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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>
>
>
>
> ------------------------------------------------------------------------------
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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

On 2014-07-30 14:51, Eric Firing wrote:
> On 2014/07/30, 7:26 AM, Benjamin Root wrote:
>> There is no --pylab for that.
>
> I don't know what development version you are using, but for 2.1.0, it
> is still there--and it does what needs to be done.

	He was talking about the normal Python interpreter, not IPython.

-- 
Brendan Barnwell
"Do not follow where the path may lead.  Go, instead, where there is 
no path, and leave a trail."
    --author unknown

On 2014/07/30, 7:26 AM, Benjamin Root wrote:
> There is no --pylab for that.

I don't know what development version you are using, but for 2.1.0, it 
is still there--and it does what needs to be done.

On Wed, Jul 30, 2014 at 10:26 AM, Nathan Goldbaum <nat...@gm...>
wrote:

> Pylab is going to be removed in IPython 3.0 (in fact it's already gone in
> master) since it has several bad interactions with the rest of the
> numpy/scipy universe and leads to un-reproducible code.


Quick clarifications:

- `--pylab` as a command-line flag is strongly discouraged and we will
likely remove it (having it in that location requires really awkward
special-case code everywhere).  But we'll probably keep the %pylab magic
indefinitely, since it's useful for quick-and-dirty command-line work where
you don't care about namespace pollution, just about minimizing typing and
namespace access for convenience.

- The %matplotlib magic can also be used without args, case in which it
works like %pylab used to, and will pick up the user's default backend:


In [1]: %matplotlib
Using matplotlib backend: TkAgg

In [2]: import matplotlib.pyplot as plt

In [3]: plt.plot([1,2,3])
Out[3]: [<matplotlib.lines.Line2D at 0x4b90ed0>]

Cheers

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 10:26 AM, Nathan Goldbaum <nat...@gm...> wrote:
> You would use "%matplotlib inline" if you want the plots to show up inline
> in the notebook.  If you want to use one of the gui backends, it would be
> "%matplotlib <backend>".  More detail here:
>
> http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib
>
> Pylab is going to be removed in IPython 3.0 (in fact it's already gone in
> master) since it has several bad interactions with the rest of the
> numpy/scipy universe and leads to un-reproducible code.  See this blog post
> for more detail on why using pylab is a bad idea:
>
> https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html

I personally use the IPython console for my just-checking interactive
work, rather than the notebook.

Checking now, '%matplotlib inline' in the console raises an error,
understandably enough, but this works:

%matplotlib osx
import matplotlib.pyplot as plt
plt.plot(range(10))

I know that's what you said, it's just to give a complete snippet for Googlers,

Cheers,

Matthew

right, thank you, it is "inline", not "interactive". I really need a memory
upgrade...

Cheers!
Ben Root


On Wed, Jul 30, 2014 at 1:26 PM, Nathan Goldbaum <nat...@gm...>
wrote:

> You would use "%matplotlib inline" if you want the plots to show up inline
> in the notebook.  If you want to use one of the gui backends, it would be
> "%matplotlib <backend>".  More detail here:
>
>
> http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib
>
> Pylab is going to be removed in IPython 3.0 (in fact it's already gone in
> master) since it has several bad interactions with the rest of the
> numpy/scipy universe and leads to un-reproducible code.  See this blog post
> for more detail on why using pylab is a bad idea:
>
> https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html
>
>
> On Wed, Jul 30, 2014 at 10:19 AM, Matthew Brett <mat...@gm...>
> wrote:
>
>>  Hi,
>>
>> On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> 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).
>>
>> Sorry for being slightly off-topic, but what is the current
>> recommendation then for interactive plots from the console, if --pylab
>> is discouraged?
>>
>> Cheers,
>>
>> Matthew
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>>
>
>

You would use "%matplotlib inline" if you want the plots to show up inline
in the notebook.  If you want to use one of the gui backends, it would be
"%matplotlib <backend>".  More detail here:

http://ipython.org/ipython-doc/2/api/generated/IPython.core.magics.pylab.html#IPython.core.magics.pylab.PylabMagics.matplotlib

Pylab is going to be removed in IPython 3.0 (in fact it's already gone in
master) since it has several bad interactions with the rest of the
numpy/scipy universe and leads to un-reproducible code.  See this blog post
for more detail on why using pylab is a bad idea:

https://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html


On Wed, Jul 30, 2014 at 10:19 AM, Matthew Brett <mat...@gm...>
wrote:

> Hi,
>
> On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> 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).
>
> Sorry for being slightly off-topic, but what is the current
> recommendation then for interactive plots from the console, if --pylab
> is discouraged?
>
> Cheers,
>
> Matthew
>
>
> ------------------------------------------------------------------------------
> 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
>

There is no change to the recommendations for interactive plots from the
console, if by console you mean the normal python REPL. There is no --pylab
for that. If you mean from the IPython console, then it is the cell magic I
mentioned previously.


On Wed, Jul 30, 2014 at 1:19 PM, Matthew Brett <mat...@gm...>
wrote:

> Hi,
>
> On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> 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).
>
> Sorry for being slightly off-topic, but what is the current
> recommendation then for interactive plots from the console, if --pylab
> is discouraged?
>
> Cheers,
>
> Matthew
>

Hi,

On Wed, Jul 30, 2014 at 9:30 AM, Benjamin Root <ben...@ou...> 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).

Sorry for being slightly off-topic, but what is the current
recommendation then for interactive plots from the console, if --pylab
is discouraged?

Cheers,

Matthew

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...> 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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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

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.
>
> I am trying to do some simple array visualizations before moving on to
> specific work.
>
> e.g. I have a 5x5x10 array and I'd like to see each 5x5 piece as a
> "frame" with a short pause in between.  I realize there are animation
> methods and such but I think the  code below ought to work and don't
> understand what I'm getting.
>
> Expect: A figure window with the first 5x5 piece of the array, a short
> pause, a new figure window overwriting the old one with the second 5x5
> piece, and so on. Equivalent code in Matlab does this.
>
> Result:  Figure window opens, nothing gets drawn in it, there's a pause,
> the window closes, and another window opens in the same location with
> nothing in it, and so on.
>
> If I refresh the kernel, create the 3D array, and manually show one
> slice, it works.  As soon as I run the loop, all I get from then on is
> blank windows whether I do it within a loop or type the matshow, show
> commands.
>
> This happens in iPython with and without the notebook interface.
>
> I'm trying to understand Matplotlib in some detail and am watching the
> SciPy2014 videos along with RTFM.
> https://www.youtube.com/watch?v=A2adyFMsut0 et.seq.
>
> So far, I've come up empty in figuring out what I'm doing wrong.
>
> I have Python 2.7.8/Anaconda 2.0.1
>
> Thanks,
>
> JBB
> ===== Test code
>
> import numpy as np
> from matplotlib.pylab import *
> import time as time
>
> # Create a 3D array of "frames"
> A = np.random.rand(5,5,10)
>
> #Turn on interactive mode
> ion()
> # Turn off interactive mode
> # ioff()
>
> # Attempt to show each frame with a short delay between frames
> for k in range(10):
>       matshow(A[:,:,k])
>       show()
>       time.sleep(1)
>       close()
>

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

>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
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> Mat...@li...
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>

Hello,

I am relatively new to Python, numpy, matplotlib, etc., with a 
reasonable amount of Matlab experience.

I am trying to do some simple array visualizations before moving on to 
specific work.

e.g. I have a 5x5x10 array and I'd like to see each 5x5 piece as a 
"frame" with a short pause in between.  I realize there are animation 
methods and such but I think the  code below ought to work and don't 
understand what I'm getting.

Expect: A figure window with the first 5x5 piece of the array, a short 
pause, a new figure window overwriting the old one with the second 5x5 
piece, and so on. Equivalent code in Matlab does this.

Result:  Figure window opens, nothing gets drawn in it, there's a pause, 
the window closes, and another window opens in the same location with 
nothing in it, and so on.

If I refresh the kernel, create the 3D array, and manually show one 
slice, it works.  As soon as I run the loop, all I get from then on is 
blank windows whether I do it within a loop or type the matshow, show 
commands.

This happens in iPython with and without the notebook interface.

I'm trying to understand Matplotlib in some detail and am watching the 
SciPy2014 videos along with RTFM.
https://www.youtube.com/watch?v=A2adyFMsut0 et.seq.

So far, I've come up empty in figuring out what I'm doing wrong.

I have Python 2.7.8/Anaconda 2.0.1

Thanks,

JBB
===== Test code

import numpy as np
from matplotlib.pylab import *
import time as time

# Create a 3D array of "frames"
A = np.random.rand(5,5,10)

#Turn on interactive mode
ion()
# Turn off interactive mode
# ioff()

# Attempt to show each frame with a short delay between frames
for k in range(10):
     matshow(A[:,:,k])
     show()
     time.sleep(1)
     close()

The solution below is maybe not optimal, but it's something you can figure
out easily enough yourself. Also, I believe this question is better asked
on stackoverflow as it is not an actual matplotlib issue, but rather a
programming problem (that shows no effort).

Let me first redefine your matrices to comply with PEP8.

nodes = np.array([[1,2,3,4],[0, 5, 2, 8]])  # What you call Q. The first
node here is (1,0)
connections = np.triu(np.random.rand(4,4))  # What you call Z
connections[0,3] = 0  # Just to make the plot a little more clear.

for row,_ in enumerate(connections):
    for col in range(row+1, connections.shape[0]):
        if connections[row, col]:
            plt.plot(
                nodes[0,[row,col]], nodes[1,[row,col]],
                color='{}'.format(connections[row, col]))  # Uses
gray-scale color-coding
plt.plot(nodes[0,:], nodes[1,:], 'ko ')


2014-07-29 14:18 GMT+02:00 Josè Luis Mietta <jos...@ya...>:

> Hi experts!
>
> I have:
>
> * a list of Q 'NODES'=[(x,y)_1,........, (x,y)_Q], where each element
> (x,y) represent the spatial position of the node in 2D Cartesian space.
> * a matrix 'H' with QxQ elements {H_k,l}.
> H_k,l=0 if nodes 'k' and 'l' aren't joined by a edge, and H_k,l = the length
> of the edge that connects these nodes.
> * a matrix 'Z' with QxQ elements {Z_k,l}.
> Z_k,l=0 if nodes 'k' and 'l' aren't joined by a edge, and Z_k,l =
> intensity_k,l (a intensity scale of the edge, 0<intensity<I-max) if these
> nodes are connected.
>
> I want to draw the nodes in their spatial position, connected by the
> edges, and use a color scale for the 'intensity'.
>
> How must I do that?
>
> Waiting for your answers.
>
> Thanks a lot!
>
> Best regards,
> José Luis
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
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>
>

Hi experts!

I have: 

* a list of Q 'NODES'=[(x,y)_1,........, (x,y)_Q], where each element 
(x,y) represent the spatial position of the node in 2D Cartesian space.
* a matrix 'H' with QxQ elements {H_k,l}. 
H_k,l=0 if nodes 'k' and 'l' aren't joined by a edge, and H_k,l = the length of the edge that connects these nodes.
* a matrix 'Z' with QxQ elements {Z_k,l}. 
Z_k,l=0 if nodes 'k' and 'l' aren't joined by a edge, and Z_k,l = intensity_k,l (a intensity scale of the edge, 0<intensity<I-max) if these nodes are connected.

I want to draw the nodes in their spatial position, connected by the edges, and use a color scale for the 'intensity'.

How must I do that?

Waiting for your answers.

Thanks a lot!

Best regards,
José Luis

No clue. This question has come up from time to time. I recommend using
Nabble to search the archives.


On Mon, Jul 28, 2014 at 2:10 AM, asmwarrior <asm...@gm...> wrote:

> Hi, can any one view the full email achieve for the matplotlib user
> maillist?
> I can only see mails up to year 2012, see image shot here:
>
> http://stackoverflow.com/questions/24971546/why-i-cant-see-all-the-matplotlib-user-maillist-email-achieve-from-sourceforge
> Thank you very much.
>
> asmwarrior(ollydbg)
>
>
> ------------------------------------------------------------------------------
> 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
>

Hi, can any one view the full email achieve for the matplotlib user maillist?
I can only see mails up to year 2012, see image shot here:
http://stackoverflow.com/questions/24971546/why-i-cant-see-all-the-matplotlib-user-maillist-email-achieve-from-sourceforge
Thank you very much.

asmwarrior(ollydbg)

Hi Mike,

I have the same problem and I am interested how dou you solve it.

Regards 

Enzo



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