matplotlib-users Mailing List for matplotlib

Hello,
One easy one harder two questions :)
My screenshot http://img213.imageshack.us/img213/3443/snapshot5.png
1-) I want to link bottom and top x axes as well as left and right y axes.
For now on the x-axis xticks are the time in seconds from midnight, not sure
how to add the secondary top x axis with time in regular HH:MM:SS
representation, without plotting the same data again. Right y-axis is there
thanks to twinx however that and left one don't snap each other when I zoom
in the plot. There is the twin function but couldn't figure out how to
achieve what I explained here.
2-) How to move plot title upwards when the new top x-axis ticks become
visible? They are overlapping each other, which I am trying to make them
nice looking.
Thanks.
-- 
Gökhan

I committed a slightly tighter version of this that uses a rectangle 
based on the size of the image plus a border to accomodate the exact 
marker size. Probably makes very little difference, but I suppose if 
there was a dense field of markers outside of view, this might speed 
things up a bit more.
A further optimization might be to use the clipping rectangle, but 
that's not necessary merely to prevent the segfault.
Mike
On 09/24/2009 12:06 AM, John Hunter wrote:
> On Wed, Sep 23, 2009 at 10:15 PM, John Hunter<jd...@gm...> wrote:
> 
>> On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls<mic...@sr...> wrote:
>> 
>>> I've encountered a segmentation fault using the Agg backend when making
>>> and saving a png plot. The segmentation fault does not seem to occur
>>> under different backends (e.g. Cairo).
>>>
>>> The sequence of commands amounts to making a plot, setting the limits of
>>> the plot, then saving the plot as a png using savefig. If the value of
>>> one of the points is too large, a segmentation fault is generated.
>>> Obviously the simple work-around is to not plot the out-of-bounds
>>> points, but the segmentation fault is probably not the desired behavior!
>>>
>>> Below is an example, which generates a segmentation fault on matplotlib
>>> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
>>> CentOS 5.3).
>>>
>>> Can others reproduce this issue?
>>> 
>> Thanks for the report -- I can confirm this on OSX and linux on svn HEAD
>>
>> I've made minor tweaks to your test case to make it deterministic::
>> 
> I applied the following patch to the branch and head -- it feels like there
> would be a more elegant way to handle it, so I'd like Michael at least to
> take a look at it::
>
> home:~/mpl> svn diff -rPREV:HEAD src/_backend_agg.cpp
> Index: src/_backend_agg.cpp
> ===================================================================
> --- src/_backend_agg.cpp (revision 7820)
> +++ src/_backend_agg.cpp (revision 7821)
> @@ -608,6 +608,14 @@
>
> x = (double)(int)x; y = (double)(int)y;
>
> + // if x or y is close to the width or height, the filled
> + // region could be inside the boundary even if the center is
> + // out. But at some point we need to cull these points
> + // because they can create segfaults of they overflow; eg
> + //
> https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
> + if (fabs(x)>(2*width)) continue;
> + if (fabs(y)>(2*height)) continue;
> +
> pixfmt_amask_type pfa(pixFmt, alphaMask);
> amask_ren_type r(pfa);
> amask_aa_renderer_type ren(r);
> @@ -629,6 +637,14 @@
>
> x = (double)(int)x; y = (double)(int)y;
>
> + // if x or y is close to the width or height, the filled
> + // region could be inside the boundary even if the center is
> + // out. But at some point we need to cull these points
> + // because they can create segfaults of they overflow; eg
> + //
> https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
> + if (fabs(x)>(2*width)) continue;
> + if (fabs(y)>(2*height)) continue;
> +
> if (face.first) {
> rendererAA.color(face.second);
> sa.init(fillCache, fillSize, x, y);
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 

There is even a simpler use case :)
Just put those three lines in a file say test.py
and try python test.py
Unless you are in ipython -pylab or threading enabled, it is required to
issue a show() to see the results on the screen.
On Thu, Sep 24, 2009 at 4:46 AM, Mark Bakker <ma...@gm...> wrote:
> Excellent. Many thanks.After all those years of using matplotlib, I
> finally find a use for show()
> Mark
>
> On Wed, Sep 23, 2009 at 11:02 PM, Gökhan Sever <gok...@gm...>wrote:
>
>>
>>
>> On Wed, Sep 23, 2009 at 3:51 PM, Mark Bakker <ma...@gm...> wrote:
>>
>>> Hello list,
>>> I recently started using Eclipse with Pydev. I like it a lot but have not
>>> been able to get interactive plotting going (which otherwise works fine).
>>>
>>> My file is simple:
>>>
>>> from pylab import *
>>>
>>> ion()
>>>
>>> plot([1,2,3])
>>>
>>>
>>>
>> You need to issue a show() here. Thus the plotting window will hang on the
>> screen until you close it.
>>
>>
>> Eclipse Platform
>> Version: 3.5.0
>> Build id: I20090611-1540
>>
>> PyDev for Eclipse 1.5.0.1251989166
>> org.python.pydev.feature.feature.group
>>
>>
>>> When I run this form within Eclipse, I do see a graphing window open up
>>> but then it disappears again when it is done, before I can even look at it.
>>>
>>> Any suggestions on how to keep the graphing window open?
>>>
>>> Thanks,
>>>
>>> Mark
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>>> is the only developer event you need to attend this year. Jumpstart your
>>> developing skills, take BlackBerry mobile applications to market and stay
>>> ahead of the curve. Join us from November 9&#45;12, 2009. Register
>>> now&#33;
>>> http://p.sf.net/sfu/devconf
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>
>>
>>
>> --
>> Gökhan
>>
>
>
-- 
Gökhan

Hi John,
Yes, works fine now, no error messages after from pylab import * .
And now my code using imshow and masked_arrays works again as 
expected, great!
Thank you,
Teemu
John Hunter kirjoitti 24.9.2009 kello 5.59:
> On Wed, Sep 23, 2009 at 4:39 PM, Christopher Barker
> <Chr...@no...> wrote:
>> Teemu Rinne wrote:
>>> from matplotlib import ft2font
>>> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/ 
>>> 2.5/
>>> lib/python
>>> 2.5/site-packages/matplotlib/ft2font.so, 2): Library not loaded: /
>>> Users/jdhunter
>>> /devbuild/lib/libfreetype.6.dylib
>>
>>> Am I missing something or is this 0.99.1 OSX package somehow broken?
>>
>> I think it's broken -- it's looking for a libfreetype in the:
>>
>> Users/jdhunter/devbuild/lib/
>>
>> dir, which you're pretty unlikely to have!
>>
>> John, did you mean to have only static lbs in your devbuild/lib dir,
>> which I think would work?
>
> I've removed the shared object libs before building the binaries, so
> now the static libs should be compiled in. Teemu, can you test again
> with the 0.99.1.1 OSX binaries at the download site?
>
> https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99.1/
>
> JDH
>

Excellent. Many thanks.After all those years of using matplotlib, I finally
find a use for show()
Mark
On Wed, Sep 23, 2009 at 11:02 PM, Gökhan Sever <gok...@gm...>wrote:
>
>
> On Wed, Sep 23, 2009 at 3:51 PM, Mark Bakker <ma...@gm...> wrote:
>
>> Hello list,
>> I recently started using Eclipse with Pydev. I like it a lot but have not
>> been able to get interactive plotting going (which otherwise works fine).
>>
>> My file is simple:
>>
>> from pylab import *
>>
>> ion()
>>
>> plot([1,2,3])
>>
>>
>>
> You need to issue a show() here. Thus the plotting window will hang on the
> screen until you close it.
>
>
> Eclipse Platform
> Version: 3.5.0
> Build id: I20090611-1540
>
> PyDev for Eclipse 1.5.0.1251989166
> org.python.pydev.feature.feature.group
>
>
>> When I run this form within Eclipse, I do see a graphing window open up
>> but then it disappears again when it is done, before I can even look at it.
>>
>> Any suggestions on how to keep the graphing window open?
>>
>> Thanks,
>>
>> Mark
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9&#45;12, 2009. Register
>> now&#33;
>> http://p.sf.net/sfu/devconf
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
>
> --
> Gökhan
>

Friends,
I have a matrix which i plotted with matshow as follows and then used text
function to write the each value inside the figure by choosing x and y
coordinate. I wish to know if there is any easy or more fancy way to do the
same.
*mat=load('tnz.txt')*
In [3]: *tmat=transpose(mat)*
In [4]: *tmat*
Out[4]:
array([[ 10.2 , 26.4 , 12.2 , 13.6 , 24.6 , 13.9 , 10.2 , 20.6 ,
 17. , 14.9 , 24.2 , 13. ],
 [ 13.6 , 26.2 , 10.5 , 13.6 , 26.8 , 9.87, 11. , 23.1 ,
 14.7 , 16.7 , 25.3 , 15.6 ],
 [ 10.7 , 22.4 , 6. , 11.8 , 23.8 , 7.4 , 6.7 , 20.9 ,
 10.3 , 12.5 , 20.9 , 7.9 ]])
In [5]: *matshow(tmat,cmap=cm.autumn)*
Out[5]: <matplotlib.image.AxesImage object at 0x9a2c7cc>
Now i wanted to give the show the values in the matrix using the text
function as follows
In [8]: *text(-.489,.511,'10.2',fontsize=12,color='b',name='serif')*
Out[8]: <matplotlib.text.Text object at 0x9a41e2c>
In [9]: *text(.495,.511,'26.4',fontsize=12,color='b',name='serif')*
Out[9]: <matplotlib.text.Text object at 0x9a489ac>

Just this afternoon I saw the same issue with the binary egg for 0.99.1 for
OS X.
Brian
On Wed, Sep 23, 2009 at 7:59 PM, John Hunter <jd...@gm...> wrote:
> On Wed, Sep 23, 2009 at 4:39 PM, Christopher Barker
> <Chr...@no...> wrote:
> > Teemu Rinne wrote:
> >> from matplotlib import ft2font
> >> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/
> >> lib/python
> >> 2.5/site-packages/matplotlib/ft2font.so, 2): Library not loaded: /
> >> Users/jdhunter
> >> /devbuild/lib/libfreetype.6.dylib
> >
> >> Am I missing something or is this 0.99.1 OSX package somehow broken?
> >
> > I think it's broken -- it's looking for a libfreetype in the:
> >
> > Users/jdhunter/devbuild/lib/
> >
> > dir, which you're pretty unlikely to have!
> >
> > John, did you mean to have only static lbs in your devbuild/lib dir,
> > which I think would work?
>
> I've removed the shared object libs before building the binaries, so
> now the static libs should be compiled in. Teemu, can you test again
> with the 0.99.1.1 OSX binaries at the download site?
>
>
> https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99.1/
>
> JDH
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Wed, Sep 23, 2009 at 3:27 PM, butterw <bu...@gm...> wrote:
>
> Hi,
>
> pickers work great to make matplotlib plots more interactive/general user
> friendly.
>
> On the subject of the legend_picker.py example, I was wondering if it was
> possible to combine both a legend picker and a line picker in the same plot.
> From what I gather they will both use the same onpick event callback.
>
> So my question is : How do I discriminate between a pick on the legend from
> a pick on a line ? The event.artist is a line2D in both cases.
As demonstrated in the above example, leg.get_lines() gives you the
list of lines inside the legend. The list of original lines is kept in
ax.lines.
So, you can check in which list the given artist is.
Regards,
-JJ
>
>
>
>
>
>
> John Hunter-4 wrote:
>>
>> On Mon, Aug 3, 2009 at 11:38 PM, Gökhan Sever<gok...@gm...>
>> wrote:
>>> Hello,
>>>
>>> I was wondering if it is possible to hide some data on figures using a
>>> say
>>> right click option to any of the legend entry and make it temporarily
>>> hidden/visible to better analyse the rest of the data?
>>>
>>> Check this screenshot for example:
>>>
>>> http://img25.imageshack.us/img25/9427/datahiding.png
>>>
>>> The red data clutters the rest of the figure, and I would like to be able
>>> to
>>> hide it temporarily so that I can investigate the other two relations
>>> more
>>> easily.
>>>
>>> Any ideas? or alternative solutions?
>>
>> It's a nice idea, and should be doable with the pick interface we have
>> for all mpl artists. Unfortunately, there were a few problems in the
>> legend implementation which blocked the pick events from hitting the
>> proxy lines they contained. I just made a few changes to mpl svn HEAD
>> to support this, and added a new example.
>>
>>  examples/event_handling/legend_picking.py
>>
>> which I'll include below.  JJ could you review the changes to legend.py?
>>
>> Instructions for checking out svn are at::
>>
>>
>> http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-svn
>>
>> Here is the example:
>>
>> """
>> Enable picking on the legend to toggle the legended line on and off
>> """
>> import numpy as np
>> import matplotlib.pyplot as plt
>>
>> t = np.arange(0.0, 0.2, 0.1)
>> y1 = 2*np.sin(2*np.pi*t)
>> y2 = 4*np.sin(2*np.pi*2*t)
>>
>> fig = plt.figure()
>> ax = fig.add_subplot(111)
>>
>> line1, = ax.plot(t, y1, lw=2, color='red', label='1 hz')
>> line2, = ax.plot(t, y2, lw=2, color='blue', label='2 hz')
>>
>> leg = ax.legend(loc='upper left', fancybox=True, shadow=True)
>> leg.get_frame().set_alpha(0.4)
>>
>>
>> lines = [line1, line2]
>> lined = dict()
>> for legline, realine in zip(leg.get_lines(), lines):
>>   legline.set_picker(5) # 5 pts tolerance
>>   lined[legline] = realine
>>
>> def onpick(event):
>>   legline = event.artist
>>   realline = lined[legline]
>>   vis = realline.get_visible()
>>   realline.set_visible(not vis)
>>   fig.canvas.draw()
>>
>> fig.canvas.mpl_connect('pick_event', onpick)
>>
>> plt.show()
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
> --
> View this message in context: http://www.nabble.com/Hiding-data-via-legend-tp24802219p25531267.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Wed, Sep 23, 2009 at 10:15 PM, John Hunter <jd...@gm...> wrote:
> On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <mic...@sr...> wrote:
>> I've encountered a segmentation fault using the Agg backend when making
>> and saving a png plot. The segmentation fault does not seem to occur
>> under different backends (e.g. Cairo).
>>
>> The sequence of commands amounts to making a plot, setting the limits of
>> the plot, then saving the plot as a png using savefig. If the value of
>> one of the points is too large, a segmentation fault is generated.
>> Obviously the simple work-around is to not plot the out-of-bounds
>> points, but the segmentation fault is probably not the desired behavior!
>>
>> Below is an example, which generates a segmentation fault on matplotlib
>> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
>> CentOS 5.3).
>>
>> Can others reproduce this issue?
>
> Thanks for the report -- I can confirm this on OSX and linux on svn HEAD
>
> I've made minor tweaks to your test case to make it deterministic::
I applied the following patch to the branch and head -- it feels like there
would be a more elegant way to handle it, so I'd like Michael at least to
take a look at it::
home:~/mpl> svn diff -rPREV:HEAD src/_backend_agg.cpp
Index: src/_backend_agg.cpp
===================================================================
--- src/_backend_agg.cpp (revision 7820)
+++ src/_backend_agg.cpp (revision 7821)
@@ -608,6 +608,14 @@
x = (double)(int)x; y = (double)(int)y;
+ // if x or y is close to the width or height, the filled
+ // region could be inside the boundary even if the center is
+ // out. But at some point we need to cull these points
+ // because they can create segfaults of they overflow; eg
+ //
https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
+ if (fabs(x)>(2*width)) continue;
+ if (fabs(y)>(2*height)) continue;
+
pixfmt_amask_type pfa(pixFmt, alphaMask);
amask_ren_type r(pfa);
amask_aa_renderer_type ren(r);
@@ -629,6 +637,14 @@
x = (double)(int)x; y = (double)(int)y;
+ // if x or y is close to the width or height, the filled
+ // region could be inside the boundary even if the center is
+ // out. But at some point we need to cull these points
+ // because they can create segfaults of they overflow; eg
+ //
https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
+ if (fabs(x)>(2*width)) continue;
+ if (fabs(y)>(2*height)) continue;
+
if (face.first) {
rendererAA.color(face.second);
sa.init(fillCache, fillSize, x, y);

On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <mic...@sr...> wrote:
> I've encountered a segmentation fault using the Agg backend when making
> and saving a png plot. The segmentation fault does not seem to occur
> under different backends (e.g. Cairo).
>
> The sequence of commands amounts to making a plot, setting the limits of
> the plot, then saving the plot as a png using savefig. If the value of
> one of the points is too large, a segmentation fault is generated.
> Obviously the simple work-around is to not plot the out-of-bounds
> points, but the segmentation fault is probably not the desired behavior!
>
> Below is an example, which generates a segmentation fault on matplotlib
> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
> CentOS 5.3).
>
> Can others reproduce this issue?
Thanks for the report -- I can confirm this on OSX and linux on svn HEAD
I've made minor tweaks to your test case to make it deterministic::
 import numpy as np
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 xdata = np.arange(10.0)
 ydata = np.arange(10.0)
 xdata[3]=1.0e9 # comment out to avoid seg fault
 fig = plt.figure()
 ax = fig.add_subplot(111)
 ax.plot(xdata,ydata,'k.')
 ax.set_xlim(0.0,1.0)
 fig.savefig('test.png')
and added a bug report to :
 https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
Platforms confirmed w/ bug:
home:~> uname -a
Darwin Macintosh-8.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT 2009; root:xnu-1228154~1/RELEASE_I386 i386
jdhunter@uqbar:~> uname -a
Linux uqbar 2.6.27-14-generic #1 SMP Tue Jun 30 19:54:46 UTC 2009
x86_64 GNU/Linux

On Wed, Sep 23, 2009 at 4:39 PM, Christopher Barker
<Chr...@no...> wrote:
> Teemu Rinne wrote:
>>   from matplotlib import ft2font
>> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/
>> lib/python
>> 2.5/site-packages/matplotlib/ft2font.so, 2): Library not loaded: /
>> Users/jdhunter
>> /devbuild/lib/libfreetype.6.dylib
>
>> Am I missing something or is this 0.99.1 OSX package somehow broken?
>
> I think it's broken -- it's looking for a libfreetype in the:
>
> Users/jdhunter/devbuild/lib/
>
> dir, which you're pretty unlikely to have!
>
> John, did you mean to have only static lbs in your devbuild/lib dir,
> which I think would work?
I've removed the shared object libs before building the binaries, so
now the static libs should be compiled in. Teemu, can you test again
with the 0.99.1.1 OSX binaries at the download site?
https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99.1/
JDH