matplotlib-users Mailing List for matplotlib

On 8/28/10 3:59 PM, Stan Schymanski wrote:
> Hi JJ,
>
> Thanks for the advice. However, the annotation_clip=False addition does
> not make a difference to me. I am using Matplotlib from within Sage,
> though; not sure if this makes it behave differently.
>


FYI, matplotlib in Sage is still at matplotlib 0.99.3.  We're working on 
upgrading it to 1.0.0.

Stan, if you want, could you try installing the 1.0.0 Sage matplotlib 
spkg and seeing if that works?  You can do it by doing:

sage -i http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg

(the ticket is http://trac.sagemath.org/sage_trac/ticket/9221 )

Matplotlib 1.0.0 changes how axes labels work, so if you want to do axes 
labels, then you'll have to also install the patch listed at the ticket.

Thanks,

Jason

Hi JJ,

Thanks for the advice. However, the annotation_clip=False addition does 
not make a difference to me. I am using Matplotlib from within Sage, 
though; not sure if this makes it behave differently.

Cheers
Stan

On 8/28/10 5:09 PM, Jae-Joon Lee wrote:
> I think this change has been there for a while.
> For recent versions of matplotlib, the default behavior of annotate is
> that, when xycoords=="data", the arrow is drawn only when the
> annotated point is inside the axes.
> To override this behavior, use annotation_clip keyword parameter.
>
>
> pylab.annotate('',(-1,3.1),(0,3.1),va='center',ha='center',
>                 arrowprops=dict(arrowstyle='<->'), annotation_clip=False)
>
> Regards,
>
> -JJ
>
>
> On Fri, Aug 27, 2010 at 9:21 PM, Stan Schymanski<ss...@bg...>  wrote:
>    
>> Dear all,
>>
>> I don't know which update it was that broke it, but this used to work:
>>
>> import numpy
>> import pylab
>> pylab.clf()
>> fig = pylab.figure(1,figsize=(8,5))
>> ax = fig.add_subplot(111, autoscale_on=False, xlim=(-1,5),
>> ylim=(-4,3))
>>
>> t = numpy.arange(0.0, 5.0, 0.01)
>> s = numpy.cos(2*numpy.pi*t)
>> line, = ax.plot(t, s, lw=3, color='purple')
>> pylab.text(-0.5,3.2,'no data',ha='center')
>> pylab.annotate('',(-1,3.1),(0,3.1),va='center',ha='center',arrowprops=dict(arrowstyle='<->'))
>> pylab.savefig('blah.png')
>>
>> This used to plot an arrow under the text 'no data' but above the main plot. Now this arrow does not appear unless at least part of it is within the plotting area. Change one of the '3.1' in the code above to, say, 3.0 and the whole arrow is displayed. Is this a bug or is there a new way of achieving what I want?
>>
>> Thanks for your help already!
>>
>> Cheers
>> Stan
>>
>>
>> ------------------------------------------------------------------------------
>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> Be part of this innovative community and reach millions of netbook users
>> worldwide. Take advantage of special opportunities to increase revenue and
>> speed time-to-market. Join now, and jumpstart your future.
>> http://p.sf.net/sfu/intel-atom-d2d
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>      

-- 
________________________________________

Stan Schymanski
Scientist
Max Planck Institute for Biogeochemistry
PO Box 10 01 64
D-07701 Jena, Germany

Phone: +49.3641.576264
Fax: +49.3641.577274
WWW: http://www.bgc-jena.mpg.de/~sschym

Biospheric Theory and Modelling Group
http://www.bgc-jena.mpg.de/bgc-theory/
_________________________________________

Thanks for reporting.
It turns out a (major) bug in gridspec, which should be fixed in r8667 & r8668.
You code should work (except the rowspan and colspan needs to be
exchanged for ax3 and ax4).

Regards,

-JJ



On Sat, Aug 28, 2010 at 2:17 PM, Erik Tollerud <eri...@gm...> wrote:
> If been playing around with the new Gridspec and subplot2grid stuff,
> and it's pretty cool... one thing is confusing me though: It doesn't
> seem to make any sense if the grid is non-square.  For example,
> suppose a 2x6 grid, which I will number like so:
>
> 1 3 5 7 9   11
> 2 4 6 8 10 12
> I want ax1 to take up 1,2,3, and 4; ax2 to be 5,6,7,8; ax3 should be 9
> and 11; and ax4 should be 10 and 12.  My assumption would be to do
> this:
>
> ax1=plt.subplot2grid((2,6),(0,0),rowspan=2,colspan=2)
> ax2=plt.subplot2grid((2,6),(0,2),rowspan=2,colspan=2)
> ax3=plt.subplot2grid((2,6),(0,4),rowspan=2,colspan=1)
> ax4=plt.subplot2grid((2,6),(1,4),rowspan=2,colspan=1)
>
> But instead, apparently random partterns of axes appear and some to
> override each other so that only one subplot is present in the end...
> what's going on here?
>
> --
> Erik Tollerud
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I think this change has been there for a while.
For recent versions of matplotlib, the default behavior of annotate is
that, when xycoords=="data", the arrow is drawn only when the
annotated point is inside the axes.
To override this behavior, use annotation_clip keyword parameter.


pylab.annotate('',(-1,3.1),(0,3.1),va='center',ha='center',
               arrowprops=dict(arrowstyle='<->'), annotation_clip=False)

Regards,

-JJ


On Fri, Aug 27, 2010 at 9:21 PM, Stan Schymanski <ss...@bg...> wrote:
> Dear all,
>
> I don't know which update it was that broke it, but this used to work:
>
> import numpy
> import pylab
> pylab.clf()
> fig = pylab.figure(1,figsize=(8,5))
> ax = fig.add_subplot(111, autoscale_on=False, xlim=(-1,5),
> ylim=(-4,3))
>
> t = numpy.arange(0.0, 5.0, 0.01)
> s = numpy.cos(2*numpy.pi*t)
> line, = ax.plot(t, s, lw=3, color='purple')
> pylab.text(-0.5,3.2,'no data',ha='center')
> pylab.annotate('',(-1,3.1),(0,3.1),va='center',ha='center',arrowprops=dict(arrowstyle='<->'))
> pylab.savefig('blah.png')
>
> This used to plot an arrow under the text 'no data' but above the main plot. Now this arrow does not appear unless at least part of it is within the plotting area. Change one of the '3.1' in the code above to, say, 3.0 and the whole arrow is displayed. Is this a bug or is there a new way of achieving what I want?
>
> Thanks for your help already!
>
> Cheers
> Stan
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On 8/27/2010 10:13 PM, Adam Gustafson wrote:
> I found a web page in which someone has done the horrible task of
> figuring out how the hell you compile in Cygwin.  Details below:
>
> http://innuendopoly.org/arch/matplotlib-cygwin
>
> In short, the Cygwin compile runs into TONS of errors as is, and it
> seems the matplotlib developers aren't really supporting it.  Trying
> their techniques to see if it works, but so far looking good....
>

What a friendly message... Matplotlib builds and works fine on cygwin 
when disabling the tkagg backend in setup.cfg.

--
Christoph

On 08/27/2010 05:17 PM, Chiara Caronna wrote:
> Ok, it is a backend issue:
> I checked and I was using Qt4Agg
> as soon as I changed to TkAgg the script worked fine...
> still is this normal or is it a bug?
> thanks for your suggestion and help!

Chiara,

As a workaround for Qt4Agg, you can follow p.draw() with 
fig.canvas.flush_events().

I think this is a bug that will be fixed easily by incorporating the 
flush functionality in the draw method, but I'm not ready to commit to 
it yet.

I wonder whether you were using a different backend when you were using 
0.99.1.1?  Or a different version of PyQt4?

Eric

> Chiara
>
> ------------------------------------------------------------------------
> From: chi...@ho...
> To: ben...@ou...
> Date: Sat, 28 Aug 2010 03:01:54 +0000
> CC: mat...@li...
> Subject: Re: [Matplotlib-users] realtime plotting was working with
> matplotlib 0.99.1.1 and it doesn't with matplotlib 1.0.0
>
> I think I am using TkAgg but I am not sure, how can I check it?
>
> ------------------------------------------------------------------------
> From: ben...@ou...
> Date: Fri, 27 Aug 2010 21:50:19 -0500
> Subject: Re: [Matplotlib-users] realtime plotting was working with
> matplotlib 0.99.1.1 and it doesn't with matplotlib 1.0.0
> To: chi...@ho...
> CC: mat...@li...
>
> On Fri, Aug 27, 2010 at 9:26 PM, Chiara Caronna
> <chi...@ho... <mailto:chi...@ho...>> wrote:
>
>     Hi all,
>     I have a script to update a plot in real time. It was working fine
>     with matplotlib 0.99.1.1 but it doesn't work anymore with the new
>     version.
>
>     Here is the script:
>
>     import numpy as n
>     import pylab as p
>
>     x=n.arange(10)
>     y=n.random.randn(10)
>     p.ion()
>     fig=p.figure(1)
>     ax=fig.add_subplot(111)
>     line,=ax.plot(x,y,'ko-')
>     for i in range(10):
>     y=n.random.randn(10)
>     line.set_data(x,y)
>     p.draw()
>
>
>     it is updating the plot correctly with matplotlib 0.99.1.1
>     when I run it with matplotlib 1.0.0
>     it doesn't show any picture at all
>
>     Interestingly, if I add a line raw_input('ok') then it shows the
>     plot and it updates it inside the loop....
>
>
>     x=n.arange(10)
>     y=n.random.randn(10)
>     p.ion()
>     fig=p.figure(1)
>     ax=fig.add_subplot(111)
>     line,=ax.plot(x,y,'ko-')
>     raw_input('ok?')
>     for i in range(10):
>     y=n.random.randn(10)
>     line.set_data(x,y)
>     p.draw()
>     raw_input('ok?')
>
>     Any idea why it is doing this? Is it a bug or am I missing something?
>
>     Thanks for your help,
>     Chiara
>
>
> It seems to work fine for me using the GTKAgg backend. Which backend are
> you using? Also, admittedly, this is the trunk build, so it might have
> some fixes that weren't in the release.
>
> Ben Root
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be
> part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue
> and speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________ Matplotlib-users mailing
> list Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

If been playing around with the new Gridspec and subplot2grid stuff,
and it's pretty cool... one thing is confusing me though: It doesn't
seem to make any sense if the grid is non-square.  For example,
suppose a 2x6 grid, which I will number like so:

1 3 5 7 9   11
2 4 6 8 10 12
I want ax1 to take up 1,2,3, and 4; ax2 to be 5,6,7,8; ax3 should be 9
and 11; and ax4 should be 10 and 12.  My assumption would be to do
this:

ax1=plt.subplot2grid((2,6),(0,0),rowspan=2,colspan=2)
ax2=plt.subplot2grid((2,6),(0,2),rowspan=2,colspan=2)
ax3=plt.subplot2grid((2,6),(0,4),rowspan=2,colspan=1)
ax4=plt.subplot2grid((2,6),(1,4),rowspan=2,colspan=1)

But instead, apparently random partterns of axes appear and some to
override each other so that only one subplot is present in the end...
what's going on here?

-- 
Erik Tollerud

I found a web page in which someone has done the horrible task of figuring
out how the hell you compile in Cygwin.  Details below:

http://innuendopoly.org/arch/matplotlib-cygwin

In short, the Cygwin compile runs into TONS of errors as is, and it seems
the matplotlib developers aren't really supporting it.  Trying their
techniques to see if it works, but so far looking good....

On 08/27/2010 05:43 PM, Benjamin Root wrote:
> On Fri, Aug 27, 2010 at 10:17 PM, Chiara Caronna
> <chi...@ho... <mailto:chi...@ho...>> wrote:
>
>     Ok, it is a backend issue:
>     I checked and I was using Qt4Agg
>     as soon as I changed to TkAgg the script worked fine...
>     still is this normal or is it a bug?
>     thanks for your suggestion and help!
>     Chiara
>
>
> I suspect that it might have been fixed since 1.0 was released, but I am
> unable to confirm that using the machine I have with me.  Can someone
> using the svn build of mpl check to see if the script works with the
> Qt4Agg backend?

No, it does not work on qt4agg, but it does work on qtagg and wxagg as 
well as gtkagg and tkagg.

Eric


>
> Ben Root
>
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Fri, Aug 27, 2010 at 10:17 PM, Chiara Caronna
<chi...@ho...>wrote:

>  Ok, it is a backend issue:
> I checked and I was using Qt4Agg
> as soon as I changed to TkAgg the script worked fine...
> still is this normal or is it a bug?
> thanks for your suggestion and help!
> Chiara
>
>
I suspect that it might have been fixed since 1.0 was released, but I am
unable to confirm that using the machine I have with me.  Can someone using
the svn build of mpl check to see if the script works with the Qt4Agg
backend?

Ben Root

Ok, it is a backend issue:
I checked and I was using Qt4Agg
as soon as I changed to TkAgg the script worked fine...
still is this normal or is it a bug?
thanks for your suggestion and help!
Chiara

From: chi...@ho...
To: ben...@ou...
Date: Sat, 28 Aug 2010 03:01:54 +0000
CC: mat...@li...
Subject: Re: [Matplotlib-users] realtime plotting was working with matplotlib 0.99.1.1 and it doesn't with matplotlib 1.0.0








I think I am using TkAgg but I am not sure, how can I check it?

From: ben...@ou...
Date: Fri, 27 Aug 2010 21:50:19 -0500
Subject: Re: [Matplotlib-users] realtime plotting was working with matplotlib 0.99.1.1 and it doesn't with matplotlib 1.0.0
To: chi...@ho...
CC: mat...@li...

On Fri, Aug 27, 2010 at 9:26 PM, Chiara Caronna <chi...@ho...> wrote:







Hi all,
I have a script to update a plot in real time. It was working fine with matplotlib 0.99.1.1 but it doesn't work anymore with the new version. 

Here is the script:

import numpy as n
import pylab as p



x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
for i in range(10):
    y=n.random.randn(10)
    line.set_data(x,y)
    p.draw()




it is updating the plot correctly with matplotlib 0.99.1.1
when I run it with matplotlib 1.0.0
it doesn't show any picture at all

Interestingly, if I add a line raw_input('ok') then it shows the plot and it updates it inside the loop....




x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
raw_input('ok?')
for i in range(10):
    y=n.random.randn(10)


    line.set_data(x,y)
    p.draw()
    raw_input('ok?')

Any idea why it is doing this? Is it a bug or am I missing something?

Thanks for your help,
Chiara




It seems to work fine for me using the GTKAgg backend.  Which backend are you using?  Also, admittedly, this is the trunk build, so it might have some fixes that weren't in the release.

Ben Root
 		 	   		  

------------------------------------------------------------------------------
Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
Be part of this innovative community and reach millions of netbook users 
worldwide. Take advantage of special opportunities to increase revenue and 
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users 		 	   		  

I think I am using TkAgg but I am not sure, how can I check it?

From: ben...@ou...
Date: Fri, 27 Aug 2010 21:50:19 -0500
Subject: Re: [Matplotlib-users] realtime plotting was working with matplotlib 0.99.1.1 and it doesn't with matplotlib 1.0.0
To: chi...@ho...
CC: mat...@li...

On Fri, Aug 27, 2010 at 9:26 PM, Chiara Caronna <chi...@ho...> wrote:







Hi all,
I have a script to update a plot in real time. It was working fine with matplotlib 0.99.1.1 but it doesn't work anymore with the new version. 

Here is the script:

import numpy as n
import pylab as p



x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
for i in range(10):
    y=n.random.randn(10)
    line.set_data(x,y)
    p.draw()




it is updating the plot correctly with matplotlib 0.99.1.1
when I run it with matplotlib 1.0.0
it doesn't show any picture at all

Interestingly, if I add a line raw_input('ok') then it shows the plot and it updates it inside the loop....




x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
raw_input('ok?')
for i in range(10):
    y=n.random.randn(10)


    line.set_data(x,y)
    p.draw()
    raw_input('ok?')

Any idea why it is doing this? Is it a bug or am I missing something?

Thanks for your help,
Chiara




It seems to work fine for me using the GTKAgg backend.  Which backend are you using?  Also, admittedly, this is the trunk build, so it might have some fixes that weren't in the release.

Ben Root
 		 	   		  

On Fri, Aug 27, 2010 at 9:26 PM, Chiara Caronna
<chi...@ho...>wrote:

>  Hi all,
> I have a script to update a plot in real time. It was working fine with
> matplotlib 0.99.1.1 but it doesn't work anymore with the new version.
>
> Here is the script:
>
> import numpy as n
> import pylab as p
>
> x=n.arange(10)
> y=n.random.randn(10)
> p.ion()
> fig=p.figure(1)
> ax=fig.add_subplot(111)
> line,=ax.plot(x,y,'ko-')
> for i in range(10):
>     y=n.random.randn(10)
>     line.set_data(x,y)
>     p.draw()
>
>
> it is updating the plot correctly with matplotlib 0.99.1.1
> when I run it with matplotlib 1.0.0
> it doesn't show any picture at all
>
> Interestingly, if I add a line raw_input('ok') then it shows the plot and
> it updates it inside the loop....
>
>
> x=n.arange(10)
> y=n.random.randn(10)
> p.ion()
> fig=p.figure(1)
> ax=fig.add_subplot(111)
> line,=ax.plot(x,y,'ko-')
> raw_input('ok?')
> for i in range(10):
>     y=n.random.randn(10)
>     line.set_data(x,y)
>     p.draw()
>     raw_input('ok?')
>
> Any idea why it is doing this? Is it a bug or am I missing something?
>
> Thanks for your help,
> Chiara
>
>
It seems to work fine for me using the GTKAgg backend.  Which backend are
you using?  Also, admittedly, this is the trunk build, so it might have some
fixes that weren't in the release.

Ben Root

Hi all,
I have a script to update a plot in real time. It was working fine with matplotlib 0.99.1.1 but it doesn't work anymore with the new version. 

Here is the script:

import numpy as n
import pylab as p

x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
for i in range(10):
    y=n.random.randn(10)
    line.set_data(x,y)
    p.draw()


it is updating the plot correctly with matplotlib 0.99.1.1
when I run it with matplotlib 1.0.0
it doesn't show any picture at all

Interestingly, if I add a line raw_input('ok') then it shows the plot and it updates it inside the loop....


x=n.arange(10)
y=n.random.randn(10)
p.ion()
fig=p.figure(1)
ax=fig.add_subplot(111)
line,=ax.plot(x,y,'ko-')
raw_input('ok?')
for i in range(10):
    y=n.random.randn(10)
    line.set_data(x,y)
    p.draw()
    raw_input('ok?')

Any idea why it is doing this? Is it a bug or am I missing something?

Thanks for your help,
Chiara