matplotlib-users Mailing List for matplotlib

OS: OSX 10.8.5 (Mountain Lion)
Matplotlib Version: 1.3.1
ipython: 2.1.0
gcc info:
Configured with: --prefix=/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix

Matplotlib Obtained: Installed via pip, auto chosen options below

BUILDING MATPLOTLIB
                matplotlib: yes [1.3.1]
                    python: yes [2.7.6 (default, Jan 28 2014, 11:09:35)  [GCC
                            4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)]]
                  platform: yes [darwin]

    REQUIRED DEPENDENCIES AND EXTENSIONS
                     numpy: yes [version 1.8.1]
                  dateutil: yes [using dateutil version 2.2]
                   tornado: yes [using tornado version 4.0]
                 pyparsing: yes [using pyparsing version 2.0.2]
                     pycxx: yes [Couldn't import.  Using local copy.]
                    libagg: yes [pkg-config information for 'libagg' could not
                            be found. Using local copy.]
                  freetype: yes [version 17.2.11]
                       png: yes [version 1.6.12]

    OPTIONAL SUBPACKAGES
               sample_data: yes [installing]
                  toolkits: yes [installing]
                     tests: yes [using nose version 1.3.3]

    OPTIONAL BACKEND EXTENSIONS
                    macosx: yes [installing, darwin]
                    qt4agg: no  [PyQt4 not found]
                   gtk3agg: no  [Requires pygobject to be installed.]
                 gtk3cairo: no  [Requires cairo to be installed.]
                    gtkagg: no  [Requires pygtk]
                     tkagg: yes [installing, version 81008]
                     wxagg: no  [requires wxPython]
                       gtk: no  [Requires pygtk]
                       agg: yes [installing]
                     cairo: no  [cairo not found]
                 windowing: no  [Microsoft Windows only]

    OPTIONAL LATEX DEPENDENCIES
                    dvipng: yes [version 1.14]
               ghostscript: yes [version 9.07]
                     latex: yes [version 3.1415926]
                   pdftops: no

Problem:

Using the default mathtext renderer, axis labels overlap the spine.
Pictures of the problem are available at
http://stackoverflow.com/questions/24997386/latex-tick-label-overlapping-axis-in-graph-generated-by-matplotlib/24999963#24999963.
Turning on tex rendering via rc('text', usetex=True), makes the
problem go away which indicates this is a possible bug in mathtext (or
perhaps the libraries used by it on OSX) and I thought I should report
it.

Minimal Code Producing Error:

from pylab import *

xticks([-np.pi, -np.pi/2, 0, np.pi/2, np.pi],
       [r'$-\pi$', r'$-\frac{\pi}{2}$',r'$0$', r'$\frac{\pi}{2}$',r'$+\pi$'])

show(block=False)

Extra Potential Relevant Information:

When calling verbose-debug, there are a bunch of lines like this one:

Using fontManager instance from /Users/wd239/.matplotlib/fontList.cache
backend MacOSX version unknown

findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
to Bitstream Vera Sans
(/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12
to STIXGeneral (/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
with score of 0.000000
......

I've followed up on several suggestions and here is what I've done/found.

(I know I don't use mlab or pylab but I pulled the import lines from 
another source and am leaving them in for the heck of it)

Code A:
import numpy as np
import matplotlib
import time
from matplotlib import pylab, mlab, pyplot

A = np.random.rand(5,5,10)
for j in range(10):
     pyplot.matshow(A[:,:,j])
     # pyplot.pause(.5)
     pyplot.show()
     time.sleep(0.5)
     pyplot.close()

Code B:
import numpy as np
import matplotlib
import time
from matplotlib import pylab, mlab, pyplot

A = np.random.rand(5,5,10)
for j in range(10):
     pyplot.matshow(A[:,:,j])
     pyplot.pause(.5)
     # pyplot.show()
     # time.sleep(0.5)
     pyplot.close()

================
1)
Code A:
Spyder Python (Mac) - A blank figure window is generated, closed, and 
repeated over ten iterations.  No user intervention needed to allow loop 
to continue.

Adding a pyplot.ioff() line after the from matplotlib line gives the 
expected/hoped behavior:  Ten arrays appear, one after the other, no 
intervention needed.

---

Ipython Notebook (no --pylab) - A figure window with an array appears. 
I have to close it using the Window Close titlebar button, then the next 
one appears, waits for close action, etc.

Adding a pyplot.ion() statement after the from matplotlib line yields 
the same result as Spyder Python w/o the pyplot.ioff() line. 10 blank 
windows appear one after the other.


Code B:
Spyder Python and Ipython Notebook (no --pylab) - Both display 
expected/hoped behavior.  Figure window appears, figure displays, 
closes, and then opens with next piece of data

So, there's something about the pause command that's special, at least 
in this case, and I'd like to understand what that is.

2) Additional interactive test following code runs:

pyplot.matshow(A[:,:,6)]

Spyder Python - Figure pops up, plot is displayed.  Zoom, pan, 
back/forth, home buttons all work

Ipython notebook (no --pylab) - Figure pops up, no plot displays.
Adding pause(x) causes figure to display.  Plot is interactive for x 
seconds.  Zoom, pan, etc. work for that time.  Notebook shows In[*] for 
x seconds.

After x seconds, In[*] <-- In[Cell number].  Plot is no longer 
interactive, mousing over plot shows spinning Mac rainbow ball.  Can't 
even close window using titlebar icons.  pyplot.close() from a cell 
required to close.

I would like to stay with the Notebook as I learn matplotlib but I'm not 
sure how to get around the plot being interactive for only a defined 
time period, spinning rainbow balls, etc.

JBB



On 7/30/14, 9:30 AM, Benjamin Root wrote:
> I think it is mostly an issue with how IPython interfaces with
> matplotlib. If you were running from a pure python prompt, then I would
> suspect it to work (haven't tried myself, though). Note that the --pylab
> option to ipython is now highly discouraged. Instead, I would try the
> "%matplotlib interactive" cell magic instead (I think that is the right
> incantation).
>
>
> On Wed, Jul 30, 2014 at 2:15 AM, JBB
> <jea...@gm...
> <mailto:jea...@gm...>> wrote:
>
>     On 7/29/14, 10:49 PM, Eric Firing wrote:
>       > On 2014/07/29, 7:04 PM, JBB wrote:
>       >> Hello,
>       >>
>       >> I am relatively new to Python, numpy, matplotlib, etc., with a
>       >> reasonable amount of Matlab experience.
>
>     ...[ Problem and test code trimmed ]
>
>       >
>       > First, at least initially for this sort of thing, run in "ipython
>       > --pylab", and don't use any "ion()" or "ioff()".
>       >
>       > Second, replace the "show(); time.sleep(1)" with "pause(1)".
>       >
>       > I think that will do it.
>       >
>       > Eric
>       >
>
>     Thank you, very much.  It did indeed work.
>
>     Is there a pointer to why this worked when my initial approach did not?
>        I thought from the documentation/videos that preparing a plot with
>     relevant commands then issuing the show() command was the preferred
>     approach within Python/Matplotlib.
>
>     JBB
>
>
>
>
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Fernando,

This information is going to be the preface of my book on using matplotlib
for making an interactive application (sorry, no IPython, the editor wanted
to keep the scope tight). So, what I am looking for are some of the major
interactive features (who supplied them, and their reasons/purpose). Also,
how has interactive matplotlib supported uses "in the wild" such as the
Mars Phoenix Lander and recently, the ISEE3 reboot project (that abandoned
satellite that was recently revived by citizen scientists).

Of, course, any insights to John's original needs/use cases in the early
years would be very valuable as well. I could have sworn he has written
such missives on the mailing lists, but I can't seem to find them.

Cheers!
Ben Root
On Jul 30, 2014 11:21 PM, "Fernando Perez" <fpe...@gm...> wrote:

> Hi Ben,
>
> if by interactive plotting you refer to using it interactively via ipython
> and other such systems, there's a good part of that history that is spread
> somewhere between the early mpl and ipython archives AND John's and my
> personal inboxes.
>
> A good chunk of that (not all, mind you, since many others contributed)
> happened with John and I working on it, and sadly he's not with us and I
> had a loss of my early email (anything older than 2005) when I left the
> University of Colorado.
>
> I'd be happy to answer some questions if you have them, to the best of my
> memory. Probably quicker over skype/phone, ping me directly (at my Berkeley
> address) if you want.
>
> Cheers
>
> f
>
>
>
> On Wed, Jul 30, 2014 at 7:20 PM, Benjamin Root <ben...@ou...> wrote:
>
>> Hello all,
>>
>> I am trying to put together notes for a writeup on a short history of
>> matplotlib (in particular, its uses for interactive plotting). I have John
>> Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
>> sources.
>>
>> Unfortunately, searching for "matplotlib" and "history" gets me lots of
>> results on our trials and tribulations with version control...
>>
>> Anybody have anything bookmarked?
>>
>> Cheers!
>> Ben Root
>>
>> P.S. - Yes... this is for a book. Stay tuned!
>>
>>
>> ------------------------------------------------------------------------------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
>
> --
> Fernando Perez (@fperez_org; http://fperez.org)
> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
> fernando.perez-at-berkeley: contact me here for any direct mail
>

Hi Ben,

if by interactive plotting you refer to using it interactively via ipython
and other such systems, there's a good part of that history that is spread
somewhere between the early mpl and ipython archives AND John's and my
personal inboxes.

A good chunk of that (not all, mind you, since many others contributed)
happened with John and I working on it, and sadly he's not with us and I
had a loss of my early email (anything older than 2005) when I left the
University of Colorado.

I'd be happy to answer some questions if you have them, to the best of my
memory. Probably quicker over skype/phone, ping me directly (at my Berkeley
address) if you want.

Cheers

f



On Wed, Jul 30, 2014 at 7:20 PM, Benjamin Root <ben...@ou...> wrote:

> Hello all,
>
> I am trying to put together notes for a writeup on a short history of
> matplotlib (in particular, its uses for interactive plotting). I have John
> Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
> sources.
>
> Unfortunately, searching for "matplotlib" and "history" gets me lots of
> results on our trials and tribulations with version control...
>
> Anybody have anything bookmarked?
>
> Cheers!
> Ben Root
>
> P.S. - Yes... this is for a book. Stay tuned!
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>


-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail

Hello all,

I am trying to put together notes for a writeup on a short history of
matplotlib (in particular, its uses for interactive plotting). I have John
Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
sources.

Unfortunately, searching for "matplotlib" and "history" gets me lots of
results on our trials and tribulations with version control...

Anybody have anything bookmarked?

Cheers!
Ben Root

P.S. - Yes... this is for a book. Stay tuned!

On Wed, Jul 30, 2014 at 6:11 PM, Matthew Brett <mat...@gm...>
wrote:

> But - for exploring plotting, I would say it was a good choice.


Yup, I'm obviously as biased as they come, but I think that the immediate
feedback and the ability to keep plots together with their source code,
makes learning and experimenting with mpl (or other plotting libs) an ideal
use case for the notebook.

The only catch to be aware of is that, in order for a simple

plot(x)

to produce a figure without having to manually call show(), we do a bit of
magic behind the scenes.  And that magic can occasionally lead to duplicate
figures when you start manually calling display(fig) yourself. So in that
more advanced scenario, you will need to add the occasional plt.close()
call.

HTH,

f


-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail

Hi,

On Wed, Jul 30, 2014 at 5:14 PM, JBB <jea...@gm...> wrote:
> Thanks for all the responses.  I'll try pure Python via the Spyder IDE
> vs. Ipython/Ipython Notebook for this and report back.  The 'No Pylab
> Thanks' was enlightening.
>
> I am confused about the role of the Notebook interface.  I've been using
> it to learn the language, do experiments, and preserve tips/tricks I
> pick up along the way.  I've also seen it used in many online
> presentations and courses on Python, numpy, matplotlib, and other
> packages. I've found it very helpful so far and would like to stick with it.
>
> But, it sounds like it there are some hidden issues in how the notebook
> i/f interacts with matplotlib?  Is it not the best choice for learning
> plotting?  If not, what's recommended - IDE?  Python from a terminal
> window? ... ?

I think the notebook is pretty good for all those things.   I have got
out of the habit of using the notebook when I'm writing code, because
it can be hard to switch between the notebook and my usual development
tools - in my case vim and bash and occasionally the IPython console.
But - for exploring plotting, I would say it was a good choice.

Cheers,

Matthew

Thanks for all the responses.  I'll try pure Python via the Spyder IDE 
vs. Ipython/Ipython Notebook for this and report back.  The 'No Pylab 
Thanks' was enlightening.

I am confused about the role of the Notebook interface.  I've been using 
it to learn the language, do experiments, and preserve tips/tricks I 
pick up along the way.  I've also seen it used in many online 
presentations and courses on Python, numpy, matplotlib, and other 
packages. I've found it very helpful so far and would like to stick with it.

But, it sounds like it there are some hidden issues in how the notebook 
i/f interacts with matplotlib?  Is it not the best choice for learning 
plotting?  If not, what's recommended - IDE?  Python from a terminal 
window? ... ?

JBB