matplotlib-users Mailing List for matplotlib

Hi,

When I make a scatter plot where the y-axis is logarithmic I expected that
points where the logarithm is not defined (0 and negative values) are
skipped (as for the plot function). But it seems that the scatter plot
assignes a value of 1e-1. So in that respect plot(x,1) and scatter (x,y)
behave differently. Is that intended or a bug? If intended, can I set the
value different than 1e-1?

For illustration I've attached a python script that shows the different
behaviour.

- Marcel

BTW: I'm using Matplotlib 0.99.1.1
http://old.nabble.com/file/p31289230/scatter_plot_bug.py scatter_plot_bug.py 
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On 03/31/2011 01:33 AM, Mike Kaufman wrote:
> how does one turn on gridlines for just the x-ticks or just the yticks?
> grid() just seems to do major or minor for both at the same time.

import matplotlib.pyplot as plt
plt.plot([1,2,3,2,1])
ax = plt.gca()
ax.xaxis.grid(True)
plt.draw()

>
> M
>
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I was thinking if its possible to shade depending on time. For
example, shade yellow for 7:00AM to 5:00PM and then leave it
white/normal for the rest of the graph. Does anyone have any example
of using axvspan? Or is there an alternative?

how does one turn on gridlines for just the x-ticks or just the yticks?
grid() just seems to do major or minor for both at the same time.

M

On 3/31/11 3:32 AM, T J wrote:
> Any chance matplotlib can get functionality similar to GraphicsArray
> in Mathematica?  It'd be nice to make a single method to draw whatever
> you want and then do this in a list comprehension.  At the end, you
> can arrange all those plots however you want.
>
> It looks like Sage has implemented something like this (built on top
> of matplotlib, I presume).  Would it be difficult to port this to
> "pure" matplotlib?
>
>     http://ask.sagemath.org/question/308/can-i-convert-a-graphicsarray-object-to-a-graphics


Sage does indeed have a (somewhat crufty) GraphicsArray object [1], 
which I've been meaning to convert to use the new GridSpec functionality 
[2].  It is built on top of matplotlib, but the code is fragile and easy 
to "break".  See 
http://doxdrum.wordpress.com/2010/08/12/graphics-array-in-sagemath/, for 
example.

One thing that would be really nice in GridSpec is if we could plot 
things recursively.  As I understand it right now, using GridSpec, we 
can arrange a bunch of axes in a grid.  However, what if we wanted to 
put a grid inside of one of the spots in the grid?  (I think the same 
question is: what if we wanted to embed a figure inside another axes?)

Jason


[1] 
http://www.sagemath.org/doc/reference/sage/plot/plot.html#sage.plot.plot.graphics_array

[2] http://matplotlib.sourceforge.net/users/gridspec.html; 
http://matplotlib.sourceforge.net/api/gridspec_api.html

Any chance matplotlib can get functionality similar to GraphicsArray
in Mathematica?  It'd be nice to make a single method to draw whatever
you want and then do this in a list comprehension.  At the end, you
can arrange all those plots however you want.

It looks like Sage has implemented something like this (built on top
of matplotlib, I presume).  Would it be difficult to port this to
"pure" matplotlib?

   http://ask.sagemath.org/question/308/can-i-convert-a-graphicsarray-object-to-a-graphics

On 03/30/2011 01:32 PM, Nat Echols wrote:
> I wanted to display a line plot with rainbow coloring based on the
> y-value, similar to what's possible for surface plots.  However, the
> 'plot' method does not appear to accept a 'cmap' argument.  The closest
> thing I was able to find was a recipe for different colored line
> segments on the SciPy examples page
> (http://www.scipy.org/Cookbook/Matplotlib/MulticoloredLine), but that's
> not really what I want - I was hoping for a continuous gradient over
> hundreds (possibly thousands) of points on a line.  Is this possible
> without too much hacking?

I don't think there is anything better than the second example here:
http://matplotlib.sourceforge.net/examples/pylab_examples/multicolored_line.html

Eric

>
> thanks,
> Nat

I wanted to display a line plot with rainbow coloring based on the y-value,
similar to what's possible for surface plots.  However, the 'plot' method
does not appear to accept a 'cmap' argument.  The closest thing I was able
to find was a recipe for different colored line segments on the SciPy
examples page (http://www.scipy.org/Cookbook/Matplotlib/MulticoloredLine),
but that's not really what I want - I was hoping for a continuous gradient
over hundreds (possibly thousands) of points on a line.  Is this possible
without too much hacking?

thanks,
Nat

Is there any way to get colormap to essentially do histogram equalization. I
would rather not touch the data. Thanks.
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I have a collection of Nx3 matrices in scipy/numpy and I'd like to
make a 3 dimensional scatter of it, where the X and Y axes are
determined by the values of first and second columns of the matrix,
the height of each bar is the third column in the matrix, and the
number of bars is determined by N.

Each matrix represents a different data group and I want each to be
plotted with a different color, and then set a legend for the entire
figure.

I have the following code:

fig = pylab.figure()
s = plt.subplot(1, 1, 1)
colors = ['k', "#B3C95A", 'b', '#63B8FF', 'g', "#FF3300",
          'r', 'k']
ax = Axes3D(fig)
plots = []
index = 0

for data, curr_color in zip(datasets, colors):
    p = ax.scatter(log2(data[:, 0]), log2(data[:, 1]),
                   log2(data[:, 2]), c=curr_color, label=my_labels[index])

    s.legend()
    index += 1

    plots.append(p)

    ax.set_zlim3d([-1, 9])
    ax.set_ylim3d([-1, 9])
    ax.set_xlim3d([-1, 9])

The issue is that ax.scatter plots things with a transparency and I'd
like that remove. Also, I'd like to set the xticks and yticks and
zticks -- how can I do that?

Finally, the legend call does not appear, even though I am calling
label="" for each scatter call. How can I get the legend to appear?

thanks very much for your help.

On 03/30/2011 04:26 AM, Giovanni Luca Ciampaglia wrote:
> Attached code for reproducing the problem
>
> python bug.py --> lc.pdf, lc.png
>
> I noticed a similar bug report posted some time ago on matplotlib-devel
> by Fernando Perez.
>
> http://www.mail-archive.com/mat...@li.../msg05133.html
>
>
> I am on 0.99.3. Has this been fixed in 1.0? I could not find any mention
> of it on the changelog ...

It is fixed in the latest development version, and probably by at least 
1.0.1, but I have not checked that.

Eric

>
> Cheers,

why? anyone knows?

TemplateSyntaxError at /accounts/profile/

Caught ViewDoesNotExist while rendering: Could not import
irrigaweb.pedotrans.views. Error was: cannot import name cbook

Request Method:GETRequest URL:
http://hirrigaweb.cpac.embrapa.br/accounts/profile/Django
Version:1.2.5Exception
Type:TemplateSyntaxErrorException Value:

Caught ViewDoesNotExist while rendering: Could not import
irrigaweb.pedotrans.views. Error was: cannot import name cbook

Exception Location:/opt/python27/lib/python2.7/site-packages/django/core/urlresolvers.py
in _get_callback, line 132Python Executable:/usr/bin/pythonPython Version:
2.7.1Python Path:['/opt/python27/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg',
'/opt/python27/lib/python2.7/site-packages/python_ldap-2.3.13-py2.7-linux-i686.egg',
'/opt/python27/lib/python2.7/site-packages/lxml-2.3-py2.7-linux-i686.egg',
'/opt/python27/lib/python2.7/site-packages/sorl_thumbnail-10.12.1-py2.7.egg',
'/opt/python27/lib/python2.7/site-packages/stripogram-1.5-py2.7.egg',
'/opt/python27/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-i686.egg',
'/opt/python27/lib/python2.7/site-packages/urwid-0.9.9.1-py2.7-linux-i686.egg',
'/opt/python27/lib/python27.zip', '/opt/python27/lib/python2.7',
'/opt/python27/lib/python2.7/plat-linux2',
'/opt/python27/lib/python2.7/lib-tk', '/opt/python27/lib/python2.7/lib-old',
'/opt/python27/lib/python2.7/lib-dynload',
'/opt/python27/lib/python2.7/site-packages',
'/opt/python27/lib/python2.7/site-packages/PIL', '/var/www/cpac',
'/var/www/cpac']Server time:Qua, 30 Mar 2011 12:17:38 -0500
Template error

In template /var/www/cpac/irrigaweb/templates/cpac/base.html, error at line
*46*
Caught ViewDoesNotExist while rendering: Could not import
irrigaweb.pedotrans.views. Error was: cannot import name cbook36 </td>
37<td width="45%" class="copyright" ><b>Usuário: </b>{{ usuarioAdmin
}}</td>
38 <td width="45%" class="copyright" ><b>Entrada: </b>{{ data }}</td> 39</tr>
40 <tr> 41 <td class="copyright" ><b>Perfil: </b>{{ lotacaoCurriculo }}</td>
42 <td class="copyright" ><span><b>IP de acesso: </b>{{ ip_addr_rem
}}</span></td> 43 </tr> 44 <td colspan="2" > 45 <div align="center"> 46 <a
href="/"> <img src="/https/sourceforge.net/publico/imagens/btInicio.jpg" alt="Menu" /></a><a
href="{%url auth_logout%}?next=/"><img src="/https/sourceforge.net/publico/imagens/btSair.jpg"
alt="Sair" /></a> 47 </div> 48 </td> 49 </tr> 50 </table></td> 51
</tr> 52</table>
53 </div> 54</div>

Please help.
-Nate


----- Forwarded Message ----
> From: Nate Gallagher <nat...@ya...>
> To: mat...@li...
> Sent: Mon, March 28, 2011 2:41:39 PM
> Subject: [Matplotlib-users] Plot show() errors, Mac OS 10.6
> 
> operating system
> $ uname -a
> Darwin nate-gallaghers-macbook-pro.local  10.6.0 Darwin Kernel Version 10.6.0: 

> Wed Nov 10 18:13:17 PST 2010;  root:xnu-1504.9.26~3/RELEASE_I386 i386
> 
> matplotlib  version:
> matplotlib-1.0.1-python.org-32bit-py2.7-macosx10.3.dmg
> 
> obtained from:
> http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0.1/
> 
> no o customizations to matplotlibrc
> 
> $ python simple_plot.py --verbose-helpful
> 
> $HOME=/Users/ibook
> CONFIGDIR=/Users/ibook/.matplotlib
> matplotlib  data path 
>/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data
>a
> 
> loaded  rc file 
>/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
>c
> 
> matplotlib  version 1.0.1
> verbose.level helpful
> interactive is False
> units is  False
> platform is darwin
> Using fontManager instance from  /Users/ibook/.matplotlib/fontList.cache
> backend TkAgg version  8.5
> findfont: Matching 
>:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
>m
>   to Bitstream Vera Sans 
>(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
>)
>   with score of 0.000000
> Exception in Tkinter callback
> Traceback (most  recent call last):
>   File 
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk/Tkinter.py",
>,
>   line 1410, in __call__
>     return self.func(*args)
>   File 
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py",
>,
>   line 245, in resize
>     self.show()
>   File 
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py",
>,
>   line 249, in draw
>     tkagg.blit(self._tkphoto,  self.renderer._renderer, colormode=2)
>   File 
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/tkagg.py",
>,
>   line 19, in blit
>     tk.call("PyAggImagePhoto", photoimage,  id(aggimage), colormode, 
> id(bbox_array))
> TclError
> 
> ------------------------------------------------------------------------------
> Create  and publish websites with WebMatrix
> Use the most popular FREE web apps or  write code yourself; 
> WebMatrix provides all the features you need to develop  and publish 
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> _______________________________________________
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> 

How can you get the title to scale when the size is changed on the image?  When I change the image size, my title is getting chopped off.

Thank you

Andrew

Attached code for reproducing the problem

python bug.py --> lc.pdf, lc.png

I noticed a similar bug report posted some time ago on matplotlib-devel 
by Fernando Perez.

http://www.mail-archive.com/mat...@li.../msg05133.html

I am on 0.99.3. Has this been fixed in 1.0? I could not find any mention 
of it on the changelog ...

Cheers,

-- 
Giovanni L. Ciampaglia
PhD Student
University of Lugano, MACS Lab

Fabrice Silva [03/30/2011 02:30 PM]:
> Le mercredi 30 mars 2011 à 13:49 +0200, Joachim Saul a écrit :
>> But speaking of zooming. How nice would it be to use the mouse wheel for
>> that! Point at a position in the figure and just zoom in towards that
>> point, keeping the (configurable) zoom factor constant for horizontal
>> and vertical axes. To restrict the zoom to either horizontal *or*
>> vertical axis one would simply hold 'x' or 'y', respectively, while
>> using the mouse wheel.
>>
>> If I had a wish list, that item would be on top. :)
>
> Look at what occurs when using the Pan button (the four-arrows button)
> and right-click (in combination with one of the w, y or CTRL keys) :)
> Documented on the same page.

Hey, that's cool! :)

> It uses drag on right click instead of mouse wheel.

Yet it would be "nice" to have that function tied to the mouse wheel 
(like in Google maps, for instance) but that's not a complaint because 
the current behaviour is already very comfortable.

Thanks for pointing that out!

Cheers,
Joachim

As far I'm concerned, I noticed indeed that the right click provide a
dezoom, while left click provide a zoom. I was confused because
gnuplot uses right click to zoom.

But I'm glad to see that this post has treshed a big discussion on the topic !

Thanks :)

On 03/30/2011 05:01 AM, Paul Ivanov wrote:
> Michael Droettboom, on 2011-03-29 10:12,  wrote:
>> On 03/29/2011 09:08 AM, xyz wrote:
>>> Hi,
>>> X and Y values are stored in a dict whereas X is the key and Y is the
>>> value in the following code:
>>>
>>> import matplotlib.pyplot as plt
>>>
>>> data = {4: 3, 5: 4, 6: 5, 7: 4, 8: 5}
>>>
>>> print data
>>> for i in sorted(data.keys()):
>>>        print i
>>>
>>> How is possible to use plot with a dict in order to get a similar
>>> picture like this
>>> http://matplotlib.sourceforge.net/_images/invert_axes.png .
>> In this case, you should be able to use:
>>
>> plt.plot(data.items())
> For me, that line produces two lines with the abscissa going from
> 0 to 4. In other words, plt.plot(data.items()) ends up being
> equivalent to plt.plot(data.values());plt.plot(data.keys())
>
> I think what xyz wants is this:
>
> x,y = zip(*sorted(data.items()))
> plt.plot(x,y)
>
> I think of the * in front of arguments to zip as being the pull
> tab or slider of the zipper (since it's at the top, you'll be
> pulling it down, or unzipping): see
> http://docs.python.org/library/functions.html#zip
>
> best,
>
Thank you it works.

Le mercredi 30 mars 2011 à 13:49 +0200, Joachim Saul a écrit :
> Fabrice Silva [03/30/2011 01:13 PM]:
> > Are you aware of the «zoom out to rectangle» feature (with right
> > click-n-drag, opposed to «zoom to rectangle» with left click-n-drag) ?
> > http://matplotlib.sourceforge.net/users/navigation_toolbar.html
> 
> This is a nice feature that I acually wasn't aware of either!
> 
> But speaking of zooming. How nice would it be to use the mouse wheel for 
> that! Point at a position in the figure and just zoom in towards that 
> point, keeping the (configurable) zoom factor constant for horizontal 
> and vertical axes. To restrict the zoom to either horizontal *or* 
> vertical axis one would simply hold 'x' or 'y', respectively, while 
> using the mouse wheel.
> 
> If I had a wish list, that item would be on top. :)

Look at what occurs when using the Pan button (the four-arrows button)
and right-click (in combination with one of the w, y or CTRL keys) :)
Documented on the same page.
It uses drag on right click instead of mouse wheel.
-- 
Fabrice

Fabrice Silva [03/30/2011 01:13 PM]:
> Are you aware of the «zoom out to rectangle» feature (with right
> click-n-drag, opposed to «zoom to rectangle» with left click-n-drag) ?
> http://matplotlib.sourceforge.net/users/navigation_toolbar.html

This is a nice feature that I acually wasn't aware of either!

But speaking of zooming. How nice would it be to use the mouse wheel for 
that! Point at a position in the figure and just zoom in towards that 
point, keeping the (configurable) zoom factor constant for horizontal 
and vertical axes. To restrict the zoom to either horizontal *or* 
vertical axis one would simply hold 'x' or 'y', respectively, while 
using the mouse wheel.

If I had a wish list, that item would be on top. :)

Cheers,
Joachim

Le mercredi 30 mars 2011 à 09:45 +0200, David Kremer a écrit :
> Hello,
> 
> I'm using archlinux, with all up-to-date packages, and matplotlib
> within a python2 environment.
> 
> When I use the zoom function, it seems the zoom is decreasing instead
> of increasing. Actually, the exact behaviour is to reproduce the old
> figure in the smaller area selected by the zoom function.
> 
> That means the zoom behaviour is completely inverted.
> 
> Does anyone here with a last version of matplotlib confirm the bug
> does still exist ?

Are you aware of the «zoom out to rectangle» feature (with right
click-n-drag, opposed to «zoom to rectangle» with left click-n-drag) ?
http://matplotlib.sourceforge.net/users/navigation_toolbar.html 

-- 
Fabrice

Hello,

I'm using archlinux, with all up-to-date packages, and matplotlib
within a python2 environment.

When I use the zoom function, it seems the zoom is decreasing instead
of increasing. Actually, the exact behaviour is to reproduce the old
figure in the smaller area selected by the zoom function.

That means the zoom behaviour is completely inverted.

Does anyone here with a last version of matplotlib confirm the bug
does still exist ?

Here a snippet to test the zoom behaviour :

$python2
<code python>
from pylab import *
plot( arange(0,pi,0.01) , sin(arange(0,pi,0.01)) )
show()
</code>

greetings.

David Kremer

Hey Matplotlib Community,

         I am trying to create a standard line plot and then overlay a 
fill_between plot that would partly grey out the line plot.  The code 
snippet I am interested in is:

import matplotlib.pyplot as plot
fig = plot.figure()
p1 = fig.add_subplot(111)
p1.plot(x,y1,'r',linewidth=5)
p1.fill_between(x,0,y2,color='k',alpha='0.7')

However, the fill_between plot is not actually covering the line plot.  
Is there another keyword I should be using?

Thanks!
Terry

-- 
P. Therese Lang
Post Doc
Alber Lab, UC Berkeley

> I would recommend running the import in the Python profiler to determine
> where most of the time is going.  When I investigated this a few years
> back, it was mainly due to loading the GUI toolkits, which are
> understandably quite large.  You can avoid most of that by using the Agg
> backend.  If you're using the Agg backend and still experiencing
> slowness, it may be that load-up issues have crept back into matplotlib
> since then -- but we need profiling data to figure out where and how.
> 
> Mike

Thank you a lot for your answer.

I noticed than _matplotlib.pyplot_ is longer to be imported the first time than 
if it has already been imported previously (maybe things are already loaded in 
ram memory), and we don't need to fetch it from the hard drive thanks to the 
kernel.

As far I see, the function calls are the same for the two logs I obtained, 
except than the first took 6s instead of 1.4s.




The two logs have been obtained using :
<code>
python -m cProfile temp.py
</code>

where temp.py consist of two lines :

<code>
#!/usr/bin/env python2

import matplotlib.pyplot
</code>

Michael Droettboom, on 2011-03-29 10:12,  wrote:
> On 03/29/2011 09:08 AM, xyz wrote:
> > Hi,
> > X and Y values are stored in a dict whereas X is the key and Y is the
> > value in the following code:
> >
> > import matplotlib.pyplot as plt
> >
> > data = {4: 3, 5: 4, 6: 5, 7: 4, 8: 5}
> >
> > print data
> > for i in sorted(data.keys()):
> >       print i
> >
> > How is possible to use plot with a dict in order to get a similar
> > picture like this
> > http://matplotlib.sourceforge.net/_images/invert_axes.png .
> In this case, you should be able to use:
> 
> plt.plot(data.items())

For me, that line produces two lines with the abscissa going from
0 to 4. In other words, plt.plot(data.items()) ends up being
equivalent to plt.plot(data.values());plt.plot(data.keys())

I think what xyz wants is this:

x,y = zip(*sorted(data.items()))
plt.plot(x,y)

I think of the * in front of arguments to zip as being the pull
tab or slider of the zipper (since it's at the top, you'll be
pulling it down, or unzipping): see
http://docs.python.org/library/functions.html#zip

best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7