matplotlib-users Mailing List for matplotlib

On Wed, Mar 14, 2012 at 5:38 PM, Will Grainger <wil...@gm...> wrote:
> Not sure if this is a bug or a feature, but
> xlabel (and ylabel) doesn't honour the rcParams['font.size']
> parameters.

I think xlabel and ylabel honor rcParams['axes.labelsize'].

Alejandro.

Hi Kevin,

Thanks for your post.  I think the short answer is that the solution 
will require some manual adjustments.

It has been a little while since I worked with the Sankey class, but 
I'll try to give some detail.  The entire Sankey diagram is a composite 
of sub-diagrams.  Each sub-diagram may have its own input and output 
branches.  The sub-diagrams are joined at matching inputs/outputs.

So, based on the images you shared, I think there are several areas that 
will need some manual work or hacks:
1.  Since the height of "Page Load" (first diagram) is greater than the 
sum of the heights of its inputs and outputs, it will be tricky.  You 
could try creating "Page Load" as a sub diagram with 5 inputs and 5 
outputs, where the first and last inputs/outputs are "dummy" branches to 
add the additional height.  You could also add page load as an 
additional rectangular patch, but that would require manual placement, 
and it would need to be placed in the proper order to overlay "Browsing 
loop."  That might require 2 unconnected Sankey diagrams.
2.  It may require tweaking or more sub-diagrams that you'd expect to 
get the +/- 30 or so degree angles on the "Organic" and "Direct" 
branches (first diagram).
3.  The second diagram introduces additional complexities.  The white 
backgrounds of the text boxes might be possible by specifying the 
properties of the existing text, but I'm not sure.
4.  It will be necessary to manually adjust the length of the 
"Electricity" branch so that it lines up with the "Steam" branch (second 
diagram).  Likewise for the "Fuel" and "Auxiliary Fuel."  That is one 
definite drawback of the matplotlib Sankey class as it is; where 
branches split and rejoin or form a circuit, manual adjustment may be 
necessary.
4. Finally, it may be difficult to reproduce the shading of the branches 
in the second diagram.

I'm sorry that there's no "out of the box" solution.  However, since 
matplotlib and Python is so flexible, it may be fairly straightforward 
to automate these additional features.  I also suspect that some of the 
features of the diagrams may be artifacts of the particular software 
used--not necessarily due to the preferences of your colleague.

Kevin


On 03/15/2012 10:56 AM, Kevin Hunter wrote:
> Hullo matplotlib list,
>
> I've discovered (with pleasure!) that matplotlib has recently learned
> how to create Sankey diagrams.  Thank you Kevin and Yannick!
>
> One of my less-technically inclined fellow graduate students is
> searching for his toolset of choice for generating these suckers, and is
> currently looking at Stan.  As I'm an open-source advocate I'd love to
> be able to say, "you can do this with X", where X in this case is
> clearly matplotlib.
>
> Specifically, I've not heavily used matplotlib before, and from the
> given examples I see on matplotlib.sf.net, I'm not clear on exactly the
> capabilities of this recently-added code.  What my fellow grad student
> has opined would be nice for his uses would be boxes that are built into
> the flows, rather than just used as labels.  Something like:
>
> "Page Load"
> http://modernl.com/images/diagrams/web-traffic-sankey-diagram.png
>
> "Input", "Gas Turbine", "HRSG", "Waste", "BP Turbine", "Output"
> http://www.bucknell.edu/images/Depts/Facilities/sankeythumb.jpg
>
> Is this currently possible, /without/ manually adjusting the graphic?
>
> Thanks!
>
> Kevin
>
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Hi all,

I'm (finally) getting started with matplotlib, and am enjoying the lovely plot quality. However, as a non-matlab user, I'm finding it *extremely* difficult to figure out how to do even the simplest tasks / understand the code samples. (e.g. what is the '111' in the boilerplate calls to add_subplot() in the various examples? I couldn't find anything in the docs, and had to resort to the matlab documentation!)

Anyhow, I've soldiered on, and have run across an issue that I don't know if is related to my non-comprehension of the right syntax, a bug in the Axes3D code, or a problem with the MacOSX backend. Here's code to duplicate the issue (Python 2.7, OS X 10.7, matplotlib 1.1.0, via pre-built installer):

import matplotlib as mpl
mpl.use('macosx')
import matplotlib.pyplot as plt
plt.ion()
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot([1,2,3], [2,3,2], [2,5,7]) # draws immediately!?
ax.cla() # plt.cla() has same effect
ax.plot([1,2,3], [2,3,2], [2,5,7]) # doesn't draw?
plt.draw() # now draws, but z-order is messed up -- grid lines on top?
# And worse, now figure can't be interactively rotated with the mouse

Nothing can restore interactivity short of making a new figure, or calling fig.clf() (which I *randomly* happened on), and then making a new set of axes.

Is this a known issue? Am I doing something wrong -- is ax.cla() or plt.cla() the wrong thing to clear the figure?

Thanks a lot,
Zach

I've been working through this excellent new book on Matplotlib:

     Tosi, Sandro.  Matplotlib for Python developers.  Packt
     Publishing, 2009, ISBN 978-1-847197-90-0.

I've been teaching Python classes for 15 years.  Until now, all I
could do in the Matplotlib unit is throw some small examples at
the students and then point them at the 800 pages of reference
documentation and say "Here is documentation for the 10,000 tiny
pieces of Matplotlib.  Good luck figuring out how to assemble
them."

Tosi's book is exactly what Matplotlib has needed for so long: a
proper tutorial.  Tosi starts with the absolute basics: plot Y
against X; add a title; add axis labels; plot two functions of
the same variable; and so on, a progression that eases the new
user first into the features that most people will use.

The writing is clear, the examples constructed and explained
well, with a nice balance of theory and practice.

In particular I appreciate the shift in chapter 4 to a more
Pythonic, object-oriented approach.  The author places Pylab in
its proper context (great for playing around) but I agree that
for serious production applications and modular design the object
approach is the way to go.

The only extremely minor quibbles I have are with the editing.
None of the editorial crew seem to be native English speakers.
Take for example the highly useful diagram on page 59, "Plot
types".  This diagram helps you figure out what kind of plot
fills your needs.  However, the title is "Chart Suggestions -- A
Tought-Starter [sic]"; that should be "Thought-Starter".  On the
same diagram, there are two references to "Tree Variables" that
probably should be "Three variables".

However, don't let that put you off.  This is just the right book
for people starting out.  I found very few typos, and none of
them reduced the book's usefulness.

Standard disclaimer:  I have no financial interest in this
book; I'm just a happy reader.

Best regards,
John Shipman (Jo...@Nm...), Applications Specialist, NM Tech Computer Center,
Speare 146, Socorro, NM 87801, (575) 835-5735, http://www.nmt.edu/~john
   ``Let's go outside and commiserate with nature.''  --Dave Farber

On 03/16/2012 08:28 AM, John W. Shipman wrote:
> We have Matplotlib 1.0.1 installed here, and it does not seem to
> have a Tkinter backend:

The backend has always been available, but it appears only if the Tk/Tcl 
headers are found when mpl is built.  So, upgrading mpl is generally a 
good thing to do anyway, but it won't help in your case unless you 
install the mpl dependencies before building mpl.  See
http://matplotlib.sourceforge.net/users/installing.html.

Eric

>
> ================================================================
> $ python
> Python 2.7.1 (r271:86832, Apr 12 2011, 16:15:16)
> [GCC 4.6.0 20110331 (Red Hat 4.6.0-2)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib as mpl
>>>> mpl.__version__
> '1.0.1'
>>>> from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
> Traceback (most recent call last):
>     File "<stdin>", line 1, in<module>
> ImportError: No module named backend_tkagg
> ----------------------------------------------------------------
>
> This page seems to imply that such a backend exists:
>
> http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_tk.html
>
> However, the official documentation of the backends module does not show
> such a back end.
>
> If we upgrade to 1.1.0, will this backend be available?
>
> I realize that there are several good GUI backends out there, but
> I have a lot of Tkinter experience and can't afford the two or
> three months it would take to learn GTK+.  Also, how come the
> oldest Python GUI hasn't been supported previously, or is the
> documentation for Matplotlib embedding hidden someplace?
>
> Best regards,
> John Shipman (jo...@nm...), Applications Specialist, NM Tech Computer Center,
> Speare 146, Socorro, NM 87801, (575) 835-5735, http://www.nmt.edu/~john
>     ``Let's go outside and commiserate with nature.''  --Dave Farber
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
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Hi;

Somewhat related to my earlier question: instead of doing a surfaceplot, 
I have also considered doing a pcolormesh of a 2D dataset in the z=0 
plane. This doesn't seem to be immediately possible though, but it would 
be a really nice feature. Is there a way to do it that doesn't require 
too much messing aroud? Otherwise, please consider this a feature request...

Best;

Emil

We have Matplotlib 1.0.1 installed here, and it does not seem to
have a Tkinter backend:

================================================================
$ python
Python 2.7.1 (r271:86832, Apr 12 2011, 16:15:16) 
[GCC 4.6.0 20110331 (Red Hat 4.6.0-2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib as mpl
>>> mpl.__version__
'1.0.1'
>>> from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
ImportError: No module named backend_tkagg
----------------------------------------------------------------

This page seems to imply that such a backend exists:

http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_tk.html

However, the official documentation of the backends module does not show
such a back end.

If we upgrade to 1.1.0, will this backend be available?

I realize that there are several good GUI backends out there, but
I have a lot of Tkinter experience and can't afford the two or
three months it would take to learn GTK+.  Also, how come the
oldest Python GUI hasn't been supported previously, or is the
documentation for Matplotlib embedding hidden someplace?

Best regards,
John Shipman (jo...@nm...), Applications Specialist, NM Tech Computer Center,
Speare 146, Socorro, NM 87801, (575) 835-5735, http://www.nmt.edu/~john
   ``Let's go outside and commiserate with nature.''  --Dave Farber

Hi,

I have been dreaming about this for a long time too,

This would really be a nice feature. I often need to come back to the 
formatting of a plot, and its formatting only, without the need to 
really access the data (which I often end up calculating again!)

Guillaume

Le 16/03/2012 09:17, David Verelst a écrit :
> Hi,
>
> This sounds actually very interesting. I have been thinking about how to
> save matplotlib figures in a way comparable to the Matlab .fig format: a
> file that holds the data (for instance using HDF5/pytables, some figures
> might hold a lot of data) and the plotting commands to exactly
> reconstruct the figure. However, I never got around of thinking about an
> actual implementation for Matplotlib. Hopefully your work can inspire me
> to actually get it started , and I will try to find some time to dig in
> your code the coming weeks.
>
> At the Spyder mailing list the idea of saving figures a la Matlab
> briefly popped before as well:
> http://groups.google.com/group/spyderlib/browse_thread/thread/bf582bac96ff875/d5e94fe9296afbe5
>
>
> I think saving figures in this manner would be a nice feature for
> matplotlib.
>
> Thanks for sharing this!
>
> Regards,
> David
>
> PS: sorry to Sebastian for sending the message twice
>
> On 15/03/12 11:22, Sebastian Berg wrote:
>> Hey,
>>
>> last weekend I wrote a hook which can track figure creation. Basically
>> it takes care of creating the new figure and wraps it to track all
>> changes to it. Its a hack, and the code is not cleaned up or tested
>> much, but I like to do scripts that I run with many parameters to create
>> plots and it works well to allow me to open the figures in a way that I
>> can zoom, etc. and would allow editing (a bit) later on too. So while I
>> doubt the approach can be made something serious, and there are probably
>> things that don't work (right now 3D Axis can be done with a bit extra
>> but mouse zooming does not work inside a 3D Axis, though I think its
>> likely not difficult to change), I thought I would put it online because
>> I am not aware of any way to save matplotlib figures:
>>
>> https://github.com/seberg/haunter-for-matplotlib-figures
>>
>> Maybe someone finds it useful or interesting :)
>>
>> Regards,
>>
>> Sebastian Berg
>>
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
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>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
> ------------------------------------------------------------------------------
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> Try Windows Azure free for 90 days Click Here
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Indeed, saving figures in the manner of Matlab would be a great feature 
enhancement for Matplotlib.
Keep Hacking ! :)

Cheers
François

Hi,

This sounds actually very interesting. I have been thinking about how to 
save matplotlib figures in a way comparable to the Matlab .fig format: a 
file that holds the data (for instance using HDF5/pytables, some figures 
might hold a lot of data) and the plotting commands to exactly 
reconstruct the figure. However, I never got around of thinking about an 
actual implementation for Matplotlib. Hopefully your work can inspire me 
to actually get it started , and I will try to find some time to dig in 
your code the coming weeks.

At the Spyder mailing list the idea of saving figures a la Matlab 
briefly popped before as well: 
http://groups.google.com/group/spyderlib/browse_thread/thread/bf582bac96ff875/d5e94fe9296afbe5 


I think saving figures in this manner would be a nice feature for 
matplotlib.

Thanks for sharing this!

Regards,
David

PS: sorry to Sebastian for sending the message twice

On 15/03/12 11:22, Sebastian Berg wrote:
> Hey,
>
> last weekend I wrote a hook which can track figure creation. Basically
> it takes care of creating the new figure and wraps it to track all
> changes to it. Its a hack, and the code is not cleaned up or tested
> much, but I like to do scripts that I run with many parameters to create
> plots and it works well to allow me to open the figures in a way that I
> can zoom, etc. and would allow editing (a bit) later on too. So while I
> doubt the approach can be made something serious, and there are probably
> things that don't work (right now 3D Axis can be done with a bit extra
> but mouse zooming does not work inside a 3D Axis, though I think its
> likely not difficult to change), I thought I would put it online because
> I am not aware of any way to save matplotlib figures:
>
> https://github.com/seberg/haunter-for-matplotlib-figures
>
> Maybe someone finds it useful or interesting :)
>
> Regards,
>
> Sebastian Berg
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Thursday, March 15, 2012, Yi Shang <mir...@gm...> wrote:
> Dear all,
> I tried to search through the mailinglist archive first, but couldn't (
http://sourceforge.net/mailarchive/forum.php?forum_name=matplotlib-users).
Is the mailinglist only for browsing by date?
>
> I did a clean install of matplotlib (following the installation webpage)
on Linux machine (x86_64 GNU/Linux), from source file matplotlib-1.1.0.tar.
>
> the building log is as follow, you could see that I did change the
basedir list in setupext.py. I didn't change the matplotlibrc file. (I
installed ActiveTcl and ActivePython trying to solve the problem, but the
installation seems unchanged.)
>
> tabasco:~/software/matplotlib-1.1.0> python setup.py build
> basedirlist is: ['/usr/local', '/usr',
'/mnt/raidc/mshang/software/libpng-1.5.9',
'/mnt/raidc/mshang/software/ActiveTcl',
'/mnt/raidc/mshang/software/ActivePython',
'/mnt/raidc/mshang/software/freetype-2.4.9',
'/mnt/raidc/mshang/software/zlib-1.2.6']
>
============================================================================
> BUILDING MATPLOTLIB
>             matplotlib: 1.1.0
>                 python: 2.7.2 (default, Mar  3 2012, 11:39:51)  [GCC 4.1.2
>                         20061115 (prerelease) (Debian 4.1.1-21)]
>               platform: linux2
>
> REQUIRED DEPENDENCIES
>                  numpy: 1.6.1
>              freetype2: found, but unknown version (no pkg-config)
>
> OPTIONAL BACKEND DEPENDENCIES
>                 libpng: found, but unknown version (no pkg-config)
>                Tkinter: no
>                         * TKAgg requires Tkinter
>                   Gtk+: no
>                         * Building for Gtk+ requires pygtk; you must be
able
>                         * to "import gtk" in your build/install
environment
>        Mac OS X native: no
>                     Qt: no
>                    Qt4: no
>                  Cairo: no
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
>               datetime: present, version unknown
>               dateutil: 1.5
>                   pytz: 2011c
>
> OPTIONAL USETEX DEPENDENCIES
>                 dvipng: no
>            ghostscript: /bin/sh: gs: command not found
>                  latex: no
>
> [Edit setup.cfg to suppress the above messages]
>
============================================================================
> .....
>
> After compilation, I can generate plots using script as blow:
>
>>cat test.py
> from matplotlib import pyplot as plt
> plt.plot([1,2],[2,3])
> plt.savefig("test.png")
> plt.savefig("test.eps")
> plt.savefig("test.pdf")
>
> But the problem I have now is that: I get no pop-up window when I type
pylab.show() in interactive mode. And below is the output of simple_plot:
>
>> cat simple_plot.py
> from pylab import *
> plot([1,2,3])
> show()
>
>> python simple_plot.py --verbose-helpful
> $HOME=/mnt/raidc/mshang
> CONFIGDIR=/mnt/raidc/mshang/.matplotlib
> matplotlib data path
/mnt/raidc/mshang/software/Python-2.7.2/lib/python2.7/site-packages/matplotlib/mpl-data
> loaded rc file
/mnt/raidc/mshang/software/Python-2.7.2/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 1.1.0
> verbose.level helpful
> interactive is False
> platform is linux2
> Using fontManager instance from
/mnt/raidc/mshang/.matplotlib/fontList.cache
> backend agg version v2.2
>
> Does anyone have any idea what's going wrong here? I can run gnuplot and
get pop-up windows fine, but I guess matplotlib doesn't use Xming...
>
> Thank you all for reading this post!!
>
> --
> Miranda
>

The build can't find the build dependencies.  At the very least, install
the tkinter-devel packages.  These dependencies are needed to make mpl
interactive, but are not required for a successful build.  The instructions
on the page for how to install from source explains how to determine all
your build requirements from the command-line.

I hope that helps!
Ben Root

Dear all,
I tried to search through the mailinglist archive first, but couldn't (
http://sourceforge.net/mailarchive/forum.php?forum_name=matplotlib-users).
Is the mailinglist only for browsing by date?

I did a clean install of matplotlib (following the installation webpage) on
Linux machine (x86_64 GNU/Linux), from source file matplotlib-1.1.0.tar.

the building log is as follow, you could see that I did change the basedir
list in setupext.py. I didn't change the matplotlibrc file. (I installed
ActiveTcl and ActivePython trying to solve the problem, but the
installation seems unchanged.)

tabasco:~/software/matplotlib-1.1.0> python setup.py build
basedirlist is: ['/usr/local', '/usr',
'/mnt/raidc/mshang/software/libpng-1.5.9',
'/mnt/raidc/mshang/software/ActiveTcl',
'/mnt/raidc/mshang/software/ActivePython',
'/mnt/raidc/mshang/software/freetype-2.4.9',
'/mnt/raidc/mshang/software/zlib-1.2.6']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.1.0
                python: 2.7.2 (default, Mar  3 2012, 11:39:51)  [GCC 4.1.2
                        20061115 (prerelease) (Debian 4.1.1-21)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.6.1
             freetype2: found, but unknown version (no pkg-config)

OPTIONAL BACKEND DEPENDENCIES
                libpng: found, but unknown version (no pkg-config)
               Tkinter: no
                        * TKAgg requires Tkinter
                  Gtk+: no
                        * Building for Gtk+ requires pygtk; you must be able
                        * to "import gtk" in your build/install environment
       Mac OS X native: no
                    Qt: no
                   Qt4: no
                 Cairo: no

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: 1.5
                  pytz: 2011c

OPTIONAL USETEX DEPENDENCIES
                dvipng: no
           ghostscript: /bin/sh: gs: command not found
                 latex: no

[Edit setup.cfg to suppress the above messages]
============================================================================
.....

After compilation, I can generate plots using script as blow:

>cat test.py
from matplotlib import pyplot as plt
plt.plot([1,2],[2,3])
plt.savefig("test.png")
plt.savefig("test.eps")
plt.savefig("test.pdf")

But the problem I have now is that: I get no pop-up window when I type
pylab.show() in interactive mode. And below is the output of simple_plot:

> cat simple_plot.py
from pylab import *
plot([1,2,3])
show()

> python simple_plot.py --verbose-helpful
$HOME=/mnt/raidc/mshang
CONFIGDIR=/mnt/raidc/mshang/.matplotlib
matplotlib data path
/mnt/raidc/mshang/software/Python-2.7.2/lib/python2.7/site-packages/matplotlib/mpl-data
loaded rc file
/mnt/raidc/mshang/software/Python-2.7.2/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 1.1.0
verbose.level helpful
interactive is False
platform is linux2
Using fontManager instance from /mnt/raidc/mshang/.matplotlib/fontList.cache
backend agg version v2.2

Does anyone have any idea what's going wrong here? I can run gnuplot and
get pop-up windows fine, but I guess matplotlib doesn't use Xming...

Thank you all for reading this post!!

-- 
Miranda