matplotlib-users Mailing List for matplotlib

On Tue, Oct 12, 2010 at 3:03 PM, Carl Karsten <ca...@pe...> wrote:
>
> Run the code, you get a window that has a 'save' button, the dialog
> has a 'type svg' option
> the svg renders with the blue/green dots everywhere (rendering using
> both rsvg-view and inkscape, which use different rendering engines.)
> save as png, display png, dots only inside circle.
>

Yup, clipping is completely broken in SVG, reported here:

http://sourceforge.net/mailarchive/forum.php?thread_name=AANLkTik-Ty-V-QFEmkjhJH%2B-%3DtEZTTXyJLXxW%2B34E_hh%40mail.gmail.com&forum_name=matplotlib-devel

Cheers,

f

I am sure this is not a matplotlib problem, but I am not sure whos it
is, so I'll start here:

http://matplotlib.sourceforge.net/examples/pylab_examples/dolphin.html
the blue and green dots should only be inside the circle.

Run the code, you get a window that has a 'save' button, the dialog
has a 'type svg' option
the svg renders with the blue/green dots everywhere (rendering using
both rsvg-view and inkscape, which use different rendering engines.)
save as png, display png, dots only inside circle.


-- 
Carl K

I just noticed the "videos" section of http://matplotlib.sourceforge.net
Here is one that I made at ChiPy (Chicago Python user group)
http://carlfk.blip.tv/file/2557425

Anyone know if this message is archived somewhere:
"Jeez, you guys have some crazy examples. I am surprised there isn't
dolphins swimming around inside a sphere."

I would like to add it to the description.

-- 
Carl K

Hi all,

Illustrating the need to *always* remember we credit in the commit
message the name of the person who made a contribution originally...

2010/10/12 Fernando Perez <fpe...@gm...>:
> Hi all,
> - New IPython Sphinx directive.  You can use this directive to mark blocks in
>  reSructuredText documents as containig IPython syntax (including figures) and
>  the will be executed during the build::
[...]
> The following people contributed to this release (please let us know if we
> omitted your name and we'll gladly fix this in the notes for the future):

...
I completely failed to note that this feature (one out of the only two
new features in 0.10.2!) was contributed by John Hunter.

John shall be generously compensated for this offense with fresh
coffee and tropical fruit candy from Colombia, so there's nothing to
worry :)

But this is a good lesson for the committers.  I wrote the release
notes last night by scanning the full changelog and running this
function:

function gauthor() {
    git log "$@" | grep '^Author' | cut -d' ' -f 2- | sort | uniq
}

Since when John sent this, I failed to record his name in the
changelog, last night I simply forgot.  It's very, very hard to
remember months after the fact where any one piece of code came from,
so let's try to be disciplined about *always*:

- if the contribution is more or less ready-to-commit as sent, and the
committer only does absolutely minimal work, use

git commit --author="Original Author <ori...@au...>"

- If the committer does significant amounts of rework, note the
original author in the long part of the commit message (after the
first summary line).  This will make it possible to find that
information later when writing the release notes.

Here are some examples from our log where I didn't screw up:

- Using --author:
commit 8323fa343e74a01394e85f3874249b955131976a
Author: Sebastian Busch <>
Date:   Sun Apr 25 10:57:39 2010 -0700

    Improvements to Vim support for visual mode.

    Patch by Sebastian Busch.

    Note: this patch was originally for the 0.10 series, I (fperez) minimally
    fixed it for 0.11 but it may still require some tweaking to work well with
    the refactored codebase.

    Closes https://bugs.launchpad.net/ipython/+bug/460359

-- Not using --author, but recording origin:
commit ffa96dbc431628218dec604d59bb80511af40751
Author: Fernando Perez <Fer...@be...>
Date:   Sat Apr 24 20:35:08 2010 -0700

    Fix readline detection bug in OSX.

    Close https://bugs.launchpad.net/ipython/+bug/411599

    Thanks to a patch by Boyd Waters.


Ideally, when a significant new feature lands, we should immediately
summarize it in the whatsnew/ docs, but I know that is often hard to
do, as features continue to evolve or a while.  All the more reason
why commit messages with sufficient, accurate information are so
important.

Cheers,

f

Thank you for your help,

but it does not seem to work.

I have downloaded simhei fonts and added it in my directory  
/usr/shared/fonts/truetype but even by using
"""fontname="simhei" """,
or:
"""mpl.rcParams['font.sans-serif'] = ['SimHei']
mpl.rcParams['axes.unicode_minus'] = False """

i still display empty boxes instead of chinese characters.

It is worth noting that these chinese characters print well on the  
console if i add the line:
"""for ytic in ytics:
     print ytic"""

Unfortunately, apart from copying lines of code, i cannot do much with  
the blog you mention, as i don't understand what is written in it.

@Mike: "monospace" family is one that enables me to display accents of  
french words, for the xticks. "fantasy" family was the last family i  
tried for the chinese labels, but to no success.

So, has anyone managed to do it? Is there something i am missing?,

regards,

Benoit.

Quoting sunqiang <sun...@gm...>:

> maybe change the line
> """axim.set_yticklabels(ytics,fontsize=15,family='fantasy')""" to
> """axim.set_yticklabels(ytics,fontsize=15, fontname= "simsun (founder
> extended)")"""
> (or replace fontname with "simhei" or "microsoft yahei") is enough.
>
>
> or, put these two lines:
> mpl.rcParams['font.sans-serif'] = ['SimHei']
> mpl.rcParams['axes.unicode_minus'] = False
>
> there is a Chinese blog (not mine) maybe worth  reading:
> http://hi.baidu.com/lijiangshui/blog/item/a0aad703cd65ee7e3812bb49.html
>
> hope this help
>
> On Mon, Oct 11, 2010 at 3:13 AM, Benoit Gaillard
> <ben...@un...> wrote:
>> Hi,
>>
>> How can one display Mandarin labels in a plot, as yticks_labels for example?
>> It looks to me that there is no font in matplotlib that can display Chinese
>> characters? I can display accentuation from 'utf8' but i could not find a
>> font family that would display Chinese characters.
>>
>> Here is an example of plot that displays empty boxes instead of Chinese
>> characters. In comments you can see various failed attempts:
>>
>> import matplotlib as mpl
>> from matplotlib import cm
>> from matplotlib import rc
>> #rc('font',**{'family':'sans-serif','sans-serif':['SimHei','Arial']})
>> #mpl.rcParams['font.sans-serif'] = ['SimHei','Arial']
>> import matplotlib.pyplot as plt
>>
>> matrix=[[skey+tkey for skey in [1,2]] for tkey in [1,2]]
>> fig = plt.figure()
>> axim = fig.add_subplot(111)
>> #ytics: caractères chinois en utf8
>> ytics=['\xe6\x8a\xb1'.decode('utf8'),'\xe6\x93\x81'.decode('utf8')]
>> xtics=['d\xc3\xa9bo\xc3\xaeter'.decode('utf8'),'diviser'.decode('utf8')]
>> axim.imshow(matrix, cmap=cm.jet, interpolation='nearest',origin='lower')
>> axim.set_xticks(range(2))
>> axim.set_xticklabels(xtics,fontsize=15,rotation=25,ha='right',family='monospace')
>> axim.set_yticks(range(2))
>> axim.set_yticklabels(ytics,fontsize=15,family='fantasy')#,fontname='AR PL
>> ungtiL GB')
>> plt.show()
>>
>> Thank you for your help,
>>
>> Benoit
>>
>>
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>> Hi,
>>
>> How can one display mandarin labels in a plot, as yticks_labels for example?
>> It looks to me that there is no font in matplotlib that can display chinese
>> characters? I can display accentuation from 'utf8' but i could not find a
>> font family that would display chinese characters.
>>
>> Here is an example of plot that displays empty boxes instead of chinese
>> characters. In comment you can see various failed attempts:
>>
>> import matplotlib as mpl
>> from matplotlib import cm
>> from matplotlib import rc
>> #rc('font',**{'family':'sans-serif','sans-serif':['SimHei','Arial']})
>> #mpl.rcParams['font.sans-serif'] = ['SimHei','Arial']
>> import matplotlib.pyplot as plt
>>
>>     matrix=[[skey+tkey for skey in [1,2]] for tkey in [1,2]]
>>     fig = plt.figure()
>>     axim = fig.add_subplot(111)
>>     #ytics: caractères chinois en utf8
>>     ytics=['\xe6\x8a\xb1'.decode('utf8'),'\xe6\x93\x81'.decode('utf8')]
>>     xtics=['d\xc3\xa9bo\xc3\xaeter'.decode('utf8'),'diviser'.decode('utf8')]
>>     axim.imshow(matrix, cmap=cm.jet, interpolation='nearest',
>> origin='lower')
>>     axim.set_xticks(range(2))
>>     axim.set_xticklabels(xtics,
>> fontsize=15,rotation=25,ha='right',family='monospace')
>>     axim.set_yticks(range(2))
>>     axim.set_yticklabels(ytics,fontsize=15,family='fantasy')#,fontname='AR
>> PL SungtiL GB')
>>     plt.show()
>>
>> Thank you for your help,
>>
>> Benoit
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>



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On Tue, Oct 12, 2010 at 9:25 AM, Benjamin Root <ben...@ou...> wrote:

> On Tue, Oct 12, 2010 at 7:57 AM, Stefan Mauerberger <
> ste...@mn...> wrote:
>
>> Hi everyone,
>>
>> I am having trouble with colormaps unsing pcolormesh. I would like to
>> plot and colorise a seismic wave field above a map. Plotting works fine
>> but I do not know how to bring transparency into colormaps. For negative
>> values I want the coloration being blue then it should become
>> transparent and the greatest value should be drawn red. I have tried a
>> lot but without any success. As far as I can see, the keyarg alpha does
>> not fit my needs at all.
>>
>> Do you have any suggestions for me?
>>
>> Regards
>>
>> Stefan
>>
>>
> Stefan,
>
> If you mean using the keyword 'alpha' in the pcolormesh function, then yes,
> that isn't the right place for it.  In your case, the right place to specify
> the alpha channel is in the colormap itself.  Unfortunately, it is currently
> designed around the idea of a scalar value specifying the transparency.
>
> What you can do is a little trick.  First, get the colormap object and then
> initialize it.  This will cause it to internally create an array called
> "_lut" which holds rgba values.
>
> >>> theCM = cm.get_cmap('somemap')
> >>> theCM._init()
>
> Then, you need to fill in the alpha values for yourself.  For this, I am
> going to use a triangle function:
>
> >>> alphas = np.abs(np.linspace(-1.0, 1.0, theCM.N))
> >>> theCM._lut[:,-1] = alphas
>
> Now that your colormap is set up, you can pass it into your pcolormesh
> call.
>
> >>> plt.pcolormesh(X, Y, C, cmap=theCM)
>
> That should work, but I have not fully tested it.  I hope that helps!
> Ben Root
>
>

Slight correction to my code example:

>>> theCM._lut[:-3,-1] = alphas

Sorry for any confusion.

Ben Root

I am preparing 3D plots and have found that the default axis labels are too
close to the tick labels, especially when large font sizes are chosen.  As
such, I would like to specify the position of the axis label.
Unfortunately, I haven't met much success.  See the code below (based on one
of the mplot3d examples).  Does anyone have any tips on how to move the axis
labels further away from the axis in 3D plots?

Thanks,
Justin

from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
X, Y, Z = axes3d.get_test_data(0.05)
ax.plot_wireframe(X, Y, Z, rstride=5, cstride=5)
ax.set_xlabel('x')

# This doesn't work:
ax.w_xaxis.set_label_coords(-0.2, -0.2)

# This doesn't work either:
# ax.w_xaxis.label.set_position((-0.2, -0.2))

# The axis label positions appear to have changed, but not in figure
print ax.w_xaxis.label.get_position()

plt.show()

On 12 October 2010 14:57, Stefan Mauerberger
<ste...@mn...> wrote:
> I am having trouble with colormaps unsing pcolormesh. I would like to
> plot and colorise a seismic wave field above a map. Plotting works fine
> but I do not know how to bring transparency into colormaps. For negative
> values I want the coloration being blue then it should become
> transparent and the greatest value should be drawn red. I have tried a
> lot but without any success. As far as I can see, the keyarg alpha does
> not fit my needs at all.
>
> Do you have any suggestions for me?

You can't make the actual colormap contain transparent color entries,
but you can easily plot a masked array using a custom colormap. The
attached script based on
http://matplotlib.sourceforge.net/examples/pylab_examples/custom_cmap.html
should help you get what you want.

The important part of the script is to create a Numpy masked array to
exclude the regions you'd like to appear transparent:

cond = (-0.1 < Z) & (Z < 0.1)
Z_masked = np.ma.masked_where(cond, Z)

Cheers,
Scott

On Tue, Oct 12, 2010 at 7:57 AM, Stefan Mauerberger <
ste...@mn...> wrote:

> Hi everyone,
>
> I am having trouble with colormaps unsing pcolormesh. I would like to
> plot and colorise a seismic wave field above a map. Plotting works fine
> but I do not know how to bring transparency into colormaps. For negative
> values I want the coloration being blue then it should become
> transparent and the greatest value should be drawn red. I have tried a
> lot but without any success. As far as I can see, the keyarg alpha does
> not fit my needs at all.
>
> Do you have any suggestions for me?
>
> Regards
>
> Stefan
>
>
Stefan,

If you mean using the keyword 'alpha' in the pcolormesh function, then yes,
that isn't the right place for it.  In your case, the right place to specify
the alpha channel is in the colormap itself.  Unfortunately, it is currently
designed around the idea of a scalar value specifying the transparency.

What you can do is a little trick.  First, get the colormap object and then
initialize it.  This will cause it to internally create an array called
"_lut" which holds rgba values.

>>> theCM = cm.get_cmap('somemap')
>>> theCM._init()

Then, you need to fill in the alpha values for yourself.  For this, I am
going to use a triangle function:

>>> alphas = np.abs(np.linspace(-1.0, 1.0, theCM.N))
>>> theCM._lut[:,-1] = alphas

Now that your colormap is set up, you can pass it into your pcolormesh call.

>>> plt.pcolormesh(X, Y, C, cmap=theCM)

That should work, but I have not fully tested it.  I hope that helps!
Ben Root

Hi everyone, 

I am having trouble with colormaps unsing pcolormesh. I would like to
plot and colorise a seismic wave field above a map. Plotting works fine
but I do not know how to bring transparency into colormaps. For negative
values I want the coloration being blue then it should become
transparent and the greatest value should be drawn red. I have tried a
lot but without any success. As far as I can see, the keyarg alpha does
not fit my needs at all. 

Do you have any suggestions for me? 

Regards

Stefan

Hi all,

we've just released IPython 0.10.1, full release notes are below.

Downloads in source and windows binary form are available in the usual location:
http://ipython.scipy.org/dist/

But since our switch to github, we also get automatic distribution of
archives there:
http://github.com/ipython/ipython/archives/rel-0.10.1

and we've also started uploading archives to the Python Package Index
(which easy_install will use by default):
http://pypi.python.org/pypi/ipython

so at any time you should find a location with good download speeds.

You can find the full documentation at:
http://ipython.scipy.org/doc/rel-0.10.1/html/index.html

Enjoy!

Fernando (on behalf of the whole IPython team)

Release 0.10.1
==============

IPython 0.10.1 was released October 11, 2010, over a year after version 0.10.
This is mostly a bugfix release, since after version 0.10 was released, the
development team's energy has been focused on the 0.11 series.  We have
nonetheless tried to backport what fixes we could into 0.10.1, as it remains
the stable series that many users have in production systems they rely on.

Since the 0.11 series changes many APIs in backwards-incompatible ways, we are
willing to continue maintaining the 0.10.x series.  We don't really have time
to actively write new code for 0.10.x, but we are happy to accept patches and
pull requests on the IPython `github site`_.  If sufficient contributions are
made that improve 0.10.1, we will roll them into future releases.  For this
purpose, we will have a branch called 0.10.2 on github, on which you can base
your contributions.

.. _github site: http://github.com/ipython

For this release, we applied approximately 60 commits totaling a diff of over
7000 lines::

    (0.10.1)amirbar[dist]> git diff --oneline rel-0.10.. | wc -l
    7296

Highlights of this release:

- The only significant new feature is that IPython's parallel computing
  machinery now supports natively the Sun Grid Engine and LSF schedulers.  This
  work was a joint contribution from Justin Riley, Satra Ghosh and Matthieu
  Brucher, who put a lot of work into it.  We also improved traceback handling
  in remote tasks, as well as providing better control for remote task IDs.

- New IPython Sphinx directive.  You can use this directive to mark blocks in
  reSructuredText documents as containig IPython syntax (including figures) and
  the will be executed during the build::

  .. ipython::

      In [2]: plt.figure()  # ensure a fresh figure

      @savefig psimple.png width=4in
      In [3]: plt.plot([1,2,3])
      Out[3]: [<matplotlib.lines.Line2D object at 0x9b74d8c>]

- Various fixes to the standalone ipython-wx application.

- We now ship internally the excellent argparse library, graciously licensed
  under BSD terms by Steven Bethard.  Now (2010) that argparse has become part
  of Python 2.7 this will be less of an issue, but Steven's relicensing allowed
  us to start updating IPython to using argparse well before Python 2.7.  Many
  thanks!

- Robustness improvements so that IPython doesn't crash if the readline library
  is absent (though obviously a lot of functionality that requires readline
  will not be available).

- Improvements to tab completion in Emacs with Python 2.6.

- Logging now supports timestamps (see ``%logstart?`` for full details).

- A long-standing and quite annoying bug where parentheses would be added to
  ``print`` statements, under Python 2.5 and 2.6, was finally fixed.

- Improved handling of libreadline on Apple OSX.

- Fix ``reload`` method of IPython demos, which was broken.

- Fixes for the ipipe/ibrowse system on OSX.

- Fixes for Zope profile.

- Fix %timeit reporting when the time is longer than 1000s.

- Avoid lockups with ? or ?? in SunOS, due to a bug in termios.

- The usual assortment of miscellaneous bug fixes and small improvements.

The following people contributed to this release (please let us know if we
omitted your name and we'll gladly fix this in the notes for the future):

* Beni Cherniavsky
* Boyd Waters.
* David Warde-Farley
* Fernando Perez
* Gökhan Sever
* Justin Riley
* Kiorky
* Laurent Dufrechou
* Mark E. Smith
* Matthieu Brucher
* Satrajit Ghosh
* Sebastian Busch
* Václav Šmilauer

maybe change the line
"""axim.set_yticklabels(ytics,fontsize=15,family='fantasy')""" to
"""axim.set_yticklabels(ytics,fontsize=15, fontname= "simsun (founder
extended)")"""
(or replace fontname with "simhei" or "microsoft yahei") is enough.


or, put these two lines:
mpl.rcParams['font.sans-serif'] = ['SimHei']
mpl.rcParams['axes.unicode_minus'] = False

there is a Chinese blog (not mine) maybe worth  reading:
http://hi.baidu.com/lijiangshui/blog/item/a0aad703cd65ee7e3812bb49.html

hope this help

On Mon, Oct 11, 2010 at 3:13 AM, Benoit Gaillard
<ben...@un...> wrote:
> Hi,
>
> How can one display Mandarin labels in a plot, as yticks_labels for example?
> It looks to me that there is no font in matplotlib that can display Chinese
> characters? I can display accentuation from 'utf8' but i could not find a
> font family that would display Chinese characters.
>
> Here is an example of plot that displays empty boxes instead of Chinese
> characters. In comments you can see various failed attempts:
>
> import matplotlib as mpl
> from matplotlib import cm
> from matplotlib import rc
> #rc('font',**{'family':'sans-serif','sans-serif':['SimHei','Arial']})
> #mpl.rcParams['font.sans-serif'] = ['SimHei','Arial']
> import matplotlib.pyplot as plt
>
> matrix=[[skey+tkey for skey in [1,2]] for tkey in [1,2]]
> fig = plt.figure()
> axim = fig.add_subplot(111)
> #ytics: caractères chinois en utf8
> ytics=['\xe6\x8a\xb1'.decode('utf8'),'\xe6\x93\x81'.decode('utf8')]
> xtics=['d\xc3\xa9bo\xc3\xaeter'.decode('utf8'),'diviser'.decode('utf8')]
> axim.imshow(matrix, cmap=cm.jet, interpolation='nearest',origin='lower')
> axim.set_xticks(range(2))
> axim.set_xticklabels(xtics,fontsize=15,rotation=25,ha='right',family='monospace')
> axim.set_yticks(range(2))
> axim.set_yticklabels(ytics,fontsize=15,family='fantasy')#,fontname='AR PL
> ungtiL GB')
> plt.show()
>
> Thank you for your help,
>
> Benoit
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> Hi,
>
> How can one display mandarin labels in a plot, as yticks_labels for example?
> It looks to me that there is no font in matplotlib that can display chinese
> characters? I can display accentuation from 'utf8' but i could not find a
> font family that would display chinese characters.
>
> Here is an example of plot that displays empty boxes instead of chinese
> characters. In comment you can see various failed attempts:
>
> import matplotlib as mpl
> from matplotlib import cm
> from matplotlib import rc
> #rc('font',**{'family':'sans-serif','sans-serif':['SimHei','Arial']})
> #mpl.rcParams['font.sans-serif'] = ['SimHei','Arial']
> import matplotlib.pyplot as plt
>
>     matrix=[[skey+tkey for skey in [1,2]] for tkey in [1,2]]
>     fig = plt.figure()
>     axim = fig.add_subplot(111)
>     #ytics: caractères chinois en utf8
>     ytics=['\xe6\x8a\xb1'.decode('utf8'),'\xe6\x93\x81'.decode('utf8')]
>     xtics=['d\xc3\xa9bo\xc3\xaeter'.decode('utf8'),'diviser'.decode('utf8')]
>     axim.imshow(matrix, cmap=cm.jet, interpolation='nearest',
> origin='lower')
>     axim.set_xticks(range(2))
>     axim.set_xticklabels(xtics,
> fontsize=15,rotation=25,ha='right',family='monospace')
>     axim.set_yticks(range(2))
>     axim.set_yticklabels(ytics,fontsize=15,family='fantasy')#,fontname='AR
> PL SungtiL GB')
>     plt.show()
>
> Thank you for your help,
>
> Benoit
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>