matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] Save pdf with plot_surface

[Derek T. <der...@gm...>]

This may be known, but the following modified example from
http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html fails with a
TypeError at matplotlib/backends/backend_pdf.pyc in draw_path_collection.
 Is it possible to save pdf files with surface plots?

from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
ax = fig.gca(projection='3d')
X = np.arange(-5, 5, 0.25)
Y = np.arange(-5, 5, 0.25)
X, Y = np.meshgrid(X, Y)
R = np.sqrt(X**2 + Y**2)
Z = np.sin(R)
surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.coolwarm,
        linewidth=0, antialiased=False)
ax.set_zlim(-1.01, 1.01)

ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))

fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('test.pdf')
plt.show()

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[John L. <joh...@sb...>]

On 04/19/2013 03:26 AM, Mark Lawrence wrote:
> On 19/04/2013 04:03, John Ladasky wrote:
>
>> Reading more, I realize that the way I was getting GUI output previously
>> (with Python 2.7 and Matplotlib 1.1) was through wxPython.
>> Unfortunately, it appears that wxPython's star is fading, and a Python
>> 3-compatible version will not be written.  In fact, wxPython hasn't
>> released a new version in nine months.
>>
> I'm surprised that you say this as months of work have gone into
> updating wxPython to make in Python 3 compatible.  Please see
> http://wxpython.org/Phoenix/snapshot-builds/ for the latest and greatest.
>
Well, that is good news.  Just before my last message to this list, I 
visited wxpython.org, as I have done many times over the years. I saw no 
announcement that there would be a Python 3.x-compatible version.  You 
would think that the developers would want everyone to know!

[Matplotlib-users] wxPython Phoenix - backend_wxagg

[Werner F. B. <wer...@fr...>]

Hi,

I am trying to get matplotlib 1.2.0 to work with wxPython Phoenix - will 
provide a patch when it is working.

Made the changes to backend_wx* for things like EmptyImage/EmptyBitmap 
and Toolbar but I am stuck on the following.

     if bbox is None:
         # agg => rgba buffer -> bitmap
         if 'phoenix' in wx.PlatformInfo:
             return wx.Bitmap.FromBufferRGBA(int(agg.width), 
int(agg.height),
memoryview(agg.buffer_rgba()))
         else:
             return wx.BitmapFromBufferRGBA(int(agg.width), int(agg.height),
                                            agg.buffer_rgba())
     else:
         # agg => rgba buffer -> bitmap => clipped bitmap
         return _WX28_clipped_agg_as_bitmap(agg, bbox)

TypeError: cannot make memory view because object does not have the 
buffer interface
File "h:\devProjectsT\aaTests\matplotlib\wxembedding-5.py", line 63, in 
<module>
   demo()
File "h:\devProjectsT\aaTests\matplotlib\wxembedding-5.py", line 60, in demo
   app.MainLoop()
File "c:\Python27\Lib\site-packages\wx-2.9.6-msw-phoenix\wx\core.py", 
line 1841, in MainLoop
   rv = wx.PyApp.MainLoop(self)
File "c:\Python27\Lib\site-packages\matplotlib\backends\backend_wx.py", 
line 1209, in _onPaint
   self.draw(drawDC=drawDC)
File 
"c:\Python27\Lib\site-packages\matplotlib\backends\backend_wxagg.py", 
line 61, in draw
   self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None)
File 
"c:\Python27\Lib\site-packages\matplotlib\backends\backend_wxagg.py", 
line 173, in _convert_agg_to_wx_bitmap
   memoryview(agg.buffer_rgba()))

I tried using "memoryview" based on a suggestion by Robin Dunn, and 
based on the following info I see in the debugger that should work no?

agg.buffer_rgba()
<read-write buffer ptr 0x05400638, size 229200 at 0x055FC680>
type(agg.buffer_rgba())
<type 'buffer'>
agg
<matplotlib.backends.backend_agg.RendererAgg instance at 0x04BA0670>

If I don't use "memoryview" (which would probably be preferred) I get 
the following exception.

Can someone help us figure this one out.

Thanks
Werner


TypeError: Bitmap.FromBufferRGBA(): argument 3 has unexpected type 'buffer'
File "h:\devProjectsT\aaTests\matplotlib\wxembedding-5.py", line 63, in 
<module>
   demo()
File "h:\devProjectsT\aaTests\matplotlib\wxembedding-5.py", line 60, in demo
   app.MainLoop()
File "c:\Python27\Lib\site-packages\wx-2.9.6-msw-phoenix\wx\core.py", 
line 1841, in MainLoop
   rv = wx.PyApp.MainLoop(self)
File "c:\Python27\Lib\site-packages\matplotlib\backends\backend_wx.py", 
line 1209, in _onPaint
   self.draw(drawDC=drawDC)
File 
"c:\Python27\Lib\site-packages\matplotlib\backends\backend_wxagg.py", 
line 61, in draw
   self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None)
File 
"c:\Python27\Lib\site-packages\matplotlib\backends\backend_wxagg.py", 
line 173, in _convert_agg_to_wx_bitmap
   agg.buffer_rgba())

[Matplotlib-users] Optimal resolution for imshow

[Christoph G. <cw...@fa...>]

Hello,

Is there a way to find out the optimal resolution that an array (of a given
aspect ratio) should have, so that imshow will not re-scale it on a
pixel-based backend?

Some background: I'm preparing an array that has a native resolution, so for
PDF output I use imshow with interpolation='none'.  For PNG-output, however,
the array has to be rescaled.  I would prefer to prepare the array in the
correct resolution right away.

Thanks in advance,
Christoph

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Michael D. <md...@st...>]

On 04/19/2013 01:59 AM, C M wrote:
>
>
> On Thu, Apr 18, 2013 at 11:03 PM, John Ladasky 
> <joh...@sb... <mailto:joh...@sb...>> wrote:
>
>     .
>     Reading more, I realize that the way I was getting GUI output
>     previously
>     (with Python 2.7 and Matplotlib 1.1) was through wxPython.
>     Unfortunately, it appears that wxPython's star is fading, and a Python
>     3-compatible version will not be written.  In fact, wxPython hasn't
>     released a new version in nine months.
>
>
> wxPython is alive and well and the newest developmental version of it 
> ("Phoenix") runs on Python 3. It should be released fairly soon.  One 
> of the wxPython list regulars mentioned getting his software to run 
> with it, with a few minor issues, just six days ago.  So you might 
> want to give Phoenix a try.
That's great news.  Unfortunately, I'm not aware of any testing with it 
and matplotlib on Python 3, so for someone who just wants to get things 
to work, I would still recommend Tk, gtk or Qt4 on Python3.

Mike

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Werner F. B. <wer...@fr...>]

On 19/04/2013 12:26, Mark Lawrence wrote:
> On 19/04/2013 04:03, John Ladasky wrote:
>
>> Reading more, I realize that the way I was getting GUI output previously
>> (with Python 2.7 and Matplotlib 1.1) was through wxPython.
>> Unfortunately, it appears that wxPython's star is fading, and a Python
>> 3-compatible version will not be written.  In fact, wxPython hasn't
>> released a new version in nine months.
>>
> I'm surprised that you say this as months of work have gone into
> updating wxPython to make in Python 3 compatible.  Please see
> http://wxpython.org/Phoenix/snapshot-builds/ for the latest and greatest.
This one to the list - sorry Mark used the wrong reply button.

I don't work on Python 3 yet but I am trying to get Phoenix to work with 
matplotlib.

Made a few changes to backend_wx:

Following don't exist in Phoenix (build r73823)  - will research later 
if they should exist.
         #wx.WXK_PRIOR           : 'pageup',
         #wx.WXK_NEXT            : 'pagedown',
         #wx.WXK_NUMPAD_PRIOR    : 'pageup',
         #wx.WXK_NUMPAD_NEXT     : 'pagedown',

There are a few EmptyBitMap creates which need to be changed to:

         if 'phoenix' in wx.PlatformInfo:
             self.bitmap = wx.Bitmap(w, h)
         else:
             self.bitmap = wx.EmptyBitmap(w, h)


But now I am stuck on the following exception and I haven't found a 
solution to this yet - any pointers would be very welcome.

Werner

AttributeError: 'BaseApp' object has no attribute 'ProcessIdle'
File "c:\dev\twcbv4\twcbsrc\controllers\app_stats.py", line 864, in <module>
   apprb = Appstats(None, standalone=True)
File "c:\dev\twcbv4\twcbsrc\controllers\app_stats.py", line 203, in __init__
   self.setupControls()
File "c:\dev\twcbv4\twcbsrc\controllers\app_stats.py", line 236, in 
setupControls
   self.createStatsPanes()
File "c:\dev\twcbv4\twcbsrc\controllers\app_stats.py", line 401, in 
createStatsPanes
   self.paneStatsDtypeCons.axes = 
self.paneStatsDtypeCons.figure.add_subplot(noRow, noCol, 1)
File "c:\Python27\Lib\site-packages\matplotlib\figure.py", line 882, in 
add_subplot
   a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "c:\Python27\Lib\site-packages\matplotlib\axes.py", line 8938, in 
__init__
   self._axes_class.__init__(self, fig, self.figbox, **kwargs)
File "c:\Python27\Lib\site-packages\matplotlib\axes.py", line 461, in 
__init__
   self._init_axis()
File "c:\Python27\Lib\site-packages\matplotlib\axes.py", line 523, in 
_init_axis
   self.spines['right'].register_axis(self.yaxis)
File "c:\Python27\Lib\site-packages\matplotlib\spines.py", line 151, in 
register_axis
   self.axis.cla()
File "c:\Python27\Lib\site-packages\matplotlib\axis.py", line 732, in cla
   self.reset_ticks()
File "c:\Python27\Lib\site-packages\matplotlib\axis.py", line 746, in 
reset_ticks
   self.minorTicks.extend([self._get_tick(major=False)])
File "c:\Python27\Lib\site-packages\matplotlib\axis.py", line 1839, in 
_get_tick
   return YTick(self.axes, 0, '', major=major, **tick_kw)
File "c:\Python27\Lib\site-packages\matplotlib\axis.py", line 140, in 
__init__
   self.tick2line = self._get_tick2line()
File "c:\Python27\Lib\site-packages\matplotlib\axis.py", line 541, in 
_get_tick2line
   l.set_transform(self.axes.get_yaxis_transform(which='tick2'))
File "c:\Python27\Lib\site-packages\matplotlib\lines.py", line 476, in 
set_transform
   Artist.set_transform(self, t)
File "c:\Python27\Lib\site-packages\matplotlib\artist.py", line 235, in 
set_transform
   self.pchanged()
File "c:\Python27\Lib\site-packages\matplotlib\artist.py", line 216, in 
pchanged
   for oid, func in self._propobservers.iteritems():

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Mark L. <bre...@ya...>]

On 19/04/2013 04:03, John Ladasky wrote:

> Reading more, I realize that the way I was getting GUI output previously
> (with Python 2.7 and Matplotlib 1.1) was through wxPython.
> Unfortunately, it appears that wxPython's star is fading, and a Python
> 3-compatible version will not be written.  In fact, wxPython hasn't
> released a new version in nine months.
>

I'm surprised that you say this as months of work have gone into 
updating wxPython to make in Python 3 compatible.  Please see 
http://wxpython.org/Phoenix/snapshot-builds/ for the latest and greatest.

-- 
If you're using GoogleCrap™ please read this 
http://wiki.python.org/moin/GoogleGroupsPython.

Mark Lawrence

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Francesco M. <fra...@gm...>]

Hi John,

on Kubuntu Precise the standard repo has at least:

python3-pyqt4
python3-pyside
python3-tk

The first two should enable Qt4Agg backend, the last TkAgg

Fra


2013/4/19 Sterling Smith <sm...@fu...>

> I have used the TkAgg backend in python2, installing the dependencies by
> hand.  Is this backend not available for python3?
>
> -Sterling
>
> On Apr 18, 2013, at 8:03PM, John Ladasky wrote:
>
> > Thanks to both Francesco Montesano and Benjamin Root.  I have done some
> > reading.  And I have made some progress, though I am not quite where I
> > want to be yet.
> >
> > So the problem appears to be that the only backend for which I had
> > suitable Python 3 libraries was agg.  It only requires libpng, which I
> > have.  I can render a Matplotlib canvas, but it appears that the only
> > output that agg offers is in the form of PNG files to disk.  I cannot
> > create a live window on the screen.
> >
> > Reading more, I realize that the way I was getting GUI output previously
> > (with Python 2.7 and Matplotlib 1.1) was through wxPython.
> > Unfortunately, it appears that wxPython's star is fading, and a Python
> > 3-compatible version will not be written.  In fact, wxPython hasn't
> > released a new version in nine months.
> >
> > The other choices for Matplotlib GUI output on Linux appear to be
> > through GTK, PySide, and PyQt.  I am not familiar with GTK, but I know
> > that it is widely-used.  Also, GTK appears to be Python 3-compatible,
> > and so that is where I need to go.
> >
> > I'm going through a trial and error process.  Unfortunately, the names
> > of the repositories in Ubuntu are not very helpful.  I installed a few
> > GTK and python-gtk related packages that I thought were relevant.  On my
> > first build attempt I got no errors, but also, I didn't get a GTKAgg
> > backend.  Upon re-reading, I saw that I should modify matplotlib's
> > setup.cfg file to force a GTK build attempt, and to report errors if it
> > fails. That's what it does.  In the "optional backend dependencies"
> > section I am not seeing any GTK libraries listed, even though I have
> > installed python-gtk2-dev (2.24.0), python-gobject-2-dev (2.28.6),
> > libgtk2.0-dev (2.24.10), libglib2.0-dev (2.32.3), python-gi-dev (3.2.2),
> > python-gobject-dev (3.2.2), python3-gi (3.2.2), and a few DOZEN packages
> > on which these depend.
> >
> > If anyone knows the way forward from here, I would appreciate your
> > advice.  Thanks again.
> >
> >
> ------------------------------------------------------------------------------
> > Precog is a next-generation analytics platform capable of advanced
> > analytics on semi-structured data. The platform includes APIs for
> building
> > apps and a phenomenal toolset for data science. Developers can use
> > our toolset for easy data analysis & visualization. Get a free account!
> > http://www2.precog.com/precogplatform/slashdotnewsletter
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Sterling S. <sm...@fu...>]

I have used the TkAgg backend in python2, installing the dependencies by hand.  Is this backend not available for python3?

-Sterling

On Apr 18, 2013, at 8:03PM, John Ladasky wrote:

> Thanks to both Francesco Montesano and Benjamin Root.  I have done some 
> reading.  And I have made some progress, though I am not quite where I 
> want to be yet.
> 
> So the problem appears to be that the only backend for which I had 
> suitable Python 3 libraries was agg.  It only requires libpng, which I 
> have.  I can render a Matplotlib canvas, but it appears that the only 
> output that agg offers is in the form of PNG files to disk.  I cannot 
> create a live window on the screen.
> 
> Reading more, I realize that the way I was getting GUI output previously 
> (with Python 2.7 and Matplotlib 1.1) was through wxPython.  
> Unfortunately, it appears that wxPython's star is fading, and a Python 
> 3-compatible version will not be written.  In fact, wxPython hasn't 
> released a new version in nine months.
> 
> The other choices for Matplotlib GUI output on Linux appear to be 
> through GTK, PySide, and PyQt.  I am not familiar with GTK, but I know 
> that it is widely-used.  Also, GTK appears to be Python 3-compatible, 
> and so that is where I need to go.
> 
> I'm going through a trial and error process.  Unfortunately, the names 
> of the repositories in Ubuntu are not very helpful.  I installed a few 
> GTK and python-gtk related packages that I thought were relevant.  On my 
> first build attempt I got no errors, but also, I didn't get a GTKAgg 
> backend.  Upon re-reading, I saw that I should modify matplotlib's 
> setup.cfg file to force a GTK build attempt, and to report errors if it 
> fails. That's what it does.  In the "optional backend dependencies" 
> section I am not seeing any GTK libraries listed, even though I have 
> installed python-gtk2-dev (2.24.0), python-gobject-2-dev (2.28.6), 
> libgtk2.0-dev (2.24.10), libglib2.0-dev (2.32.3), python-gi-dev (3.2.2), 
> python-gobject-dev (3.2.2), python3-gi (3.2.2), and a few DOZEN packages 
> on which these depend.
> 
> If anyone knows the way forward from here, I would appreciate your 
> advice.  Thanks again.
> 
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[C M <cmp...@gm...>]

On Thu, Apr 18, 2013 at 11:03 PM, John Ladasky
<joh...@sb...>wrote:

> .
> Reading more, I realize that the way I was getting GUI output previously
> (with Python 2.7 and Matplotlib 1.1) was through wxPython.
> Unfortunately, it appears that wxPython's star is fading, and a Python
> 3-compatible version will not be written.  In fact, wxPython hasn't
> released a new version in nine months.
>

wxPython is alive and well and the newest developmental version of it
("Phoenix") runs on Python 3. It should be released fairly soon.  One of
the wxPython list regulars mentioned getting his software to run with it,
with a few minor issues, just six days ago.  So you might want to give
Phoenix a try.

Che

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[John L. <joh...@sb...>]

Thanks to both Francesco Montesano and Benjamin Root.  I have done some 
reading.  And I have made some progress, though I am not quite where I 
want to be yet.

So the problem appears to be that the only backend for which I had 
suitable Python 3 libraries was agg.  It only requires libpng, which I 
have.  I can render a Matplotlib canvas, but it appears that the only 
output that agg offers is in the form of PNG files to disk.  I cannot 
create a live window on the screen.

Reading more, I realize that the way I was getting GUI output previously 
(with Python 2.7 and Matplotlib 1.1) was through wxPython.  
Unfortunately, it appears that wxPython's star is fading, and a Python 
3-compatible version will not be written.  In fact, wxPython hasn't 
released a new version in nine months.

The other choices for Matplotlib GUI output on Linux appear to be 
through GTK, PySide, and PyQt.  I am not familiar with GTK, but I know 
that it is widely-used.  Also, GTK appears to be Python 3-compatible, 
and so that is where I need to go.

I'm going through a trial and error process.  Unfortunately, the names 
of the repositories in Ubuntu are not very helpful.  I installed a few 
GTK and python-gtk related packages that I thought were relevant.  On my 
first build attempt I got no errors, but also, I didn't get a GTKAgg 
backend.  Upon re-reading, I saw that I should modify matplotlib's 
setup.cfg file to force a GTK build attempt, and to report errors if it 
fails. That's what it does.  In the "optional backend dependencies" 
section I am not seeing any GTK libraries listed, even though I have 
installed python-gtk2-dev (2.24.0), python-gobject-2-dev (2.28.6), 
libgtk2.0-dev (2.24.10), libglib2.0-dev (2.32.3), python-gi-dev (3.2.2), 
python-gobject-dev (3.2.2), python3-gi (3.2.2), and a few DOZEN packages 
on which these depend.

If anyone knows the way forward from here, I would appreciate your 
advice.  Thanks again.

Re: [Matplotlib-users] TypeError: unsupported operand type(s) for +: 'NoneType' and 'float' on 1.2.1

[Michael D. <md...@st...>]

Can you please provide a complete, minimal and self-contained script 
that reproduces the error?  The example below has many undefined 
variables etc.

Cheers,
Mike

On 04/16/2013 07:09 PM, Christophe Pettus wrote:
> # preamble code collecting data
>
>      ind = np.arange(len(table_name))
>      
>      width = 0.35
>      
>      fig = plot.figure(figsize=DEFAULT_FIGURE_SIZE)
>      ax = fig.add_subplot(111, axisbg='#fafafa', alpha=0.9)
>      
>      ax.set_title('Largest Tables')
>      
>      ax.set_xlabel('Size (log scale)')
>      
>      ax.set_xscale('log')
>      ax.grid(True)
>      
>      ax.xaxis.set_major_formatter(FuncFormatter(magnitude_ticks))
>
>      dbar = ax.barh(ind, data_size, width, linewidth=0, color='blue', label='Main Data')  # exception here
>      ibar = ax.barh(ind, index_toast_size, width, left=data_size, linewidth=0, color='red', label='Toast/Indexes')
>      ax.set_yticks(ind + width/2)
>      ax.set_yticklabels(table_name, fontproperties=xx_small_font)
>
>      ax.legend(loc='lower right', prop=x_small_font)
>
>      plot.tight_layout()
>      
>      plot.savefig(REPORT_DIR_PATH + '/table_sizes.pdf')
>
>      plot.close()

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Benjamin R. <ben...@ou...>]

On Thu, Apr 18, 2013 at 3:34 AM, John Ladasky <joh...@sb...>wrote:

> Hello everyone,
>
> After not using Matplotlib for over a year, I'm returning to it.
> Meanwhile, I have upgraded from Python 2.7 to Python 3.2, and I want to
> do all of my software development in Python 3 from now on.
>
> My OS is Ubuntu 12.04.1.  Python 2.7 is still the default Python for
> Ubuntu, and many of the Python 3 packages are not offered as official
> repositories yet. I downloaded Matplotlib 1.2.1, then built it using
> Python 3.  Eventually, I got no build error messages, and proceeded to
> install. (I always have to pick through dependency problems one error
> message at a time.  I wish there was a better way.  The Matplotlib docs
> could be a little better in this respect.)
>
> When I open a Python3 interpreter, I can import matplotlib.  But I am
> not seeing ANYTHING with commands like plt.show().  It executes, and
> then returns.  No output is generated.
>
> This very short and simple test program of mine used to produce output
> with Python 2.7 and Matplotlib 1.1.0.  But with Python 3 and Matplolib
> 1.2.1, I am getting nothing...
>
> import numpy as np
> import matplotlib.pyplot as plt
>
> x = np.arange(0, 5, 0.1);
> y = np.sin(x)
> plt.plot(x, y)
> plt.show()
>
> It runs.  No error messages are generated.  But I don't get a graph. I
> don't even see a graph flicker on to the screen and disappear an instant
> later.
>
> Any advice will be appreciated!
>
>
You will need to make sure you install the gtk packages (both the libraries
and the dev packages) *before* building from source.  If it can't find the
dev packages, then it won't build the interactive backend for it.  I can't
remember if there are python3 specific packages for gtk (or any other gui
for that matter).

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Francesco M. <fra...@gm...>]

Hi John,

2013/4/18 John Ladasky <joh...@sb...>

> On 04/18/2013 01:01 AM, Francesco Montesano wrote:
>
>> does plt.savefig('test.png') work?
>>
> Yes, it does!  Thank you, that was a useful hint.


Good, than I would say that is a clear sign that you have a non interactive
backend.
Can you please give use the output of plt.get_backend() ?


>
>  If the figure get saved, it can be that you are using a non interactive
>> backend
>>
> Ugh, the one thing that I never understood about Matplotlib was backends.
>  So, what am I missing?  (Whatever I am missing now, I had it working a
> year ago when I was using matplotlib 1.1.0 on Python 2.7.)
>

This link http://matplotlib.org/faq/usage_faq.html#what-is-a-backend should
explain you what a backend is.

If you want to use always a specific backend, you should select it in the
matplotlibrc file

You should have a line like this
#backend      : TkAgg
Just uncomment it and put the backend that you want to use


> I have also just tried ipython3.  Nothing that I do in the live
> interpreter displays any graphs.
>
>
That is not surprising: if matplotlib doesn't use an interactive backend,
you can't show the figures, whatever interpreter you use.

I hope that now is clearer,

Fra

ps: try to remember to reply to the list :D

Re: [Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[Francesco M. <fra...@gm...>]

Hi John,

does plt.savefig('test.png') work?

If the figure get saved, it can be that you are using a non interactive
backend

Cheers
Fra


2013/4/18 John Ladasky <joh...@sb...>

> Hello everyone,
>
> After not using Matplotlib for over a year, I'm returning to it.
> Meanwhile, I have upgraded from Python 2.7 to Python 3.2, and I want to
> do all of my software development in Python 3 from now on.
>
> My OS is Ubuntu 12.04.1.  Python 2.7 is still the default Python for
> Ubuntu, and many of the Python 3 packages are not offered as official
> repositories yet. I downloaded Matplotlib 1.2.1, then built it using
> Python 3.  Eventually, I got no build error messages, and proceeded to
> install. (I always have to pick through dependency problems one error
> message at a time.  I wish there was a better way.  The Matplotlib docs
> could be a little better in this respect.)
>
> When I open a Python3 interpreter, I can import matplotlib.  But I am
> not seeing ANYTHING with commands like plt.show().  It executes, and
> then returns.  No output is generated.
>
> This very short and simple test program of mine used to produce output
> with Python 2.7 and Matplotlib 1.1.0.  But with Python 3 and Matplolib
> 1.2.1, I am getting nothing...
>
> import numpy as np
> import matplotlib.pyplot as plt
>
> x = np.arange(0, 5, 0.1);
> y = np.sin(x)
> plt.plot(x, y)
> plt.show()
>
> It runs.  No error messages are generated.  But I don't get a graph. I
> don't even see a graph flicker on to the screen and disappear an instant
> later.
>
> Any advice will be appreciated!
>
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

[Matplotlib-users] Trying to migrate to Python 3.2, Matplotlib 1.2.1

[John L. <joh...@sb...>]

Hello everyone,

After not using Matplotlib for over a year, I'm returning to it. 
Meanwhile, I have upgraded from Python 2.7 to Python 3.2, and I want to 
do all of my software development in Python 3 from now on.

My OS is Ubuntu 12.04.1.  Python 2.7 is still the default Python for 
Ubuntu, and many of the Python 3 packages are not offered as official 
repositories yet. I downloaded Matplotlib 1.2.1, then built it using 
Python 3.  Eventually, I got no build error messages, and proceeded to 
install. (I always have to pick through dependency problems one error 
message at a time.  I wish there was a better way.  The Matplotlib docs 
could be a little better in this respect.)

When I open a Python3 interpreter, I can import matplotlib.  But I am 
not seeing ANYTHING with commands like plt.show().  It executes, and 
then returns.  No output is generated.

This very short and simple test program of mine used to produce output 
with Python 2.7 and Matplotlib 1.1.0.  But with Python 3 and Matplolib 
1.2.1, I am getting nothing...

import numpy as np
import matplotlib.pyplot as plt

x = np.arange(0, 5, 0.1);
y = np.sin(x)
plt.plot(x, y)
plt.show()

It runs.  No error messages are generated.  But I don't get a graph. I 
don't even see a graph flicker on to the screen and disappear an instant 
later.

Any advice will be appreciated!

[Matplotlib-users] After close the plot window the process keeps running.

[<car...@ya...>]

Hi guys,

Im new in matplotlib and having some hard times. From the user point of view
everything works fine.
I have a window with a button. Pressing the button a new window pops showing
the plot. After play
with it i click at X to close this window. And click at X again to close the
window with the button.
BUT im not dropped back to a free prompt. The main window is locked and
still running in background.

Here goes the important parts of code:

import matplotlib
import matplotlib.pyplot as Plt
from matplotlib.figure import Figure

class MainPanel(wx.Panel):

    def __init__(self, parent): #=None

        wx.Panel.__init__(self, parent)

                       .... wxpython stuff goes here....

              self.btn1.Bind(wx.EVT_BUTTON, self.cplot)

                       ....

    def cplot(self, event):
        self.new = NewWindow(self)
        self.new.cidplot(self)
        self.new.Show()
        return


class NewWindow(wx.Frame):

    def __init__(self,event):
        wx.Frame.__init__(self, None, -1, 'Plot', size=(556, 618))
        wx.Frame.CenterOnScreen(self)
        self.Bind(wx.EVT_CLOSE, self.OnClose)


    def OnClose(self,event):
        self.Destroy()


    def cidplot(self,event):


        self.fig = Figure()
        
        self.axes = self.fig.add_subplot(111)
        self.canvas = FigCanvas(self, -1, self.fig)

        self.axes.set_ylabel("Parts")
        self.axes.set_ylim(0,100)
        self.axes.grid(True)

        ....more axes settings...

       bars = self.axes.bar(left=self.ii, height=self.tt, width=0.2,
align='center', alpha=0.8)

        ....

        self.canvas.draw()

        Plt.savefig("Parts.pdf", dpi=300)



class MainFrame(wx.Frame):

    def __init__(self):

        wx.Frame.__init__(self, None, title = "System Test")

        self.SetSize((556, 618))

        panel = MainPanel(self)

        self.Show()


if __name__ == "__main__":

    app = wx.App(False)
    frame = MainFrame()
    app.MainLoop()


I think the problem is at self.fig = Figure() (Same happens if i use
Plt.figure())

Im doing something wrong when i create a new window or is at my matplotlib
part?
Some better way to do it?

Thanks in advance. Any ideia is welcome.



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/After-close-the-plot-window-the-process-keeps-running-tp40919.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] Trouble with x-axis labeling

[Alexa <ale...@gm...>]

Hi Ben,

Thank you for your quick reply. That did the trick! I will into
ax.label_outer() , thanks for the suggestion.

- Alexa



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Trouble-with-x-axis-labeling-tp40916p40918.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] Trouble with x-axis labeling

[Benjamin R. <ben...@ou...>]

On Wed, Apr 17, 2013 at 11:54 AM, Alexa <ale...@gm...> wrote:

> Hello All!
>
> I searched for my problem and while I found similar questions this seemed
> to
> be a unique problem.
>
> I am creating an image that is six vertically stacked subplots and I want
> only the axis of the bottom subplot to be labelled. However, as you can see
> from the image I attached it's picking the wrong subplot to label. It's as
> if the program is not understanding that there is one more plot. If I just
> plot five plots than everything works. I'm not sure what is going wrong
> with
> me code. It would be extremely helpful if someone could take a look.
>
> xlabel = ["",5000,5500,6000,6500,7000,""]
> plt.figure()
>
> night = (glob.glob('*_sci.txt'))
> for i in range(0,len(night)):
>         # Read in data for each night
>         wave = np.loadtxt(night[i], usecols=[0])
>         flux = np.loadtxt(night[i], usecols=[1])
>         # Create subplots
>         temp = 610 +i
>         spect = plt.subplot(temp,sharex=True)
>         # Draw plot
>         plt.plot(wave, flux, color="green")
>         plt.subplots_adjust(hspace = 0.001)
>         spect.set_autoscaley_on(False)
>         pylab.ylim([0,0.5e-13])
>         # Make y tick makers
>         temp = tic.MaxNLocator(3)
>         plt.gca().yaxis.set_major_locator(tic.MaxNLocator(prune='lower'))
>         plt.gca().yaxis.set_major_locator(tic.MaxNLocator(prune='upper'))
>         spect.yaxis.set_major_locator(temp)
>         # Get rid of redundant x tick labels
>         if i < len(night)-1:
>                 plt.setp(spect.get_xticklabels(), visible=False)
>
>
> spect.set_xticklabels(xlabel, minor=False)
> plt.xlabel("Observed Wavelength $(\AA)$",fontsize=16)
>
>
> <http://matplotlib.1069221.n5.nabble.com/file/n40916/Example.png>
>
>
>
plt.subplot() uses 1-based indexing.  So, the first plot you make is "610"
because i == 0 in the first iteration.  This corresponds to the *last"
subplot you actually want (i.e., the bottom one).  If you just have a 611 +
i, the problem would be fixed.  Btw, there is an ax.label_outer() function
that would make the code easier to read.

Ben Root

[Matplotlib-users] Trouble with x-axis labeling

[Alexa <ale...@gm...>]

Hello All!

I searched for my problem and while I found similar questions this seemed to
be a unique problem.

I am creating an image that is six vertically stacked subplots and I want
only the axis of the bottom subplot to be labelled. However, as you can see
from the image I attached it's picking the wrong subplot to label. It's as
if the program is not understanding that there is one more plot. If I just
plot five plots than everything works. I'm not sure what is going wrong with
me code. It would be extremely helpful if someone could take a look.

xlabel = ["",5000,5500,6000,6500,7000,""]
plt.figure()

night = (glob.glob('*_sci.txt'))
for i in range(0,len(night)):
        # Read in data for each night
        wave = np.loadtxt(night[i], usecols=[0])
        flux = np.loadtxt(night[i], usecols=[1])
        # Create subplots
        temp = 610 +i  
        spect = plt.subplot(temp,sharex=True)
        # Draw plot
        plt.plot(wave, flux, color="green")
        plt.subplots_adjust(hspace = 0.001)
        spect.set_autoscaley_on(False)  
        pylab.ylim([0,0.5e-13])
        # Make y tick makers 
        temp = tic.MaxNLocator(3)
        plt.gca().yaxis.set_major_locator(tic.MaxNLocator(prune='lower'))
        plt.gca().yaxis.set_major_locator(tic.MaxNLocator(prune='upper'))
        spect.yaxis.set_major_locator(temp)
        # Get rid of redundant x tick labels
        if i < len(night)-1:
                plt.setp(spect.get_xticklabels(), visible=False)


spect.set_xticklabels(xlabel, minor=False)
plt.xlabel("Observed Wavelength $(\AA)$",fontsize=16)


<http://matplotlib.1069221.n5.nabble.com/file/n40916/Example.png> 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Trouble-with-x-axis-labeling-tp40916.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] AnchoredSizeBar Color

[Jae-Joon L. <lee...@gm...>]

The anchored_artists needs improvements and things are still opaque.
For now you can do something like below,

```
a = AnchoredSizeBar(ax.transData, 0.1, "test",
                    loc=8, pad=0.1, borderpad=0.1, sep=2, prop=None,
                    frameon=False)
rect = a.size_bar._children[0]
rect.set_ec("g")
```

`rect` is a patch instance responsible for the bar. By default its height
is 0 and facecolor="none".

Similarly, the text label can be accessed via `a.txt_label._text`.

Regards,

-JJ



On Wed, Apr 17, 2013 at 1:47 AM, Mathew Topper <mat...@ed...>wrote:

> Hi,
>
> Is there anyway to set the color of an AnchoredSizeBar artist from the
> mpl_toolkits.axes_grid.anchored_artists toolkit?
>
> Thanks,
>
> Mat
> --
> Dr. Mathew Topper
> Institute for Energy Systems
> School of Engineering
> The University of Edinburgh
> Faraday Building
> The King’s Buildings
> Edinburgh EH9 3JL
> Tel: +44 (0)131 650 5570
> School fax: +44 (0)131 650 6554
> mat...@ed... <mailto:mat...@ed...>
> http://www.see.ed.ac.uk <http://www.see.ed.ac.uk/>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

[Matplotlib-users] TypeError: unsupported operand type(s) for +: 'NoneType' and 'float' on 1.2.1

[Christophe P. <xo...@th...>]

After upgrading to 1.2.1 from 1.1, I'm getting an exception on the below-noted line; any thoughts what might have changed?

  File "/Users/xof/Documents/Dev/tuneup/reports/tables.py", line 60, in table_sizes
    dbar = ax.barh(ind, data_size, width, linewidth=0, color='blue', label='Main Data')
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/axes.py", line 5021, in barh
    orientation='horizontal', **kwargs)
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/axes.py", line 4901, in bar
    self.add_patch(r)
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/axes.py", line 1570, in add_patch
    self._update_patch_limits(p)
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/axes.py", line 1588, in _update_patch_limits
    xys = patch.get_patch_transform().transform(vertices)
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/patches.py", line 581, in get_patch_transform
    self._update_patch_transform()
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/patches.py", line 577, in _update_patch_transform
    bbox = transforms.Bbox.from_bounds(x, y, width, height)
  File "/Users/xof/Documents/Dev/environments/tuneup/lib/python2.6/site-packages/matplotlib/transforms.py", line 786, in from_bounds
    return Bbox.from_extents(x0, y0, x0 + width, y0 + height)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'float'

The code is:

    # preamble code collecting data

    ind = np.arange(len(table_name))
    
    width = 0.35
    
    fig = plot.figure(figsize=DEFAULT_FIGURE_SIZE)
    ax = fig.add_subplot(111, axisbg='#fafafa', alpha=0.9)
    
    ax.set_title('Largest Tables')
    
    ax.set_xlabel('Size (log scale)')
    
    ax.set_xscale('log')
    ax.grid(True)
    
    ax.xaxis.set_major_formatter(FuncFormatter(magnitude_ticks))

    dbar = ax.barh(ind, data_size, width, linewidth=0, color='blue', label='Main Data')  # exception here
    ibar = ax.barh(ind, index_toast_size, width, left=data_size, linewidth=0, color='red', label='Toast/Indexes')
    ax.set_yticks(ind + width/2)
    ax.set_yticklabels(table_name, fontproperties=xx_small_font)

    ax.legend(loc='lower right', prop=x_small_font)

    plot.tight_layout()
    
    plot.savefig(REPORT_DIR_PATH + '/table_sizes.pdf')

    plot.close()

--
-- Christophe Pettus
   xo...@th...

[Matplotlib-users] AnchoredSizeBar Color

[Mathew T. <mat...@ed...>]

Hi,

Is there anyway to set the color of an AnchoredSizeBar artist from the 
mpl_toolkits.axes_grid.anchored_artists toolkit?

Thanks,

Mat
-- 
Dr. Mathew Topper
Institute for Energy Systems
School of Engineering
The University of Edinburgh
Faraday Building
The King’s Buildings
Edinburgh EH9 3JL
Tel: +44 (0)131 650 5570
School fax: +44 (0)131 650 6554
mat...@ed... <mailto:mat...@ed...>
http://www.see.ed.ac.uk <http://www.see.ed.ac.uk/>

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [Matplotlib-users] Linewidths in data space?

[Joe K. <jof...@gm...>]

> Apart from implementing this natively in matplotlib, I was thinking if
> I could work around this limitation for our purposes in the following
> way: My objects to draw will always sit in a Collection. I could derive
> my own Collection class with a draw() method that changes the
> linewidth of the collections, taking into account the current
> axes.transData and figure.dpi. Using that I should be able to
> achieve my goal, right? (given that I restrict myself to plots with
> the same scaling in all directions)
>
>
Not to plug one of my own answers, but there's an example of using a
callback to keep linewidths in data coordinates here:
http://stackoverflow.com/a/15673254/325565

Have a look at the second example in the answer for the callback approach.
Using something like ``shapely`` to buffer your lines as the first example
does is also an option.

Hope that helps a bit anyway,
-Joe

Re: [Matplotlib-users] Linewidths in data space?

[Michael W. <wim...@gm...>]

Dear Mike,

thanks for your quick answer! Sorry for the late reply, I was away over the
weekend.

We are using matplotlib to plot two-dimensional and three-dimensional
(mostly regular) lattices (it's a physics application), with grid sites being
represented by a symbol and links representes by lines. The size of these
grids varies strongly (i.e. how many symbols and lines are plotted), and it
would be easiest if I could specify linewidths relative to some data coordinate
system (e.g. the line width being 5% of the grid spacing).

Arguably, this is not what matplotlib is intended for, but sometimes we also
want to plot data information on top of that lattice, and then the
tools of matplotlib are extremely handy.

Also, what I have in mind will always be for a linear-scale, unit
aspect-ratio plot, so that the problems you mentioned (log-scale,
different scaling in different directions) would not be applicable.
In the general case I agree one would need to make the lines
actually a filled stroke.

I'll nevertheless file a ticket. On github?

Apart from implementing this natively in matplotlib, I was thinking if
I could work around this limitation for our purposes in the following
way: My objects to draw will always sit in a Collection. I could derive
my own Collection class with a draw() method that changes the
linewidth of the collections, taking into account the current
axes.transData and figure.dpi. Using that I should be able to
achieve my goal, right? (given that I restrict myself to plots with
the same scaling in all directions)

Michael

2013/4/12 Michael Droettboom <md...@st...>:
> Unfortunately, I don't think there is a way to do this at present.  Out
> of curiosity, what is the use case?
>
> I wonder if the best way to do this would be to expose the stroking to
> the Python level, so given a line one could get a filled path that is
> the stroked line.  I'm not sure how else this could work, since the
> zooming could be different in each direction, etc., or could even by
> log-scaled etc.
>
> Would you mind creating an issue ticket for this?  (Patches welcome,
> too, of course, and I can provide pointers if you want to take this on
> yourself...)
>
> Mike
>
> On 04/12/2013 05:34 AM, Michael Wimmer wrote:
>> I have a collection of Patches and Lines that have their coordinates in
>> data space, i.e. like in the following example:
>>
>>
>> import matplotlib.pyplot as plt
>> import matplotlib.patches as mpatches
>> import matplotlib.collections as mcollections
>> import matplotlib.lines as mlines
>>
>> fig = plt.figure()
>> ax = fig.add_subplot(111)
>>
>> patches = []
>> patches.append(mlines.Line2D((0,1),(0,1), linewidth=1))
>> patches.append(mpatches.Circle((0,0), 0.25, linewidth=1))
>> patches.append(mpatches.Circle((1,1), 0.25, linewidth=1))
>>
>> coll = mcollections.PatchCollection(patches)
>> ax.add_collection(coll)
>> ax.autoscale_view()
>>
>> plt.show()
>>
>>
>> Now, in this example the line width is always given with respect to the
>> screen space, i.e. does not change when I zoom into the plot. Is it
>> possible to specify a linewidth with respect to data space? I.e. to say
>> that a line (in both the Line2D and the Circle) should be let's say 0.1
>> in data space, and thus scale accordingly if I zoom in?
>>
>> -Michael
>>
>> ------------------------------------------------------------------------------
>> Precog is a next-generation analytics platform capable of advanced
>> analytics on semi-structured data. The platform includes APIs for building
>> apps and a phenomenal toolset for data science. Developers can use
>> our toolset for easy data analysis & visualization. Get a free account!
>> http://www2.precog.com/precogplatform/slashdotnewsletter
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users