matplotlib-users Mailing List for matplotlib (Page 6)

I am trying use matplotlib on CentOS through a PHP script. If I run it on
the command line it works fine and generates a PNG figure. If I run with
another user,

sudo -u apache python filename.py

it gives error: Cannot obtain dvipng version.

Any ideas? I search the net but no answers. It looks like a bug? In the
script I am using TeX.

rc('text', usetex=True)

Texlive and dvipng are installed and paths are set correctly.

How is the space between the axis and the outer margins of a figure defined?
How much space is between the upper most plot and the upper end of the figure?
This is the space e.g for the titles etc. but can this be space be increased?

Or how can a some text be placed above the axis but with a lot of space?
I hope it is now clearer...

/johannes

Am 13.05.2011 um 16:59 schrieb Michael Droettboom:

> I think there's a confusion of definition here:
> 
>   figure: The entire image
> 
>   axes: A box within the figure containing a plot
> 
> Mike
> 
> On 05/13/2011 10:20 AM, Johannes Radinger wrote:
>> That is not what I want, to put the text inside the figure.
>> 
>> I want the text above the figure with some space (e.g 2 cm) to the figure
>> thats why I tried 0, 1.2 but then the text is outside the margins
>> 
>> /j
>> -------- Original-Nachricht --------
>> 
>>> Datum: Fri, 13 May 2011 14:03:16 +0000 (UTC)
>>> Von: Pauli Virtanen<pa...@ik...>
>>> An: mat...@li...
>>> Betreff: Re: [Matplotlib-users] Text outside the graphs "box"
>>> 
>> 
>>> Fri, 13 May 2011 15:58:37 +0200, Johannes Radinger wrote:
>>> 
>>>> Hello again I tried:
>>>> 
>>>> plt.figtext(0, 1.2, r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
>>>> 
>>>> but then the text is outside the printed area and therefore not
>>>> displayed. Does that mean that the printed area has to be changed as
>>>> well?
>>>> 
>>> The first two parameters are the x and y coordinates of the text,
>>> in range [0, 1]. Adjust them to put the text inside the figure.
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Achieve unprecedented app performance and reliability
>>> What every C/C++ and Fortran developer should know.
>>> Learn how Intel has extended the reach of its next-generation tools
>>> to help boost performance applications - inlcuding clusters.
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>>> 
>> 
> 
> 
> -- 
> Michael Droettboom
> Science Software Branch
> Space Telescope Science Institute
> Baltimore, Maryland, USA
> 
> 
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Thanks!
-Joe

On Sun, May 15, 2011 at 12:50 AM, Eric Firing <ef...@ha...> wrote:

> On 05/14/2011 12:22 PM, Joe Kington wrote:
> > Hi,
> >
> > When getting an axis's extents through "axis", the autoscaling state of
> > the axis is turned off, regardless of the state it was in before calling
> > "ax.axis()"
> >
> > E.g.
> > import matplotlib.pyplot as plt
> > fig = plt.figure()
> > ax = fig.add_subplot(111)
> > print ax.get_autoscale_on()
> > limits = ax.axis()
> > print ax.get_autoscale_on()
> >
> > It makes sense that it would be turned off if the axis's limits are
> > manually set, but calling ax.get_xlim() or ax.get_ylim() doesn't change
> > the autoscaling state, so why should getting the extents by calling
> > ax.axis()?
>
> It is now fixed in v1.0.x and master on github.
>
> Eric
> >
> > This seems like confusing and/or inconsistent behavior to me. Would this
> > be considered a bug?  If not, is it worth clarifying in the docstring to
> > axis?
> >
> > Thanks,
> > -Joe
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Achieve unprecedented app performance and reliability
> > What every C/C++ and Fortran developer should know.
> > Learn how Intel has extended the reach of its next-generation tools
> > to help boost performance applications - inlcuding clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> >
> >
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On 05/14/2011 12:22 PM, Joe Kington wrote:
> Hi,
>
> When getting an axis's extents through "axis", the autoscaling state of
> the axis is turned off, regardless of the state it was in before calling
> "ax.axis()"
>
> E.g.
> import matplotlib.pyplot as plt
> fig = plt.figure()
> ax = fig.add_subplot(111)
> print ax.get_autoscale_on()
> limits = ax.axis()
> print ax.get_autoscale_on()
>
> It makes sense that it would be turned off if the axis's limits are
> manually set, but calling ax.get_xlim() or ax.get_ylim() doesn't change
> the autoscaling state, so why should getting the extents by calling
> ax.axis()?

It is now fixed in v1.0.x and master on github.

Eric
>
> This seems like confusing and/or inconsistent behavior to me. Would this
> be considered a bug?  If not, is it worth clarifying in the docstring to
> axis?
>
> Thanks,
> -Joe
>
>
>
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On 05/14/2011 12:22 PM, Joe Kington wrote:
> Hi,
>
> When getting an axis's extents through "axis", the autoscaling state of
> the axis is turned off, regardless of the state it was in before calling
> "ax.axis()"
>
> E.g.
> import matplotlib.pyplot as plt
> fig = plt.figure()
> ax = fig.add_subplot(111)
> print ax.get_autoscale_on()
> limits = ax.axis()
> print ax.get_autoscale_on()
>
> It makes sense that it would be turned off if the axis's limits are
> manually set, but calling ax.get_xlim() or ax.get_ylim() doesn't change
> the autoscaling state, so why should getting the extents by calling
> ax.axis()?

It's a bug.

Eric

>
> This seems like confusing and/or inconsistent behavior to me. Would this
> be considered a bug?  If not, is it worth clarifying in the docstring to
> axis?
>
> Thanks,
> -Joe

Hi,

When getting an axis's extents through "axis", the autoscaling state of the
axis is turned off, regardless of the state it was in before calling
"ax.axis()"

E.g.
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
print ax.get_autoscale_on()
limits = ax.axis()
print ax.get_autoscale_on()

It makes sense that it would be turned off if the axis's limits are manually
set, but calling ax.get_xlim() or ax.get_ylim() doesn't change the
autoscaling state, so why should getting the extents by calling ax.axis()?

This seems like confusing and/or inconsistent behavior to me. Would this be
considered a bug?  If not, is it worth clarifying in the docstring to axis?

Thanks,
-Joe

Hello,

I'm a new matplotlib user and i have some question on embeded mpl into WxPython app. It's true that i a lot of doc but i don't find my solution (my poor english it's maybe  for somethings).
My problem is not to how to embeded it but how customize customize my y axe whit barh chart.

Whit pylab i can do this't
pylab.yticks(pos, testNames)

But how can i do this when i work with wx. 

This a part off my code :

def draw_figure(self):

        self.axes.clear()
        self.axes.grid(True)
        
        
        self.axes.barh([1], 10, 0.2, 4, align='center')
        self.axes.barh([2], 4, 0.2, 2, align='center')
        self.axes.barh([3], 0.5, 0.2, 0.2, align='center')
        self.axes.yaxis.set_label_text("Grp de sauvegarde")
        
        self.axes.set_yticklabels(('G1', 'G2', 'G3'))
        for i in dir(self.axes):
            print i

        
        self.canvas.draw()
 

Thank's

Bruno

This message has been scanned for viruses and
dangerous content by  Amavisd-new, and is
believed to be clean.

On 05/13/2011 05:19 AM, Johannes Radinger wrote:
>
> -------- Original-Nachricht --------
>> Datum: Fri, 13 May 2011 10:58:15 -0400
>> Von: Michael Droettboom<md...@st...>
>> An: mat...@li...
>> Betreff: Re: [Matplotlib-users] eps output and fill_between
>
>> Running it through gs (ghostscript) gives this error:
>>
>> =====
>>
>> GPL Ghostscript 8.70 (2009-07-31)
>> Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
>> This software comes with NO WARRANTY: see the file PUBLIC for details.
>> Error: /stackoverflow in -file-
>> Operand stack:
>>      --nostringval--
>> Execution stack:
>>      %interp_exit   .runexec2   --nostringval--   --nostringval--
>> --nostringval--   2   %stopped_push   --nostringval--
>> --nostringval--   --nostringval--   false   1   %stopped_push   1846
>> 1   3   %oparray_pop   1845   1   3   %oparray_pop   --nostringval--
>> 1829   1   3   %oparray_pop   1723   1   3   %oparray_pop
>> --nostringval--   %errorexec_pop   .runexec2   --nostringval--
>> --nostringval--   --nostringval--   2   %stopped_push
>> Dictionary stack:
>>      --dict:1148/1684(ro)(G)--   --dict:0/20(G)--   --dict:75/200(L)--
>> --dict:7/8(L)--
>> Current allocation mode is local
>> Current file position is 675310
>> GPL Ghostscript 8.70: Unrecoverable error, exit code 1
>>
>> =====
>>
>> This indicates that the Postscript is running out of stack space
>> (memory).  Indeed, the file has a very large path in it.
>>
>> A little background: matplotlib includes an algorithm to "simplify"
>> really long paths by removing points that don't actually contribute to
>> the resulting image.  Unfortunately, this algorithm only works for
>> unfilled paths -- dealing with the more general case of filled paths is
>> more difficult.  That's why you only see this problem when using
>> "fill_between" and not just when plotting lines.
>>
>> The problem here is that it's hard to trap for this error -- the size of
>> the Postscript stack is dependent on the Postscript interpreter being
>> used, so what works in one place may not in another.
>>
>> A simple way around this is to just decimate the data, i.e.:
>>
>>     plt.plot(x[::5], pdf_min[::5], x[::5], pdf_max[::5], color="k")
>>     plt.fill_between(x[::5], pdf_min[::5], pdf_max[::5], color='0.85')
>>
>> but obviously that's not doing anything terribly smart, so it won't work
>> with all data.
>
> First thank you for that way how it works...
>
> just some short questions, after I tried it this way (and it is working:)):
> 1) What does this decimate [::5] actually mean, what does it?

It takes every 5th point and ignores the rest.  It is an example of 
python slicing, which means taking a uniformly-spaced subset of a sequence.

> 2) In which case will it fail if you say it won't work with all data?

Two failure modes: (1) if taking every 5th point still leaves too many 
points; (2) if taking every 5th point leaves out points that would have 
an important effect on the shape of the curve, so the figure you end up 
with is not an accurate representation of what you are trying to plot.

> 3) Actually I have to use that [::5] only for the fill_between as the usual  line plot works, or am I wrong?

Correct.  What Mike is saying is that for ordinary lines, mpl has a 
sophisticated algorithm for eliminating points that don't affect what 
one sees in the figure, so it is much less likely that the postscript 
renderer will run out of stack space; but this algorithm is not used for 
filled regions because points that are not needed for representing a 
line might still be needed for a filled region.

Eric

>
> /johannes

On Wed, May 11, 2011 at 12:29 AM, Jae-Joon Lee <lee...@gm...> wrote:
> I think I fixed a similar bug at some point but I'm not sure if that
> is related with this.
> Are you using the *make_axes_area_auto_adjustable* from the current
> git master (check
> examples/axes_grid/make_room_for_ylabel_using_axesgrid.py)? If not can
> you try that? Also please post your code.

It seems I can't build matplotlib from source. Would it be possible to
attach the amended files to this list and I'll try them?

Thank you,
Che

On Fri, May 13, 2011 at 6:23 AM, Pauli Virtanen <pa...@ik...> wrote:
> Thu, 12 May 2011 15:16:43 -0400, C M wrote:
> [clip: installing Python modules]
>> Is there a step-by-step method on the
>> website that shows how to do this?
>
> Here: http://docs.python.org/install/index.html

Thanks, but I guess I can't install matplotlib since I can't build it,
since I don't have VS2003.

-------- Original-Nachricht --------
> Datum: Fri, 13 May 2011 10:58:15 -0400
> Von: Michael Droettboom <md...@st...>
> An: mat...@li...
> Betreff: Re: [Matplotlib-users] eps output and fill_between

> Running it through gs (ghostscript) gives this error:
> 
> =====
> 
> GPL Ghostscript 8.70 (2009-07-31)
> Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
> This software comes with NO WARRANTY: see the file PUBLIC for details.
> Error: /stackoverflow in -file-
> Operand stack:
>     --nostringval--
> Execution stack:
>     %interp_exit   .runexec2   --nostringval--   --nostringval--   
> --nostringval--   2   %stopped_push   --nostringval--   
> --nostringval--   --nostringval--   false   1   %stopped_push   1846   
> 1   3   %oparray_pop   1845   1   3   %oparray_pop   --nostringval--   
> 1829   1   3   %oparray_pop   1723   1   3   %oparray_pop   
> --nostringval--   %errorexec_pop   .runexec2   --nostringval--   
> --nostringval--   --nostringval--   2   %stopped_push
> Dictionary stack:
>     --dict:1148/1684(ro)(G)--   --dict:0/20(G)--   --dict:75/200(L)--   
> --dict:7/8(L)--
> Current allocation mode is local
> Current file position is 675310
> GPL Ghostscript 8.70: Unrecoverable error, exit code 1
> 
> =====
> 
> This indicates that the Postscript is running out of stack space 
> (memory).  Indeed, the file has a very large path in it.
> 
> A little background: matplotlib includes an algorithm to "simplify" 
> really long paths by removing points that don't actually contribute to 
> the resulting image.  Unfortunately, this algorithm only works for 
> unfilled paths -- dealing with the more general case of filled paths is 
> more difficult.  That's why you only see this problem when using 
> "fill_between" and not just when plotting lines.
> 
> The problem here is that it's hard to trap for this error -- the size of 
> the Postscript stack is dependent on the Postscript interpreter being 
> used, so what works in one place may not in another.
> 
> A simple way around this is to just decimate the data, i.e.:
> 
>    plt.plot(x[::5], pdf_min[::5], x[::5], pdf_max[::5], color="k")
>    plt.fill_between(x[::5], pdf_min[::5], pdf_max[::5], color='0.85')
> 
> but obviously that's not doing anything terribly smart, so it won't work 
> with all data.

First thank you for that way how it works...

just some short questions, after I tried it this way (and it is working:)):
1) What does this decimate [::5] actually mean, what does it?
2) In which case will it fail if you say it won't work with all data?
3) Actually I have to use that [::5] only for the fill_between as the usual  line plot works, or am I wrong?

/johannes


> 
> Mike
> 
> On 05/13/2011 10:00 AM, Johannes Radinger wrote:
> > Does anyone already know what causes the problem with the fill_between
> and the eps output?
> >
> > /johannes
> >
> >
> > -------- Original-Nachricht --------
> >    
> >> Datum: Thu, 12 May 2011 17:10:43 +0200
> >> Von: Johannes Radinger<JRa...@gm...>
> >> An: John Hunter<jd...@gm...>
> >> CC: mat...@li...
> >> Betreff: Re: [Matplotlib-users] eps output and fill_between
> >>      
> >    
> >> Hello again,
> >>
> >> I tried the script you provided to test the PolyCollection and that
> works
> >> fine.
> >> I am working under Mac OS X 10.6.6 Snow Leopard and use matplotlib
> 1.0.1.
> >>
> >> That is the script where I fail with eps but not with pdf:
> >>
> >>
> >>
> >> import matplotlib.pyplot as plt
> >> import numpy
> >> from scipy import stats
> >>
> >> p=0.3
> >> m=0
> >> s1min=120
> >> s1max=140
> >> s2min=1200
> >> s2max=1600
> >>
> >> x = numpy.arange((s2max*-1.5), (s2max*1.5), 0.2)
> >>
> >> def pdf(x,s1,s2):
> >>      return p * stats.norm.pdf(x, loc=m, scale=s1) + (1-p) *
> >> stats.norm.pdf(x, loc=m, scale=s2)
> >>
> >>
> >> pdf_min = pdf(x,s1min,s2min)
> >> pdf_max = pdf(x,s1max,s2max)
> >>
> >> plt.plot(x, pdf_min, x, pdf_max, color="k")
> >> plt.fill_between(x, pdf_min, pdf_max, color='0.85')
> >>
> >>
> >> #plt.show()
> >> #plt.savefig("testplot.eps")
> >> plt.savefig("testplot.pdf")
> >>
> >>
> >> /Johannes
> >>
> >> Am 12.05.2011 um 15:28 schrieb John Hunter:
> >>
> >>      
> >>>
> >>> On Thu, May 12, 2011 at 3:42 AM, Johannes Radinger<JRa...@gm...>
> >>>        
> >> wrote:
> >>      
> >>> Hello ,
> >>>
> >>> sofar I know how to safe a plot into a *.eps file and it works good,
> >>> but there is one issue with filled areas between two functions.
> >>>
> >>> When I try to use:
> >>> plt.fill_between(x, pdf_min, pdf_max, color='0.85')
> >>>
> >>> and I try to open it on my mac I fail. So far as I know
> >>> is the mac converting the eps internally to pdf to be
> >>> displayed, but it seems it can't be converted.
> >>>
> >>> If I try to set the output to *.pdf it works perfectly and I can
> >>> open the file. Something in the combination of fill_between
> >>> and eps is causing the error. I tried also color="red" but with
> >>> the same problems.
> >>>
> >>> Is there anything I've to set because I need the output as
> >>> a working eps.
> >>>
> >>>
> >>> under the hool, fill_between uses a PolyCollection.  Below is a simple
> >>>        
> >> example which uses a PolyCollection directly.  Does this crash when you
> >> convert eps ->  pdf.  If not, maybe we can hone in on what is special
> about the
> >> vertices in your fill_between example.  Also, you should give us some
> >> information about what version of matplotlib and OSX you are running.
> >>      
> >>>
> >>> import numpy as np
> >>> import matplotlib.collections as mcollections
> >>> import matplotlib.pyplot as plt
> >>>
> >>> theta = np.linspace(0, 2*np.pi, 20)
> >>> x1 = np.cos(theta)
> >>> y1 = np.sin(theta)
> >>>
> >>> x2 = x1 + 5
> >>> y2 = y1 + 5
> >>>
> >>> verts1 = zip(x1, y1)
> >>> verts2 = zip(x2, y2)
> >>>
> >>> c = mcollections.PolyCollection([verts1, verts2], facecolors=['red',
> >>>        
> >> 'green'])
> >>      
> >>> ax = plt.subplot(111)
> >>> ax.add_collection(c)
> >>> ax.axis([-5, 10, -5, 10])
> >>>
> >>> plt.savefig('test.eps')
> >>> plt.show()
> >>>
> >>>        
> >>      
> >    
> 
> 
> -- 
> Michael Droettboom
> Science Software Branch
> Space Telescope Science Institute
> Baltimore, Maryland, USA
> 
> 
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

-- 
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I think there's a confusion of definition here:

   figure: The entire image

   axes: A box within the figure containing a plot

Mike

On 05/13/2011 10:20 AM, Johannes Radinger wrote:
> That is not what I want, to put the text inside the figure.
>
> I want the text above the figure with some space (e.g 2 cm) to the figure
> thats why I tried 0, 1.2 but then the text is outside the margins
>
> /j
> -------- Original-Nachricht --------
>    
>> Datum: Fri, 13 May 2011 14:03:16 +0000 (UTC)
>> Von: Pauli Virtanen<pa...@ik...>
>> An: mat...@li...
>> Betreff: Re: [Matplotlib-users] Text outside the graphs "box"
>>      
>    
>> Fri, 13 May 2011 15:58:37 +0200, Johannes Radinger wrote:
>>      
>>> Hello again I tried:
>>>
>>> plt.figtext(0, 1.2, r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
>>>
>>> but then the text is outside the printed area and therefore not
>>> displayed. Does that mean that the printed area has to be changed as
>>> well?
>>>        
>> The first two parameters are the x and y coordinates of the text,
>> in range [0, 1]. Adjust them to put the text inside the figure.
>>
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
>> to help boost performance applications - inlcuding clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>      
>    


-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA

On Friday, May 13, 2011, Johannes Radinger <JRa...@gm...> wrote:
> That is not what I want, to put the text inside the figure.
>
> I want the text above the figure with some space (e.g 2 cm) to the figure
> thats why I tried 0, 1.2 but then the text is outside the margins
>

"figure" is the term for the entire printable space.  The graphs that
are made in a figure are called "plots".  figtext() lets you put text
anywhere you want in the normalized domain of 0 to 1.  If you want the
text exactly in the middle, the specify 0.5, 0.5.  Want it in a
corner, then you can do 0.0, 1.0.  Figtext is what you want.

Ben Root

Running it through gs (ghostscript) gives this error:

=====

GPL Ghostscript 8.70 (2009-07-31)
Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Error: /stackoverflow in -file-
Operand stack:
    --nostringval--
Execution stack:
    %interp_exit   .runexec2   --nostringval--   --nostringval--   
--nostringval--   2   %stopped_push   --nostringval--   
--nostringval--   --nostringval--   false   1   %stopped_push   1846   
1   3   %oparray_pop   1845   1   3   %oparray_pop   --nostringval--   
1829   1   3   %oparray_pop   1723   1   3   %oparray_pop   
--nostringval--   %errorexec_pop   .runexec2   --nostringval--   
--nostringval--   --nostringval--   2   %stopped_push
Dictionary stack:
    --dict:1148/1684(ro)(G)--   --dict:0/20(G)--   --dict:75/200(L)--   
--dict:7/8(L)--
Current allocation mode is local
Current file position is 675310
GPL Ghostscript 8.70: Unrecoverable error, exit code 1

=====

This indicates that the Postscript is running out of stack space 
(memory).  Indeed, the file has a very large path in it.

A little background: matplotlib includes an algorithm to "simplify" 
really long paths by removing points that don't actually contribute to 
the resulting image.  Unfortunately, this algorithm only works for 
unfilled paths -- dealing with the more general case of filled paths is 
more difficult.  That's why you only see this problem when using 
"fill_between" and not just when plotting lines.

The problem here is that it's hard to trap for this error -- the size of 
the Postscript stack is dependent on the Postscript interpreter being 
used, so what works in one place may not in another.

A simple way around this is to just decimate the data, i.e.:

   plt.plot(x[::5], pdf_min[::5], x[::5], pdf_max[::5], color="k")
   plt.fill_between(x[::5], pdf_min[::5], pdf_max[::5], color='0.85')

but obviously that's not doing anything terribly smart, so it won't work 
with all data.

Mike

On 05/13/2011 10:00 AM, Johannes Radinger wrote:
> Does anyone already know what causes the problem with the fill_between and the eps output?
>
> /johannes
>
>
> -------- Original-Nachricht --------
>    
>> Datum: Thu, 12 May 2011 17:10:43 +0200
>> Von: Johannes Radinger<JRa...@gm...>
>> An: John Hunter<jd...@gm...>
>> CC: mat...@li...
>> Betreff: Re: [Matplotlib-users] eps output and fill_between
>>      
>    
>> Hello again,
>>
>> I tried the script you provided to test the PolyCollection and that works
>> fine.
>> I am working under Mac OS X 10.6.6 Snow Leopard and use matplotlib 1.0.1.
>>
>> That is the script where I fail with eps but not with pdf:
>>
>>
>>
>> import matplotlib.pyplot as plt
>> import numpy
>> from scipy import stats
>>
>> p=0.3
>> m=0
>> s1min=120
>> s1max=140
>> s2min=1200
>> s2max=1600
>>
>> x = numpy.arange((s2max*-1.5), (s2max*1.5), 0.2)
>>
>> def pdf(x,s1,s2):
>>      return p * stats.norm.pdf(x, loc=m, scale=s1) + (1-p) *
>> stats.norm.pdf(x, loc=m, scale=s2)
>>
>>
>> pdf_min = pdf(x,s1min,s2min)
>> pdf_max = pdf(x,s1max,s2max)
>>
>> plt.plot(x, pdf_min, x, pdf_max, color="k")
>> plt.fill_between(x, pdf_min, pdf_max, color='0.85')
>>
>>
>> #plt.show()
>> #plt.savefig("testplot.eps")
>> plt.savefig("testplot.pdf")
>>
>>
>> /Johannes
>>
>> Am 12.05.2011 um 15:28 schrieb John Hunter:
>>
>>      
>>>
>>> On Thu, May 12, 2011 at 3:42 AM, Johannes Radinger<JRa...@gm...>
>>>        
>> wrote:
>>      
>>> Hello ,
>>>
>>> sofar I know how to safe a plot into a *.eps file and it works good,
>>> but there is one issue with filled areas between two functions.
>>>
>>> When I try to use:
>>> plt.fill_between(x, pdf_min, pdf_max, color='0.85')
>>>
>>> and I try to open it on my mac I fail. So far as I know
>>> is the mac converting the eps internally to pdf to be
>>> displayed, but it seems it can't be converted.
>>>
>>> If I try to set the output to *.pdf it works perfectly and I can
>>> open the file. Something in the combination of fill_between
>>> and eps is causing the error. I tried also color="red" but with
>>> the same problems.
>>>
>>> Is there anything I've to set because I need the output as
>>> a working eps.
>>>
>>>
>>> under the hool, fill_between uses a PolyCollection.  Below is a simple
>>>        
>> example which uses a PolyCollection directly.  Does this crash when you
>> convert eps ->  pdf.  If not, maybe we can hone in on what is special about the
>> vertices in your fill_between example.  Also, you should give us some
>> information about what version of matplotlib and OSX you are running.
>>      
>>>
>>> import numpy as np
>>> import matplotlib.collections as mcollections
>>> import matplotlib.pyplot as plt
>>>
>>> theta = np.linspace(0, 2*np.pi, 20)
>>> x1 = np.cos(theta)
>>> y1 = np.sin(theta)
>>>
>>> x2 = x1 + 5
>>> y2 = y1 + 5
>>>
>>> verts1 = zip(x1, y1)
>>> verts2 = zip(x2, y2)
>>>
>>> c = mcollections.PolyCollection([verts1, verts2], facecolors=['red',
>>>        
>> 'green'])
>>      
>>> ax = plt.subplot(111)
>>> ax.add_collection(c)
>>> ax.axis([-5, 10, -5, 10])
>>>
>>> plt.savefig('test.eps')
>>> plt.show()
>>>
>>>        
>>      
>    


-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA

Hello everyone,

I am having regular segmentation fault crashes using matplotlib under the
configuration describes in the title. This is particularly annoying. I have
not been able to identify a common pattern in the different things I do
before it crashes (just regular plotting, resizing, xlabeling,
ylabeling,...).

I have python, numpy, scipy and matplotlib installed following the
instructions given at
http://www.bytemining.com/2011/03/instructions-for-installing-64bit-scipy-python-2-7-1-on-macos-x-10-6/

I have a bunch of diagnostic reports of the crashes ; I am not very sure of
what I read in there. I have reported two of them below.

If anybody has had a similar problem or knows how to read those reports, I
would appreciate if you gave me a hint.

Have a nice day,


Sirdouille.


-----------------------------------------------------------------------------------------------------------------

Process:         Python [1999]
Path:           
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:      org.python.python
Version:         2.7.1 (2.7.1)
Code Type:       X86-64 (Native)
Parent Process:  bash [900]

Date/Time:       2011-05-13 16:01:45.466 +0200
OS Version:      Mac OS X 10.6.7 (10J869)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: 0x000000000000000d, 0x0000000000000000
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Application Specific Information:
objc_msgSend() selector name: removeFromSuperviewWithoutNeedingDisplay


Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   libobjc.A.dylib               	0x00007fff807be13e objc_msgSend + 74
1   com.apple.CoreFoundation      	0x00007fff86ec8d4e CFArrayApplyFunction +
222
2   com.apple.AppKit              	0x00007fff82ee94cc -[NSView
_finalizeWithReferenceCounting] + 831
3   com.apple.AppKit              	0x00007fff82ee9164 -[NSView dealloc] + 38
4   com.apple.CoreFoundation      	0x00007fff86ed21e6 _CFAutoreleasePoolPop
+ 230
5   com.apple.Foundation          	0x00007fff82bc3ecb -[NSAutoreleasePool
release] + 158
6   _macosx.so                    	0x0000000102b79f75 wait_for_stdin + 597
7   readline.so                   	0x00000001012cffc5 call_readline + 309
8   org.python.python             	0x0000000100008ee2 PyOS_Readline + 274
9   org.python.python             	0x00000001000b6a95 builtin_raw_input +
597
10  org.python.python             	0x00000001000c124d PyEval_EvalFrameEx +
22397
11  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
12  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
13  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
14  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
15  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
16  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
17  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
18  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
19  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
20  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
21  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
22  org.python.python             	0x00000001000c3066 PyEval_EvalCode + 54
23  org.python.python             	0x00000001000e7b2e PyRun_FileExFlags +
174
24  org.python.python             	0x00000001000e7de9
PyRun_SimpleFileExFlags + 489
25  org.python.python             	0x00000001000fe75c Py_Main + 2940
26  org.python.python             	0x0000000100000f14 0x100000000 + 3860

Thread 1:  com.apple.CFSocket.private
0   libSystem.B.dylib             	0x00007fff81820e52 select$DARWIN_EXTSN +
10
1   com.apple.CoreFoundation      	0x00007fff86f0b498 __CFSocketManager +
824
2   libSystem.B.dylib             	0x00007fff818164f6 _pthread_start + 331
3   libSystem.B.dylib             	0x00007fff818163a9 thread_start + 13

Thread 2:  Dispatch queue: com.apple.libdispatch-manager
0   libSystem.B.dylib             	0x00007fff817f612a kevent + 10
1   libSystem.B.dylib             	0x00007fff817f7ffd _dispatch_mgr_invoke +
154
2   libSystem.B.dylib             	0x00007fff817f7cd4 _dispatch_queue_invoke
+ 185
3   libSystem.B.dylib             	0x00007fff817f77fe
_dispatch_worker_thread2 + 252
4   libSystem.B.dylib             	0x00007fff817f7128 _pthread_wqthread +
353
5   libSystem.B.dylib             	0x00007fff817f6fc5 start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00000001030f72f8  rbx: 0x0000000000000000  rcx: 0x0000000000000000 
rdx: 0x00000001030f72c0
  rdi: 0x0000000103411d70  rsi: 0x00007fff835dd6e0  rbp: 0x00007fff5fbfde70 
rsp: 0x00007fff5fbfde18
   r8: 0x00000001034e000e   r9: 0x0000000000000000  r10: 0x0000000103253dc0 
r11: 0x000101d8c9f01699
  r12: 0x0000000000000000  r13: 0x0000000103442ca0  r14: 0x0000000000000009 
r15: 0x0000000000000000
  rip: 0x00007fff807be13e  rfl: 0x0000000000010246  cr2: 0x0000000086ee2000

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    0x7fff8678d000 -     0x7fff867c6fef  libcups.2.dylib 2.8.0
(compatibility 2.0.0) <F8E0672F-C0B4-B161-E50D-A1405D14F21C>
/usr/lib/libcups.2.dylib
    0x7fff86d18000 -     0x7fff86d26ff7  libkxld.dylib ??? (???)
<27713C39-0E51-8F5A-877B-C5539C96A520> /usr/lib/system/libkxld.dylib
    0x7fff86d2d000 -     0x7fff86de2fe7  com.apple.ink.framework 1.3.3 (107)
<8C36373C-5473-3A6A-4972-BC29D504250F>
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
    0x7fff86e9d000 -     0x7fff87014fe7  com.apple.CoreFoundation 6.6.4
(550.42) <770C572A-CF70-168F-F43C-242B9114FCB5>
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
    0x7fff87015000 -     0x7fff87056fff  com.apple.SystemConfiguration
1.10.5 (1.10.2) <FB39F09C-57BB-D8CC-348D-93E00C602F7D>
/System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
    0x7fff872d7000 -     0x7fff873a9fe7  com.apple.CFNetwork 454.11.12
(454.11.12) <B1C9008A-4A5D-609D-5D10-C93DAD6FFB4C>
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
    0x7fff873aa000 -     0x7fff87467fff  com.apple.CoreServices.OSServices
359 (359) <8F509D8D-4C94-9A1C-3A87-5B775D9F6075>
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
    0x7fff87499000 -     0x7fff875ceff7 
com.apple.audio.toolbox.AudioToolbox 1.6.6 (1.6.6)
<AFAB42A2-A3A8-83D8-D583-613625706690>
/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
    0x7fff875cf000 -     0x7fff8770dfff  com.apple.CoreData 102.1 (251)
<9DFE798D-AA52-6A9A-924A-DA73CB94D81A>
/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
    0x7fff8770e000 -     0x7fff878c6fef  com.apple.ImageIO.framework 3.0.4
(3.0.4) <EFB373AE-FE02-40C4-ABDC-09D61AFD25EA>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
    0x7fff8794a000 -     0x7fff8795efff  libGL.dylib ??? (???)
<0FA671EB-6FA0-BA97-C00A-C42247C22B26>
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
    0x7fff87dc9000 -     0x7fff87e03fff  libssl.0.9.8.dylib 0.9.8
(compatibility 0.9.8) <C7153747-50E3-32DA-426F-CC4C505D1D6C>
/usr/lib/libssl.0.9.8.dylib
    0x7fff87edd000 -     0x7fff87f2cff7 
com.apple.DirectoryService.PasswordServerFramework 6.1 (6.1)
<01B370FB-D524-F660-3826-E85B7F0D85CD>
/System/Library/PrivateFrameworks/PasswordServer.framework/Versions/A/PasswordServer
    0x7fff87fbb000 -     0x7fff882b9fff  com.apple.HIToolbox 1.6.5 (???)
<AD1C18F6-51CB-7E39-35DD-F16B1EB978A8>
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
    0x7fff882bb000 -     0x7fff882c8fe7  libCSync.A.dylib 545.0.0
(compatibility 64.0.0) <45B5B514-7CEB-38A9-F34A-1D96F010EC42>
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    0x7fff882c9000 -     0x7fff889c606f  com.apple.CoreGraphics 1.545.0
(???) <F0A5F62D-4C66-5B1F-4F13-322932915901>
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    0x7fff88a85000 -     0x7fff88aa2ff7  libPng.dylib ??? (???)
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/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
    0x7fff88aac000 -     0x7fff88ad2fe7  libJPEG.dylib ??? (???)
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<9BAEB2F2-B485-6349-E1AB-637FE12EE770> /usr/lib/libSystem.B.dylib

-----------------------------------------------------------------------------------------------------------------


















-----------------------------------------------------------------------------------------------------------------

Process:         Python [1603]
Path:           
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:      org.python.python
Version:         2.7.1 (2.7.1)
Code Type:       X86-64 (Native)
Parent Process:  bash [900]

Date/Time:       2011-05-13 15:58:23.219 +0200
OS Version:      Mac OS X 10.6.7 (10J869)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000010
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Application Specific Information:
objc_msgSend() selector name: _propagateDirtyRectsToOpaqueAncestors


Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   libobjc.A.dylib               	0x00007fff807be11c objc_msgSend + 40
1   com.apple.CoreFoundation      	0x00007fff86ec8d4e CFArrayApplyFunction +
222
2   com.apple.AppKit              	0x00007fff83485c55 -[NSView
_propagateDirtyRectsToOpaqueAncestors] + 168
3   com.apple.AppKit              	0x00007fff82eef934 -[NSView
displayIfNeeded] + 355
4   com.apple.AppKit              	0x00007fff82eeaa46
_handleWindowNeedsDisplay + 678
5   com.apple.CoreFoundation      	0x00007fff86f0db37 __CFRunLoopDoObservers
+ 519
6   com.apple.CoreFoundation      	0x00007fff86ee9464 __CFRunLoopRun + 468
7   com.apple.CoreFoundation      	0x00007fff86ee8dbf CFRunLoopRunSpecific +
575
8   com.apple.HIToolbox           	0x00007fff87fe97ee
RunCurrentEventLoopInMode + 333
9   com.apple.HIToolbox           	0x00007fff87fe9551 ReceiveNextEventCommon
+ 148
10  com.apple.HIToolbox           	0x00007fff87fe94ac
BlockUntilNextEventMatchingListInMode + 59
11  com.apple.AppKit              	0x00007fff82ebfe64 _DPSNextEvent + 718
12  com.apple.AppKit              	0x00007fff82ebf7a9 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 155
13  _macosx.so                    	0x00000001029cff22 wait_for_stdin + 514
14  readline.so                   	0x00000001012cffc5 call_readline + 309
15  org.python.python             	0x0000000100008ee2 PyOS_Readline + 274
16  org.python.python             	0x00000001000b6a95 builtin_raw_input +
597
17  org.python.python             	0x00000001000c124d PyEval_EvalFrameEx +
22397
18  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
19  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
20  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
21  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
22  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
23  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
24  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
25  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
26  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
27  org.python.python             	0x00000001000c0d8a PyEval_EvalFrameEx +
21178
28  org.python.python             	0x00000001000c2f49 PyEval_EvalCodeEx +
2137
29  org.python.python             	0x00000001000c3066 PyEval_EvalCode + 54
30  org.python.python             	0x00000001000e7b2e PyRun_FileExFlags +
174
31  org.python.python             	0x00000001000e7de9
PyRun_SimpleFileExFlags + 489
32  org.python.python             	0x00000001000fe75c Py_Main + 2940
33  org.python.python             	0x0000000100000f14 0x100000000 + 3860

Thread 1:  com.apple.CFSocket.private
0   libSystem.B.dylib             	0x00007fff81820e52 select$DARWIN_EXTSN +
10
1   com.apple.CoreFoundation      	0x00007fff86f0b498 __CFSocketManager +
824
2   libSystem.B.dylib             	0x00007fff818164f6 _pthread_start + 331
3   libSystem.B.dylib             	0x00007fff818163a9 thread_start + 13

Thread 2:  Dispatch queue: com.apple.libdispatch-manager
0   libSystem.B.dylib             	0x00007fff817f612a kevent + 10
1   libSystem.B.dylib             	0x00007fff817f7ffd _dispatch_mgr_invoke +
154
2   libSystem.B.dylib             	0x00007fff817f7cd4 _dispatch_queue_invoke
+ 185
3   libSystem.B.dylib             	0x00007fff817f77fe
_dispatch_worker_thread2 + 252
4   libSystem.B.dylib             	0x00007fff817f7128 _pthread_wqthread +
353
5   libSystem.B.dylib             	0x00007fff817f6fc5 start_wqthread + 13

Thread 3:
0   libSystem.B.dylib             	0x00007fff817dd29a mach_msg_trap + 10
1   libSystem.B.dylib             	0x00007fff817dd90d mach_msg + 59
2   com.apple.CoreFoundation      	0x00007fff86ee9932 __CFRunLoopRun + 1698
3   com.apple.CoreFoundation      	0x00007fff86ee8dbf CFRunLoopRunSpecific +
575
4   com.apple.CoreFoundation      	0x00007fff86ee8b46 CFRunLoopRun + 70
5   com.apple.DesktopServices     	0x00007fff862c34d2
TSystemNotificationTask::SystemNotificationTaskProc(void*) + 514
6   ...ple.CoreServices.CarbonCore	0x00007fff83def335 PrivateMPEntryPoint +
63
7   libSystem.B.dylib             	0x00007fff818164f6 _pthread_start + 331
8   libSystem.B.dylib             	0x00007fff818163a9 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000010d823470  rbx: 0x0000000000000018  rcx: 0x0000000000000086 
rdx: 0x000000010d823430
  rdi: 0x0000000152a36ee0  rsi: 0x00007fff835eb47f  rbp: 0x00007fff5fbfcb40 
rsp: 0x00007fff5fbfcae8
   r8: 0x0000000000000001   r9: 0x0000000139de2a40  r10: 0x00007fff86ec6f40 
r11: 0x0000000000000000
  r12: 0x0000000000000003  r13: 0x000000010d822f30  r14: 0x0000000000000004 
r15: 0x0000000000000000
  rip: 0x00007fff807be11c  rfl: 0x0000000000010202  cr2: 0x0000000000000010

Binary Images:
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<9FD4D128-BF5C-532C-5D86-D6CFCCBC9B4B>
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
       0x100003000 -        0x10016bfff +org.python.python 2.7.1, (c)
2004-2008 Python Software Foundation. (2.7.1)
<B1D40343-7092-B922-B649-F20CBDC8BD2A>
/Library/Frameworks/Python.framework/Versions/2.7/Python
       0x1002ee000 -        0x1002f0fff +time.so ??? (???)
<938FAE54-0299-FACF-C957-247FDC411623>
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       0x1002f6000 -        0x1002fafff +_collections.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_collections.so
       0x1004de000 -        0x1004e2ff7 +operator.so ??? (???)
<7EEDE83B-7A43-9C46-D37D-A901A46C6DE3>
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so
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       0x1004fb000 -        0x1004fbfff +_bisect.so ??? (???)
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       0x100640000 -        0x100641ff7 +_heapq.so ??? (???)
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       0x100645000 -        0x100648ff7 +strop.so ??? (???)
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       0x10068d000 -        0x100690fef +binascii.so ??? (???)
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       0x100694000 -        0x1006a2ff7 +datetime.so ??? (???)
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       0x1006ae000 -        0x1006affff +cStringIO.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/math.so
       0x10120c000 -        0x10120dfff +_hashlib.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_hashlib.so
       0x101211000 -        0x101212fff +_random.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_random.so
       0x101215000 -        0x101216ff7 +fcntl.so ??? (???)
<810DE937-99C9-04F3-EAE9-E4F6F910AE12>
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/fcntl.so
       0x101259000 -        0x101259fff +grp.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/grp.so
       0x10125c000 -        0x10125ffff +select.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/select.so
       0x101265000 -        0x101269fff +_struct.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so
       0x101270000 -        0x10127dff7 +_curses.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_curses.so
       0x101288000 -        0x101289fff +termios.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline-6.1.0-py2.7-macosx-10.6-intel.egg/readline.so
       0x10131b000 -        0x10131cff7 +resource.so ??? (???)
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cPickle.so
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/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_lsprof.so
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[truncated message content]

That is not what I want, to put the text inside the figure.

I want the text above the figure with some space (e.g 2 cm) to the figure
thats why I tried 0, 1.2 but then the text is outside the margins

/j
-------- Original-Nachricht --------
> Datum: Fri, 13 May 2011 14:03:16 +0000 (UTC)
> Von: Pauli Virtanen <pa...@ik...>
> An: mat...@li...
> Betreff: Re: [Matplotlib-users] Text outside the graphs "box"

> Fri, 13 May 2011 15:58:37 +0200, Johannes Radinger wrote:
> > Hello again I tried:
> > 
> > plt.figtext(0, 1.2, r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
> > 
> > but then the text is outside the printed area and therefore not
> > displayed. Does that mean that the printed area has to be changed as
> > well?
> 
> The first two parameters are the x and y coordinates of the text,
> in range [0, 1]. Adjust them to put the text inside the figure.
> 
> 
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
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Fri, 13 May 2011 15:58:37 +0200, Johannes Radinger wrote:
> Hello again I tried:
> 
> plt.figtext(0, 1.2, r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
> 
> but then the text is outside the printed area and therefore not
> displayed. Does that mean that the printed area has to be changed as
> well?

The first two parameters are the x and y coordinates of the text,
in range [0, 1]. Adjust them to put the text inside the figure.

Does anyone already know what causes the problem with the fill_between and the eps output?

/johannes


-------- Original-Nachricht --------
> Datum: Thu, 12 May 2011 17:10:43 +0200
> Von: Johannes Radinger <JRa...@gm...>
> An: John Hunter <jd...@gm...>
> CC: mat...@li...
> Betreff: Re: [Matplotlib-users] eps output and fill_between

> Hello again,
> 
> I tried the script you provided to test the PolyCollection and that works
> fine.
> I am working under Mac OS X 10.6.6 Snow Leopard and use matplotlib 1.0.1.
> 
> That is the script where I fail with eps but not with pdf:
> 
> 
> 
> import matplotlib.pyplot as plt
> import numpy
> from scipy import stats
> 
> p=0.3
> m=0
> s1min=120
> s1max=140
> s2min=1200
> s2max=1600
> 
> x = numpy.arange((s2max*-1.5), (s2max*1.5), 0.2)
> 
> def pdf(x,s1,s2):
>     return p * stats.norm.pdf(x, loc=m, scale=s1) + (1-p) *
> stats.norm.pdf(x, loc=m, scale=s2)
> 
> 
> pdf_min = pdf(x,s1min,s2min)
> pdf_max = pdf(x,s1max,s2max)
> 
> plt.plot(x, pdf_min, x, pdf_max, color="k")
> plt.fill_between(x, pdf_min, pdf_max, color='0.85')
> 
> 
> #plt.show()
> #plt.savefig("testplot.eps")
> plt.savefig("testplot.pdf")
> 
> 
> /Johannes
> 
> Am 12.05.2011 um 15:28 schrieb John Hunter:
> 
> > 
> > 
> > On Thu, May 12, 2011 at 3:42 AM, Johannes Radinger <JRa...@gm...>
> wrote:
> > Hello ,
> > 
> > sofar I know how to safe a plot into a *.eps file and it works good,
> > but there is one issue with filled areas between two functions.
> > 
> > When I try to use:
> > plt.fill_between(x, pdf_min, pdf_max, color='0.85')
> > 
> > and I try to open it on my mac I fail. So far as I know
> > is the mac converting the eps internally to pdf to be
> > displayed, but it seems it can't be converted.
> > 
> > If I try to set the output to *.pdf it works perfectly and I can
> > open the file. Something in the combination of fill_between
> > and eps is causing the error. I tried also color="red" but with
> > the same problems.
> > 
> > Is there anything I've to set because I need the output as
> > a working eps.
> > 
> > 
> > under the hool, fill_between uses a PolyCollection.  Below is a simple
> example which uses a PolyCollection directly.  Does this crash when you
> convert eps -> pdf.  If not, maybe we can hone in on what is special about the
> vertices in your fill_between example.  Also, you should give us some
> information about what version of matplotlib and OSX you are running.
> > 
> > 
> > import numpy as np
> > import matplotlib.collections as mcollections
> > import matplotlib.pyplot as plt
> > 
> > theta = np.linspace(0, 2*np.pi, 20)
> > x1 = np.cos(theta)
> > y1 = np.sin(theta)
> > 
> > x2 = x1 + 5
> > y2 = y1 + 5
> > 
> > verts1 = zip(x1, y1)
> > verts2 = zip(x2, y2)
> > 
> > c = mcollections.PolyCollection([verts1, verts2], facecolors=['red',
> 'green'])
> > 
> > ax = plt.subplot(111)
> > ax.add_collection(c)
> > ax.axis([-5, 10, -5, 10])
> > 
> > plt.savefig('test.eps')
> > plt.show()
> > 
> 

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Hello again I tried:

plt.figtext(0, 1.2, r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)

but then the text is outside the printed area and therefore not displayed.
Does that mean that the printed area has to be changed as well?


/j

-------- Original-Nachricht --------
> Datum: Fri, 13 May 2011 09:27:24 -0400
> Von: Michael Droettboom <md...@st...>
> An: mat...@li...
> Betreff: Re: [Matplotlib-users] Text outside the graphs "box"

> figtext will let you place text relative to the figure, not the axes:
> 
> http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.figtext
> 
> Cheers,
> Mike
> 
> On 05/13/2011 08:46 AM, Johannes Radinger wrote:
> > Hej
> >
> >
> > I want to include a mathematical expression but want to position it
> > outside the graphs box. I want it above the graph, so i tried to set it
> as title but there is to less space between the title and the graphs box.
> >
> > how can that be done? how to set a position outside the box?
> >
> > I tried eg:
> >
> > plt.title(r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
> >
> > thanks
> >
> > /johannes
> >    
> 
> 
> -- 
> Michael Droettboom
> Science Software Branch
> Space Telescope Science Institute
> Baltimore, Maryland, USA
> 
> 
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

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figtext will let you place text relative to the figure, not the axes:

http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.figtext

Cheers,
Mike

On 05/13/2011 08:46 AM, Johannes Radinger wrote:
> Hej
>
>
> I want to include a mathematical expression but want to position it
> outside the graphs box. I want it above the graph, so i tried to set it as title but there is to less space between the title and the graphs box.
>
> how can that be done? how to set a position outside the box?
>
> I tried eg:
>
> plt.title(r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)
>
> thanks
>
> /johannes
>    


-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA

Hej


I want to include a mathematical expression but want to position it
outside the graphs box. I want it above the graph, so i tried to set it as title but there is to less space between the title and the graphs box.

how can that be done? how to set a position outside the box?

I tried eg: 

plt.title(r'$F(x)=p*\frac{1}{s1\sqrt{2\pi}}$', fontsize=20)

thanks

/johannes
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Thu, 12 May 2011 15:16:43 -0400, C M wrote:
[clip: installing Python modules]
> Is there a step-by-step method on the
> website that shows how to do this?

Here: http://docs.python.org/install/index.html

On Thu, May 12, 2011 at 2:50 PM, Michael Droettboom <md...@st...> wrote:
> On 05/12/2011 02:34 PM, C M wrote:
>>
>> On Thu, May 12, 2011 at 1:26 PM, Michael Droettboom<md...@st...>
>>  wrote:
>>
>>>
>>> You can always get a tarball of the current git master by going here:
>>>
>>> https://github.com/matplotlib/matplotlib
>>>
>>> clicking on "Download" and choosing one of the "download source" options
>>> at the top of the popup box.
>>>
>>> Mike
>>>
>>
>> Thanks, but I'm having trouble using that.  I downloaded the .zip
>> file, unzipped the archive, moved the folder to
>> C:\Python25\Lib\site-packages, renamed my current matplotlib folder to
>> matplotlib_OLD, ran these commands from the new directory:
>>
>> python setup.py build
>> python setup.py install
>>
>> And finally renamed the new folder to just matplotlib.  It is not
>> finding the modules when I go to run it.  If revert the names of the
>> folders, my old folder still works.  What am I doing wrong?
>>
>
> You should not expand the directory tree under site-packages -- "python
> setup.py install" is what does that for you.  You should expand it anywhere
> else (most people create a "src" directory somewhere on their machine for
> source code).  Then run those commands.

I unzipped it in a download directory, changed the directory to that
folder, and ran the commands again...and it did not put a matplotlib
folder under site-packages.  Is there a step-by-step method on the
website that shows how to do this?

But all I really want is the changes that Jae Joon made as mentioned
above.  Is there a way to just grab them from the new folders?  (I
thought not because the folder structure from what I downloaded from
git master doesn't match the folder structure I had from mpl 1.0,
downloaded from the main mpl page).

Thanks,
Che

On 05/12/2011 02:34 PM, C M wrote:
> On Thu, May 12, 2011 at 1:26 PM, Michael Droettboom<md...@st...>  wrote:
>    
>> You can always get a tarball of the current git master by going here:
>>
>> https://github.com/matplotlib/matplotlib
>>
>> clicking on "Download" and choosing one of the "download source" options
>> at the top of the popup box.
>>
>> Mike
>>      
> Thanks, but I'm having trouble using that.  I downloaded the .zip
> file, unzipped the archive, moved the folder to
> C:\Python25\Lib\site-packages, renamed my current matplotlib folder to
> matplotlib_OLD, ran these commands from the new directory:
>
> python setup.py build
> python setup.py install
>
> And finally renamed the new folder to just matplotlib.  It is not
> finding the modules when I go to run it.  If revert the names of the
> folders, my old folder still works.  What am I doing wrong?
>    
You should not expand the directory tree under site-packages -- "python 
setup.py install" is what does that for you.  You should expand it 
anywhere else (most people create a "src" directory somewhere on their 
machine for source code).  Then run those commands.

Cheers,
Mike

-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA

On Thu, May 12, 2011 at 1:26 PM, Michael Droettboom <md...@st...> wrote:
> You can always get a tarball of the current git master by going here:
>
> https://github.com/matplotlib/matplotlib
>
> clicking on "Download" and choosing one of the "download source" options
> at the top of the popup box.
>
> Mike

Thanks, but I'm having trouble using that.  I downloaded the .zip
file, unzipped the archive, moved the folder to
C:\Python25\Lib\site-packages, renamed my current matplotlib folder to
matplotlib_OLD, ran these commands from the new directory:

python setup.py build
python setup.py install

And finally renamed the new folder to just matplotlib.  It is not
finding the modules when I go to run it.  If revert the names of the
folders, my old folder still works.  What am I doing wrong?

Thanks,
Che