-config support I would like to rule that out as the problem though.
>
> I think it's more likely that the libpng isn't being built correctly to
> match the kind of binary matplotlib is building. I'm afraid that's where I
> hit the end of my knowledge as a non-Mac user, but I'm sure another Mac
> developer will chime in.
>
Okay, I just installed pkg-config, and it now finds the proper libpng...
 libpng: 1.2.37
However, I still get exactly the same compile problem:
g++ -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
-bundle -u
ndefined dynamic_lookup build/temp.macosx-10.3-fat-2.6/src/ft2font.o
build/temp.
macosx-10.3-fat-2.6/src/mplutils.o
build/temp.macosx-10.3-fat-2.6/CXX/cxx_extens
ions.o build/temp.macosx-10.3-fat-2.6/CXX/cxxsupport.o
build/temp.macosx-10.3-fa
t-2.6/CXX/IndirectPythonInterface.o
build/temp.macosx-10.3-fat-2.6/CXX/cxxextens
ions.o -L/usr/local/lib -L/usr/lib -L/usr/X11R6/lib -lfreetype -lz -lstdc++
-lm
-o build/lib.macosx-10.3-fat-2.6/matplotlib/ft2font.so
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libPng.dylib, file is
not o
f required architecture for architecture ppc
collect2: ld returned 1 exit status
lipo: can't open input file:
/var/folders/tu/tuLdYMqlEm00c5EVXrMQ+U+++TQ/-Tmp-//
ccU5pNn1.out (No such file or directory)
error: command 'g++' failed with exit status 1
-- 
Rick Muller
rpm...@gm...

On Tue, Jun 30, 2009 at 9:14 AM, Michael Droettboom <md...@st...> wrote:
> What does
>
> pkg-config libpng --modversion --libs --cflags
>
> give?
I guess I don't have pkg-config installed. Is this a requirement? I haven't
had it installed before?
>
>
> The pkg-config error may actually be a red herring, since matplotlib will
> look in /usr/local even if pkg-config fails, and it obviously found the
> headers or it wouldn't have gotten to the linking stage. As the author of
> the pkg-config support I would like to rule that out as the problem though.
>
> I think it's more likely that the libpng isn't being built correctly to
> match the kind of binary matplotlib is building. I'm afraid that's where I
> hit the end of my knowledge as a non-Mac user, but I'm sure another Mac
> developer will chime in.
I think it's just finding the wrong version of libpng. For whatever reason,
it has decided that an old version in
/Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libPng.dylib is the proper
version, despite there being a newer version in /usr/local/lib.
Is there any way I can rearrange the search path so that it finds the
/usr/local/lib version?
Rick
-- 
Rick Muller
rpm...@gm...

What does
 pkg-config libpng --modversion --libs --cflags
give?
The pkg-config error may actually be a red herring, since matplotlib 
will look in /usr/local even if pkg-config fails, and it obviously found 
the headers or it wouldn't have gotten to the linking stage. As the 
author of the pkg-config support I would like to rule that out as the 
problem though.
I think it's more likely that the libpng isn't being built correctly to 
match the kind of binary matplotlib is building. I'm afraid that's 
where I hit the end of my knowledge as a non-Mac user, but I'm sure 
another Mac developer will chime in.
Cheers,
Mike
Rick Muller wrote:
> I've been a long time, happy user of MPL, but I'm having some problems 
> building the latest version (0.98.5.3) on the Mac (python 2.6.2).
>
> The bottom line is that when I build, I get the error message:
>
> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libPng.dylib, 
> file is not o
> f required architecture for architecture ppc
> collect2: ld returned 1 exit status
> lipo: can't open input file: 
> /var/folders/tu/tuLdYMqlEm00c5EVXrMQ+U+++TQ/-Tmp-//
> cci4zDq4.out (No such file or directory)
> error: command 'g++' failed with exit status 1
>
> However, I have a freshly-built version of libpng installed from 
> source in /usr/local/lib. I don't think MPL is finding it, though, 
> since during config I see:
>
> libpng: found, but unknown version (no pkg-config)
>
> (However, when I install libpng, I do install the pc file, viz:
> cd /usr/local/lib/pkgconfig; rm -f libpng.pc
> cd /usr/local/lib/pkgconfig; ln -s libpng12.pc libpng.pc)
>
> I'm probably doing something dumb. Is there a workaround to this?
>
> Thanks in advance,
>
> Rick
>
> -- 
> Rick Muller
> rpm...@gm... <mailto:rpm...@gm...>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

I've been a long time, happy user of MPL, but I'm having some problems
building the latest version (0.98.5.3) on the Mac (python 2.6.2).
The bottom line is that when I build, I get the error message:
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libPng.dylib, file is
not o
f required architecture for architecture ppc
collect2: ld returned 1 exit status
lipo: can't open input file:
/var/folders/tu/tuLdYMqlEm00c5EVXrMQ+U+++TQ/-Tmp-//
cci4zDq4.out (No such file or directory)
error: command 'g++' failed with exit status 1
However, I have a freshly-built version of libpng installed from source in
/usr/local/lib. I don't think MPL is finding it, though, since during config
I see:
 libpng: found, but unknown version (no pkg-config)
(However, when I install libpng, I do install the pc file, viz:
cd /usr/local/lib/pkgconfig; rm -f libpng.pc
cd /usr/local/lib/pkgconfig; ln -s libpng12.pc libpng.pc)
I'm probably doing something dumb. Is there a workaround to this?
Thanks in advance,
Rick
-- 
Rick Muller
rpm...@gm...

Hi Ryan,
This is currently not supported. Since also the 2D PatchCollection
does not support it I don't see how to easily add it either...
Cheers,
Reinier
On Mon, Jun 29, 2009 at 11:40 PM, Ryan Wagner<rw...@vn...> wrote:
> Can anyone help me out? I’m trying to do the following equivalent in a
> scatter3d call...
>
>
>
> line, = ax.plot(data1, data2)
>
> line.set_data(data3, data4)
>
> line.axes.figure.canvas.draw()
>
>
>
> So I’m looking to do:
>
>
>
> ax = axes3d.Axes3D(fig)
>
> s = ax.scatter(data1, data2, data3)
>
> s.set_data(data2,data3,data4)  ß but this function doesn’t exist... what is
> the equivalent that I’m missing?
>
> s.axes.figure.canvas.draw()
>
>
>
>
>
> TIA
>
> -Ryan
>
-- 
Reinier Heeres
Tel: +31 6 10852639

Le lundi 29 juin 2009 à 16:11 -0400, Jae-Joon Lee a écrit :
> I think the issue here is to connect points in two different axes,
> which is possible but can be a bit difficult.
That was my problem
> In the svn version of matplotlib, there are some helper classes to
> ease this job a bit.
Thanks for your pointer. Sadly the mpl.toolkits.axes_grid is not shipped
by debian package, and downloading it requires other stuff. So I adapted
from the inset_locator.py the attached file.
Finally I can "zoom" with the mere script :
 import matplotlib.pyplot as plt
 from mpl_axes_grid_inset_locator import zoom_effect
 S1 = plt.subplot(211)
 S1.plot(... # xlim (0.,1.2)
 S2 = plt.subplot(223)
 S2.plot(... # xlim (0.0095,.012)
 S3 = plt.subplot(224)
 S3.plot(... # xlim (0.84,1.)
 # Labels stuff
 # [...]
 
 patch_props=dict(ec="r", alpha=0.5, fc="r")
 zoom_effect(S1,S2, 0.01, 0.011, **patch_props)
 zoom_effect(S1,S3, 0.90, 0.95, **patch_props)
It produces two zoom subplots with the wanted patch.

Hello,
I know how to remove a line from an axes. But a I also want to remove the
label of the line from the legend of the axes.
In the sample code you can see two labels in the legend, while there is only
one line in the axes left.
import numpy as N
from matplotlib.pyplot import *
x = N.linspace(-10,10,201)
ax = figure().add_subplot(111)
ax.plot(x, x**2, label="$x^2$")
ax.plot(x, x**3, label="$x^3$")
ax.legend()
ax.lines[0].remove()
show()
Regards
Magnus

per freem <per...@gm...> writes:
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
> rc('pdf', use14corefonts=True)
>
> then when i open the generated pdf in adobe illustrator i get the error:
> "The font "Helvetica-Narrow" contains a bad /BBox."
Helvetica-Narrow is not one of the pdf core fonts. I suspect that the
matplotlib font selection system is matching your specification of
Helvetica with Helvetica-Narrow because it is available on your system
and its name begins with "Helvetica". This must be a bug. I don't have
time to investigate now, so unless someone else has any comments, I
suggest filing this on the sourceforge tracker.
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

I am developing an application in which I would like the user to be
able to click on a chart and have the application detect whether the
click has occurred over a specific piece of text. For example, I have
multiple lines on a chart with two y-axes, and I have the titles of
the series stacked up at the top of the chart. I would like the user
to be able to click one of the titles which would then cause the
corresponding series to switch to the other axis. Unfortunately I
still cannot figure how to retrieve the area that a piece of text
fills on the chart.
(in case it makes a difference, note that the chart can be resized at
any time, so the pixel coordinates of the text could change at any
time).
Thanks very much
Abiel

more information on this. if i try to use pdf.use14corefonts, like was
suggested by Jouni, as follows:
from scipy import *
import matplotlib
matplotlib.use('PDF')
from matplotlib import rc
import matplotlib.pyplot as plt
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
rc('pdf', use14corefonts=True)
then when i open the generated pdf in adobe illustrator i get the error:
"The font "Helvetica-Narrow" contains a bad /BBox." -- then no labels are
shown in the graph, only the nontextual elements.
On Mon, Jun 29, 2009 at 4:46 PM, per freem <per...@gm...> wrote:
> hi all,
>
> I am not sure if I have helvetica installed as a TTF -- how can i install
> it if i don't?
>
> i followed the debug suggestion and here are the results. when i set the
> font to arial, using:
>
> from matplotlib import rc
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
>
> then the relevant output i get using --verbose-debug is:
>
> matplotlib version 0.98.5.2
> Using fontManager instance from /Users/perf/.matplotlib/fontList.cache
> backend pdf version unknown
> findfont: Matching
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
> to Arial (/Library/Fonts/Arial.ttf) with score of 0.000000
> findfont: Matching
> :family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBol.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXGeneral:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize3:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize3
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz3Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize4:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize4
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz4Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize5:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize5
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz5Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize1:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize1
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz1Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize2:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize2
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz2Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXGeneral:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmb10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmb10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmtt10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmtt10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmmi10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmmi10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmex10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmex10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmsy10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmsy10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmsy10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmr10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmr10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmss10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmss10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf)
> with score of 0.000000
>
> with the same line but this time setting the font to 'Helvetica', I get:
>
> matplotlib version 0.98.5.2
> Using fontManager instance from /Users/perf/.matplotlib/fontList.cache
> backend pdf version unknown
> findfont: Could not match
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium.
> Returning
> /Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
> findfont: Matching
> :family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBol.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXGeneral:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize3:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize3
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz3Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize4:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize4
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz4Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize5:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize5
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz5Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize1:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize1
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz1Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXSize2:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXSize2
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz2Sym.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXGeneral:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXGeneral
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf)
> with score of 0.000000
> findfont: Matching
> :family=STIXNonUnicode:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to STIXNonUnicode
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmb10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmb10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmtt10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmtt10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmmi10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmmi10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmex10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmex10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmsy10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmsy10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmsy10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmr10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmr10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf)
> with score of 0.000000
> findfont: Matching
> :family=cmss10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to cmss10
> (/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf)
> with score of 0.000000
>
> any idea what might be wrong here?
>
>
> On Mon, Jun 29, 2009 at 8:47 AM, Michael Droettboom <md...@st...>wrote:
>
>> Are you certain you have Helvetica installed as a TrueType font? If you
>> don't, the only way to get the Postscript Helvetica is to set "ps.useafm" to
>> True.
>>
>> Cheers,
>> Mike
>>
>> per freem wrote:
>>
>>> I just wanted to add: if i simply set the font to Arial, using
>>>
>>> rc('font',**{'family':'sans-serif','sans-serif':['Arial']})
>>>
>>> then it works. But the same call with Helvetica still defaults to that
>>> Bitstream/default font of matplotlib. any idea why this might be? could
>>> matplotlib be confusing helvetica with bitstream?
>>>
>>> On Sun, Jun 28, 2009 at 11:28 AM, per freem <per...@gm... <mailto:
>>> per...@gm...>> wrote:
>>>
>>> hi,
>>>
>>> i am trying to use the Helvetica font on matplotlib. i am using
>>> mac os x (so i definitely have helvetica installed) with version
>>> 0.98.5.2 of matplotlib. my code is:
>>>
>>> from scipy import *
>>> import matplotlib
>>> matplotlib.use('PDF')
>>> from matplotlib import rc
>>> import matplotlib.pyplot as plt
>>> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
>>> plt.hist(rand(100))
>>> xlabel(r"My x axis $\alpha$")
>>> ylabel(r"My y axis $\beta$")
>>>
>>> i verified that plt.rcParams gets modified to use 'Helvetica' as
>>> the value for font.family, etc. but i still get the default font
>>> used in all of these figures. i tried using the PS backend using
>>> matplotlib.use('PS') but the problem persists. i am interested in
>>> getting out PDFs that use helvetica everywhere.
>>>
>>> does anyone know how to fix this? thank you.
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>
>>
>> --
>> Michael Droettboom
>> Science Software Branch
>> Operations and Engineering Division
>> Space Telescope Science Institute
>> Operated by AURA for NASA
>>
>>
>
>

Can anyone help me out? I'm trying to do the following equivalent in a scatter3d call...
line, = ax.plot(data1, data2)
line.set_data(data3, data4)
line.axes.figure.canvas.draw()
So I'm looking to do:
ax = axes3d.Axes3D(fig)
s = ax.scatter(data1, data2, data3)
s.set_data(data2,data3,data4) <-- but this function doesn't exist... what is the equivalent that I'm missing?
s.axes.figure.canvas.draw()
TIA
-Ryan

hi all,
I am not sure if I have helvetica installed as a TTF -- how can i install it
if i don't?
i followed the debug suggestion and here are the results. when i set the
font to arial, using:
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
then the relevant output i get using --verbose-debug is:
matplotlib version 0.98.5.2
Using fontManager instance from /Users/perf/.matplotlib/fontList.cache
backend pdf version unknown
findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
to Arial (/Library/Fonts/Arial.ttf) with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBol.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize3:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize3
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz3Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize4:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize4
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz4Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize5:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize5
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz5Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize1:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize1
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz1Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize2:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize2
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz2Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf)
with score of 0.000000
findfont: Matching
:family=cmb10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmb10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf)
with score of 0.000000
findfont: Matching
:family=cmtt10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmtt10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf)
with score of 0.000000
findfont: Matching
:family=cmmi10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmmi10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf)
with score of 0.000000
findfont: Matching
:family=cmex10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmex10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10.ttf)
with score of 0.000000
findfont: Matching
:family=cmsy10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmsy10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmsy10.ttf)
with score of 0.000000
findfont: Matching
:family=cmr10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmr10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf)
with score of 0.000000
findfont: Matching
:family=cmss10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmss10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf)
with score of 0.000000
with the same line but this time setting the font to 'Helvetica', I get:
matplotlib version 0.98.5.2
Using fontManager instance from /Users/perf/.matplotlib/fontList.cache
backend pdf version unknown
findfont: Could not match
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium.
Returning
/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBol.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize3:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize3
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz3Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize4:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize4
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz4Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize5:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize5
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz5Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize1:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize1
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz1Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXSize2:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXSize2
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSiz2Sym.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf)
with score of 0.000000
findfont: Matching
:family=STIXNonUnicode:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXNonUnicode
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf)
with score of 0.000000
findfont: Matching
:family=cmb10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmb10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf)
with score of 0.000000
findfont: Matching
:family=cmtt10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmtt10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf)
with score of 0.000000
findfont: Matching
:family=cmmi10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmmi10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf)
with score of 0.000000
findfont: Matching
:family=cmex10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmex10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10.ttf)
with score of 0.000000
findfont: Matching
:family=cmsy10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmsy10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmsy10.ttf)
with score of 0.000000
findfont: Matching
:family=cmr10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmr10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf)
with score of 0.000000
findfont: Matching
:family=cmss10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to cmss10
(/Library/Python/2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf)
with score of 0.000000
any idea what might be wrong here?
On Mon, Jun 29, 2009 at 8:47 AM, Michael Droettboom <md...@st...> wrote:
> Are you certain you have Helvetica installed as a TrueType font? If you
> don't, the only way to get the Postscript Helvetica is to set "ps.useafm" to
> True.
>
> Cheers,
> Mike
>
> per freem wrote:
>
>> I just wanted to add: if i simply set the font to Arial, using
>>
>> rc('font',**{'family':'sans-serif','sans-serif':['Arial']})
>>
>> then it works. But the same call with Helvetica still defaults to that
>> Bitstream/default font of matplotlib. any idea why this might be? could
>> matplotlib be confusing helvetica with bitstream?
>>
>> On Sun, Jun 28, 2009 at 11:28 AM, per freem <per...@gm... <mailto:
>> per...@gm...>> wrote:
>>
>> hi,
>>
>> i am trying to use the Helvetica font on matplotlib. i am using
>> mac os x (so i definitely have helvetica installed) with version
>> 0.98.5.2 of matplotlib. my code is:
>>
>> from scipy import *
>> import matplotlib
>> matplotlib.use('PDF')
>> from matplotlib import rc
>> import matplotlib.pyplot as plt
>> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
>> plt.hist(rand(100))
>> xlabel(r"My x axis $\alpha$")
>> ylabel(r"My y axis $\beta$")
>>
>> i verified that plt.rcParams gets modified to use 'Helvetica' as
>> the value for font.family, etc. but i still get the default font
>> used in all of these figures. i tried using the PS backend using
>> matplotlib.use('PS') but the problem persists. i am interested in
>> getting out PDFs that use helvetica everywhere.
>>
>> does anyone know how to fix this? thank you.
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
> --
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>
>

I think the issue here is to connect points in two different axes,
which is possible but can be a bit difficult.
In the svn version of matplotlib, there are some helper classes to
ease this job a bit.
I'm attaching the example.
I think you can also run the example with 0.98.5.3. Just download
inset_locator.py and modify your import statement.
http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/matplotlib/lib/mpl_toolkits/axes_grid/inset_locator.py?revision=7084&view=markup
Regards,
-JJ
On Mon, Jun 29, 2009 at 1:22 PM, Fabrice Silva<si...@lm...> wrote:
> Le lundi 29 juin 2009 à 14:39 +0200, Fabrice Silva a écrit :
>> I merely wanted to add a Polygon patch between the upper and the lower
>> subplots, but using data coordinates from these axes.
>
> One more precision : my intent is to draw a figure 'statically', I do
> not need event handling, ie handling manual zoom through an interactive
> backend. The figure is generated from a script and directly saved
> without human interaction.
> --
> Fabrice Silva <si...@lm...>
> LMA UPR CNRS 7051
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>