matplotlib-users Mailing List for matplotlib (Page 2)

Hi,

I've made a matplotlib plot with frequency  on the x-axis, and I would 
like to add an additional x-axis at the top that is measured in 
wavelength , i.e. wavelength = 3e8 / frequency

Is there anyway to do this transformation automatically in matplotlib?

I tried to give a transformation argument to the ax.twin() axes_grid 
command, as shown in the axes_grid parasite_simple2.py example,  but 
I've not managed to get this to work with a transformation more 
complicated than a scaling by a constant factor. I tried looking at the 
matplotlib.transforms documentation but I couldn't see a way to do this 
transformation there. I'm not sure I understood it very well though. I 
can't simply use the twiny( ) command and manually set the limits as the 
wavelength ticks will not occur at the points corresponding to the 
correct frequency.

At the moment I am using the twin() command, and then I  manually choose 
a sensible set of tickvalues  I want in wavelength units,  calculate the 
corresponding frequency values, and then set the tick locations to be 
the frequency values and the tick labels to be the wavelength values.

Thanks,
Sarah

Example code:
import numpy as np
import matplotlib
from mpl_toolkits.axes_grid1.parasite_axes import SubplotHost
import matplotlib.pyplot as plt
#create xaxis range of values -- 200 -- 1000 Ghz
xvals = np.arange(199.9, 999.9, 0.1)
#make some test data
data = np.sin(0.03*xvals)
#set up the figure
fig = plt.figure()
ax = SubplotHost(fig, 111)
fig.add_subplot(ax)
ax2 = ax.twin()
#plot data
ax.plot(xvals, data)
ax.set_xlim(200.0, 1000.0)
#set up ax2 with chosen values
wavelength_labels = np.array([0.4, 0.6, 0.8,1.0,1.2, 1.4]) #in mm
frequency_points = 3e2/wavelength_labels #in GHz
ax2.set_xticks(frequency_points)
ax2.set_xticklabels(wavelength_labels)
ax2.set_xlabel('Wavelength (mm)')
ax.set_xlabel('Frequency (GHz)')
plt.show()

Hi,

This is probably easy to do but I didn't work it out from the 
documentation so far. How do I remove the tick lines on a plot but keep 
the labels?

Thanks,
John.

Hi John and George,

I did of course rtfm :)
However when I do this for the latest svn checkout I get:

matplotlib $ PREFIX=/usr/local sudo make -f make.osx fetch deps mpl_install
Password:
python2.6 -c 'import urllib;
urllib.urlretrieve("http://www.zlib.net/zlib-1.2.3.tar.gz",
"zlib-1.2.3.tar.gz")'  &&\
	python2.6 -c 'import urllib;
urllib.urlretrieve("http://downloads.sourceforge.net/project/libpng/libpng-stable/1.2.39/libpng-1.2.39.tar.gz",
"libpng-1.2.39.tar.gz")' &&\
	python2.6 -c 'import urllib;
urllib.urlretrieve("http://download.savannah.gnu.org/releases/freetype/freetype-2.3.11.tar.bz2",
"freetype-2.3.11.tar.bz2")'
export PKG_CONFIG_PATH="/lib/pkgconfig" &&\
	rm -rf zlib-1.2.3 &&\
	tar xvfj zlib-1.2.3.tar.gz &&\
	cd zlib-1.2.3 &&\
	export MACOSX_DEPLOYMENT_TARGET=10.6 &&\
	export CFLAGS="-arch i386 -arch x86_64 -I/include
-I/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk" &&\
	export LDFLAGS="-arch i386 -arch x86_64 -L/lib
-syslibroot,/Developer/SDKs/MacOSX10.6.sdk" &&\
	./configure --prefix=&&\
	MACOSX_DEPLOYMENT_TARGET=10.6 CFLAGS="-arch i386 -arch x86_64
-I/include -I/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk" LDFLAGS="-arch i386 -arch x86_64
-L/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk" make -j3 install&&
\
	unset MACOSX_DEPLOYMENT_TARGET
tar: Unrecognized archive format: Inappropriate file type or format
tar: Error exit delayed from previous errors.
make: *** [zlib] Error 1

However I would prefer to use my independently installed freetype2 and
libpng libraries, rather than installing them again.
Does anyone have an idea where the architecture error comes from, or
how to check this?
Also, why is a separate make.osx file needed?
Could the same functionality not have been integrated into the setup.py script?
This is not a rant, just a question :)

Kind regards,

Pim Schellart

2010/5/25 George Nurser <gn...@gm...>:
> If what John suggests doesn't work, and you really only need 64 bit,
> then the nuclear option is to remove all occurrences of
>  -arch i386
> from the makefile (assuming you have a framework build) at
>
> /Library/Frameworks/Python.framework/Versions/Current/lib/python2.6/config/Makefile
>
> This should only generate x86_64.
>
> Obviously, save the current one, so you can go back to it.
>
> HTH, George.
>
> On 25 May 2010 16:58, John Hunter <jd...@gm...> wrote:
>> On Tue, May 25, 2010 at 10:45 AM, Pim Schellart <p.s...@gm...> wrote:
>>> Hi John and George,
>>>
>>> I tried both and although it now seems to find the libraries it still
>>> fails to link something.
>>>
>>> matplotlib-0.99.1.1 $ sudo python setup.py install
>>
>> According to the README I pointed you too, this isn't the command you
>> should be running.  Rather,
>>
>> Example usage::
>>
>>  PREFIX=/Users/jdhunter/dev make -f make.osx fetch deps mpl_install
>>
>> But I advise you work from the svn trunk if you want to go this route,
>> as I have made some updates for 64bit/python2.6 OSX there
>>
>>  > svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/matplotlib
>> matplotlib
>>
>> JDH
>>
>

>w/o seeing the entire code it is difficult to diagnose.  Nothing looks
>wrong with your code.  However, for full control I suggest you use the
>API; see examples at
>http://matplotlib.sourceforge.net/examples/api/index.html and take a
>look at the "artist tutorial" at
>http://matplotlib.sourceforge.net/users/artists.html.

Thank you.  The tutorial was very helpful.  For a moment I thought I might
have found the answer with the lines.remove() function but alas, it did not
make a difference yet again.  :(  I am starting to feel that this is a
problem with my setup rather than my code.  I may have to try this on
someone else's computer.

>In a nutshell

>fig = plt.figure()
>ax = fig.add_subplot(111)
>for param in myparams:
>    fig.clf()
>    ax.plot(something_with(param))
>    ax.set_ylabel('Sum Squared Error')
>    ax.set_title('Plot of Iris Training Errors')
>    ax.set_ylim(ymin=0)
>    outfilename = '%d.png'%param
>    fig.savefig(outfilename)

This is almost exactly the same as something else I have tried but this is
all to no avail.  I have posted all of my code at
http://code-bin.homedns.org/653 if anyone has time to look at it.
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2) In which case, it's not a framework install.  Fink puts everything into
/sw/; there's nothing to do with pyton in /Library/Frameworks.
Thanks for the clarification; I'm tempted to get Python from source and try
this...

-dw

On Tue, May 25, 2010 at 10:41 PM, Michiel de Hoon <mjl...@ya...>wrote:

>
> > 1)The problem does manifest in the same manner through the normal python
> prompt.
>
> OK that is good to know.
>
>
> > 2) I'm not sure what is meant by a "framework install."  Everything
> (except MPL 99.1.1)
> > was installed through fink.
>
> This is important. Check where python is installed. If 'which python' shows
> /Library/Frameworks/Python.framework/Versions/2.6/bin/python or something
> similar, you have a framework version. If on the other hand it shows
> /usr/bin/python, /usr/local/bin/python, or something similar, you don't have
> a framework version. I don't know what fink installs by default. If you
> don't have Python installed as a framework, some backends (including the
> MacOSX backend) will not interact properly with the window manager. This is
> a Mac peculiarity. If you build Python from source, you can specify to
> install a framework version by passing the --enable-framework option to the
> configure script.
>
>
> > 6) Although I use x11 and not the native Mac terminal, I'm not sure if
> this requires me to > install different packages for the gui stuff.  Could
> you guys expand on this, please?
>
> Some backends go make use of X11 (e.g., the gtkcairo backend), others do
> not (e.g., the MacOSX backend). The MacOSX backend should work with both the
> native Mac terminal and with an X11 terminal.
>
> --Michiel.
>
>

> 1)The problem does manifest in the same manner through the normal python
 prompt.

OK that is good to know.

> 2) I'm not sure what is meant by a "framework install."  Everything 
(except MPL 99.1.1)
> was installed through fink.

This is important. Check where python is installed. If 'which python' shows /Library/Frameworks/Python.framework/Versions/2.6/bin/python or something similar, you have a framework version. If on the other hand it shows /usr/bin/python, /usr/local/bin/python, or something similar, you don't have a framework version. I don't know what fink installs by default. If you don't have Python installed as a framework, some backends (including the MacOSX backend) will not interact properly with the window manager. This is a Mac peculiarity. If you build Python from source, you can specify to install a framework version by passing the --enable-framework option to the configure script.



> 6) Although I use x11 and not the native Mac terminal, I'm not sure if this requires me to > install different packages for the gui stuff.  Could you guys expand on this, please?

Some backends go make use of X11 (e.g., the gtkcairo backend), others do not (e.g., the MacOSX backend). The MacOSX backend should work with both the native Mac terminal and with an X11 terminal.

--Michiel.



      

Hi,
I am a real newbie at matplotlib, so I apologize if this is an obvious
question.
I am running ipython in emacs and while the first time I use the show()
command in the ipython buffer the graph shows up fine, subsequent times that
I call the command it, the graph does not show up.  I am on ubuntu 10.04
(64) and I built the matplotlib library from source.
I am trying to get the graphs to show up the subsequent times as well (sorry
for the pun).
Thanks for any help.

----------------------------------------
Ted Rosenbaum
Graduate Student
Department of Economics
Yale University

Thanks for the info...
1)The problem does manifest in the same manner through the normal python
prompt.
2) I'm not sure what is meant by a "framework install."  Everything (except
MPL 99.1.1) was installed through fink.
3) I've never had problems with Fink software before, and I have a crapload
(technical term) of stuff installed.  This is neither here nor there,
however, as it seems that not all Pythons are created equal.
4) A colleague of mine claims to have everything working on a new Intel mac
(I'm guessing 10.5.8) right out of MacPorts; I'll talk to him more and try
to find out what is different between our two cases.
5) I have yet to try installing wxPython for python 2.5; this may work in
the end.  It's not in fink, so I've put off installing it manually.  I'll
give it a shot and let you know how it works.
6) Although I use x11 and not the native Mac terminal, I'm not sure if this
requires me to install different packages for the gui stuff.  Could you guys
expand on this, please?

Finally, I've had some measure of success by installing Qt4 (through Fink)
and using the Qt4Agg backend.  Because the current stable fink Qt4 release
(4.6.1) has a bug, I need to apply the fix found here:
http://old.nabble.com/Qt4-backend:-critical-bug-with-PyQt4-v4.6%2B-td26205716.html
in order to allow more than one plot per session to be shown.  I'll re-write
the fix here for convenience and clarity (the original did not have the
proper module references in it, so this saves some 5 minutes of
tab-completion work in ipython...)

# Add this before "FigureManagerQT" class
class FigureWindow(QtGui.QMainWindow):
    def __init__(self):
        super(FigureWindow, self).__init__()
    def closeEvent(self, event):
        super(FigureWindow, self).closeEvent(event)
        if QtCore.PYQT_VERSION_STR.startswith('4.6'):
            self.emit(QtCore.SIGNAL('destroyed()'))
# Replace "QtGui.QMainWindow" by "FigureWindow" in
"FigureManagerQT"'s constructor

This works perfectly on my Intel machine running MPL 99.1.1.  It's fast and
looks sharp.  I'll report back on the PPC/99.0 combo tomorrow; Qt4 takes a
thousand hours to compile.

Thanks for the input.

On Tue, May 25, 2010 at 8:48 PM, Jonathan Stickel <jjs...@vc...> wrote:

> On 05/25/2010 mat...@li... wrote:
> > From: Christopher Barker <Chr...@no...>
> > Subject: Re: [Matplotlib-users] Mac backend problems for nearly all
> >     backends.
> > To: mat...@li...
> > Message-ID: <4BF...@no...>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Jonathan Stickel wrote:
> > > > I've experienced many of the same problems on Mac OS X 10.6.3
> > (Snow
> > > > Leopard).  I have python/scipy/numpy/matplotlib/ipython all
> > installed
> > > > via Macports.
> >
> > Just to be clear -- this sounds like a MacPorts problem, not
> > necessarily
> > an OS-X problem.
> >
> >
> > > >  I finally have the WXagg backend
> > > > working, but that required installed WXPython with the gtk/X11
> > backend.
> >
> > Does MacPorts not allow a native wx? Maybe becasue you're running 64
> > bit?
> >
>
> Right, I am running Snow Leopard and have Python 2.6 installed 64 bit.
> Apparently, Carbon requires 32 bit and wxWidgets/wxPython does not (yet)
> support Cocoa.  This problem will bite you in one form or another on Mac
> OS X, regardless of whether you are using Macports or something else.
>
> > Anyway, I guess that's why I don't use macports for python.
>
> See above.
>
> >
> >
> > >> >> In any case, I have been having royal problems with GUI
> > backends and
> > >> >> matplotlib.
> > >> >> Some background on where I've been having these problems:
> > >> >> Machine 1: OSX 10.5.8 G5 PPC
> >
> > That's what I've been running, and I've had no real issues (Haven't
> > tried the OS-X back-end) -- but I'm using the python.org python.
> >
> > >> >> Machine 2: OSX 10.5.7 Macbook pro/Intel
> > >> >> Code versions: python 2.5.4, Numpy 1.3.0, Scipy 0.7.0 (all
> > obtained through
> > >> >> fink.)
> >
> > OK -- then a fink issue, rather than a Macports one -- same idea,
> > though.
> >
> > My impression is that neither fink nor macports do well with Mac GUI
> > stuff -- unless you're talking X11.
>
> Not exactly true.  Fink and Macports are tools and have their
> shortcomings, but both can be immensely useful for installing all this
> stuff.  Otherwise, you do it manually, which of course can cause you
> trouble as well.  Anyway, getting off topic.  I only intended to report
> some form of success with the wx backend.
>
> Jonathan
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On 05/25/2010 mat...@li... wrote:
> From: Christopher Barker <Chr...@no...>
> Subject: Re: [Matplotlib-users] Mac backend problems for nearly all
>     backends.
> To: mat...@li...
> Message-ID: <4BF...@no...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Jonathan Stickel wrote:
> > > I've experienced many of the same problems on Mac OS X 10.6.3 
> (Snow 
> > > Leopard).  I have python/scipy/numpy/matplotlib/ipython all 
> installed 
> > > via Macports.
> 
> Just to be clear -- this sounds like a MacPorts problem, not 
> necessarily 
> an OS-X problem.
> 
> 
> > >  I finally have the WXagg backend 
> > > working, but that required installed WXPython with the gtk/X11 
> backend.
> 
> Does MacPorts not allow a native wx? Maybe becasue you're running 64 
> bit?
> 

Right, I am running Snow Leopard and have Python 2.6 installed 64 bit. 
Apparently, Carbon requires 32 bit and wxWidgets/wxPython does not (yet) 
support Cocoa.  This problem will bite you in one form or another on Mac 
OS X, regardless of whether you are using Macports or something else.

> Anyway, I guess that's why I don't use macports for python.

See above.

> 
> 
> >> >> In any case, I have been having royal problems with GUI 
> backends and
> >> >> matplotlib.
> >> >> Some background on where I've been having these problems:
> >> >> Machine 1: OSX 10.5.8 G5 PPC
> 
> That's what I've been running, and I've had no real issues (Haven't 
> tried the OS-X back-end) -- but I'm using the python.org python.
> 
> >> >> Machine 2: OSX 10.5.7 Macbook pro/Intel
> >> >> Code versions: python 2.5.4, Numpy 1.3.0, Scipy 0.7.0 (all 
> obtained through
> >> >> fink.)
> 
> OK -- then a fink issue, rather than a Macports one -- same idea, 
> though.
> 
> My impression is that neither fink nor macports do well with Mac GUI 
> stuff -- unless you're talking X11.

Not exactly true.  Fink and Macports are tools and have their 
shortcomings, but both can be immensely useful for installing all this 
stuff.  Otherwise, you do it manually, which of course can cause you 
trouble as well.  Anyway, getting off topic.  I only intended to report 
some form of success with the wx backend.

Jonathan

Dears, I want to interpolate some irregular data using radial basis.
Can I interpolate only the data that falls inside a circle (or a
polygon)?

TIA

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Institute of Geosciences - Univ. of São Paulo, Brazil
http://www.igc.usp.br/pessoais/guano
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