matplotlib-users Mailing List for matplotlib

On 4/4/07, Simon Kammerer <sim...@we...> wrote:
> Hi list,
>
> I guess it's not limited to the basemap toolkit, but it fits to explain
> my problem:
>
> I'd like to produce time series with basemap. As drawing coastlines,
> countrys etc. is expensive, but stays the same for every time step, I'd
> like to draw the basemap "background" only once and the reuse I.

This can probably be solved with the copy/blit/animate stuff described
at the end of
http://www.scipy.org/Cookbook/Matplotlib/Animations

Tim Hirzel wrote:
> Its a little tough right now that os x doesn't have one python 
> install to rule them all.

Yes it does.

  http://www.python.org/download/

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco

My understanding is that currently the best way to get all these 
packages (wxpython, matplotlib, numpy, etc) running together on os x is 
via these packages:
http://pythonmac.org/packages/

at least, I can say for sure that the 2.5 builds worked without a hitch 
for me.  Its a little tough right now that os x doesn't have one python 
install to rule them all.  Instead, there are about 5 (not an actual 
count) ways to do it, most with gotchas.
tim


Simson Garfinkel wrote:
> Alas, tried the easy_install matplotlib. It downloaded and installed  
> matplotlib, but didn't install wx, so I got this error:
>
>  >>> from pylab import *;
> Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
> pylab.py", line 1, in <module>
>      from matplotlib.pylab import *
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
> matplotlib/pylab.py", line 222, in <module>
>      new_figure_manager, draw_if_interactive, show = pylab_setup()
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
> matplotlib/backends/__init__.py", line 24, in pylab_setup
>      globals(),locals(),[backend_name])
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
> matplotlib/backends/backend_wxagg.py", line 19, in <module>
>      import wx
> ImportError: No module named wx
>  >>>
>
>
> When I tried to use easy_install to install wxPython, I got this:
>
> Computer:/Users/simsong root# easy_install wxPython
> Searching for wxPython
> Reading http://cheeseshop.python.org/pypi/wxPython/
> Reading http://wxPython.org/
> Reading http://wxPython.org/download.php
> Reading http://cheeseshop.python.org/pypi/wxPython/2.6.3.2
> Best match: wxPython src-2.8.3.0
> Downloading http://prdownloads.sourceforge.net/wxpython/wxPython- 
> src-2.8.3.0.tar.bz2
> Processing wxPython-src-2.8.3.0.tar.bz2
> error: Couldn't find a setup script in /tmp/easy_install-UB-WlK/ 
> wxPython-src-2.8.3.0.tar.bz2
> Computer:/Users/simsong root#
>
> Why do we make this so hard?
>
> The wyPython page for Mac says:
>
> ========
>
> Mac OS X
>
> wxPython needs a special Mac OS X-specific build of Python, called a  
> Framework build, in order to work. Panther and Tiger include a  
> Framework build of Python 2.3, but on Jaguar you'll need to get the  
> MacPython installer from Jack's MacPython page.
> ============
> (I really can't keep track of all these cat names. )
>
> Then I need to choose one of 8 different versions to install,  
> dependin gon whether I am using py2.3, 2.4 or 2.5, and whether I want  
> unicode or ansi, and whether I want PPC or Universal.
>
> But I finally got it installed. Thanks.
>
>
> On Apr 4, 2007, at 7:38 AM, Edin Salkovic wrote:
>
>   
>> On 4/4/07, Simson Garfinkel <si...@ac...> wrote:
>>     
>>> 2. How do I install an EGG file?
>>>       
>> For detailed instructions about eggs see:
>> http://peak.telecommunity.com/DevCenter/EasyInstall
>>
>> Quick instructions:
>> Download:
>> http://peak.telecommunity.com/dist/ez_setup.py
>> and run it.
>>
>> then run
>> easy_install matplotlib
>> or
>> easy_install /path/to/matplotlib-xxx.egg
>>
>>
>> HTH,
>> Edin
>>
>>     
>
>
>
>
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>
>   

Alas, tried the easy_install matplotlib. It downloaded and installed  
matplotlib, but didn't install wx, so I got this error:

 >>> from pylab import *;
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
pylab.py", line 1, in <module>
     from matplotlib.pylab import *
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
matplotlib/pylab.py", line 222, in <module>
     new_figure_manager, draw_if_interactive, show = pylab_setup()
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
matplotlib/backends/__init__.py", line 24, in pylab_setup
     globals(),locals(),[backend_name])
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg/ 
matplotlib/backends/backend_wxagg.py", line 19, in <module>
     import wx
ImportError: No module named wx
 >>>


When I tried to use easy_install to install wxPython, I got this:

Computer:/Users/simsong root# easy_install wxPython
Searching for wxPython
Reading http://cheeseshop.python.org/pypi/wxPython/
Reading http://wxPython.org/
Reading http://wxPython.org/download.php
Reading http://cheeseshop.python.org/pypi/wxPython/2.6.3.2
Best match: wxPython src-2.8.3.0
Downloading http://prdownloads.sourceforge.net/wxpython/wxPython- 
src-2.8.3.0.tar.bz2
Processing wxPython-src-2.8.3.0.tar.bz2
error: Couldn't find a setup script in /tmp/easy_install-UB-WlK/ 
wxPython-src-2.8.3.0.tar.bz2
Computer:/Users/simsong root#

Why do we make this so hard?

The wyPython page for Mac says:

========

Mac OS X

wxPython needs a special Mac OS X-specific build of Python, called a  
Framework build, in order to work. Panther and Tiger include a  
Framework build of Python 2.3, but on Jaguar you'll need to get the  
MacPython installer from Jack's MacPython page.
============
(I really can't keep track of all these cat names. )

Then I need to choose one of 8 different versions to install,  
dependin gon whether I am using py2.3, 2.4 or 2.5, and whether I want  
unicode or ansi, and whether I want PPC or Universal.

But I finally got it installed. Thanks.


On Apr 4, 2007, at 7:38 AM, Edin Salkovic wrote:

> On 4/4/07, Simson Garfinkel <si...@ac...> wrote:
>> 2. How do I install an EGG file?
>
> For detailed instructions about eggs see:
> http://peak.telecommunity.com/DevCenter/EasyInstall
>
> Quick instructions:
> Download:
> http://peak.telecommunity.com/dist/ez_setup.py
> and run it.
>
> then run
> easy_install matplotlib
> or
> easy_install /path/to/matplotlib-xxx.egg
>
>
> HTH,
> Edin
>

On Wed, 2007-04-04 at 16:26 +0200, David Fokkema wrote:
> Hi group,
> 
> I have the following ipython 'session':
> 
> In [23]: data = [0, 0.4, 0.6, 1, 2, 3]
> 
> In [24]: bins = [0, 1, 2, 3]
> 
> In [25]: hist(data, bins, align='edge')
> Out[25]: (array([3, 1, 1, 1]), [0, 1, 2, 3], <a list of 4 Patch
> objects>)
> 
> In [26]: hist(data, bins, align='center')
> Out[26]: (array([3, 1, 1, 1]), [0, 1, 2, 3], <a list of 4 Patch
> objects>)
> 
> 
> I would suspect that the histogram output from 'center' should be [2, 2,
> 1, 1]. Why is this not so? At least, the two should be different? I
> would say that with edge, my bins would be 0-1, 1-2, 2-3, 3-4, and that
> center should give me -0.5-0.5, 0.5-1.5, 1.5-2.5, 2.5-3.5, but this
> seems not to be the case??? Any help understanding this would be greatly
> appreciated!

It seems that the hist function simply calls matplotlib.mlab.hist
without any regard to the bins (be they edge or centered values) and
passes the plotting through to the 'bar' function. This function places
the bar with either the edge at the bin value or the center at the bin
value. If I choose center, the result is that my histogram is calculated
for edge values but the bars are placed at center values which is
completely misleading and wrong! I'd say this is a bug, but I may be
overlooking something here...

Thanks,

David


> 
> Thanks,
> 
> David
> 
> 
> -------------------------------------------------------------------------
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> 

Hi group,

I have the following ipython 'session':

In [23]: data = [0, 0.4, 0.6, 1, 2, 3]

In [24]: bins = [0, 1, 2, 3]

In [25]: hist(data, bins, align='edge')
Out[25]: (array([3, 1, 1, 1]), [0, 1, 2, 3], <a list of 4 Patch
objects>)

In [26]: hist(data, bins, align='center')
Out[26]: (array([3, 1, 1, 1]), [0, 1, 2, 3], <a list of 4 Patch
objects>)


I would suspect that the histogram output from 'center' should be [2, 2,
1, 1]. Why is this not so? At least, the two should be different? I
would say that with edge, my bins would be 0-1, 1-2, 2-3, 3-4, and that
center should give me -0.5-0.5, 0.5-1.5, 1.5-2.5, 2.5-3.5, but this
seems not to be the case??? Any help understanding this would be greatly
appreciated!

Thanks,

David

On 4/4/07, Simson Garfinkel <si...@ac...> wrote:
> 2. How do I install an EGG file?

For detailed instructions about eggs see:
http://peak.telecommunity.com/DevCenter/EasyInstall

Quick instructions:
Download:
http://peak.telecommunity.com/dist/ez_setup.py
and run it.

then run
easy_install matplotlib
or
easy_install /path/to/matplotlib-xxx.egg


HTH,
Edin

Hi list,

I guess it's not limited to the basemap toolkit, but it fits to explain 
my problem:

I'd like to produce time series with basemap. As drawing coastlines, 
countrys etc. is expensive, but stays the same for every time step, I'd 
like to draw the basemap "background" only once and the reuse I.

copy / deepcopy (module copy) the current axes doesn't work:
copy.Error: un(deep)copyable object of type <type 'Affine'>

Creating two identical axes with different label='XXX' doesn't work, 
because contourf will overwrite my background.
Same for adding a subplot to my figure.

Whats the way to "clone" an axes instance (or any other form of my 
background), so I can reuse it after I plotted the first time step and 
then called cla()?


Thanks
Simon

I'm embarrassed to ask that I'm having trouble building/installing  
matplotlib on an intel Mac.

The version at http://matplotlib.sourceforge.net/ wants to give me  
an .egg file for my Mac, and I have yet to figure out how to load and  
install .egg files. (How come python is such a mess?)

So I tried to install with darwinports. Darwinports proceeded to  
upgrade my python from 2.4 to 2.5 (thanks!) and then gave me an error  
installing numeric because the fortran compiler wouldn't build or  
something.

So I manually installed numeric (I don't need fortran support) and  
manually downloaded matplotlib to install with setup.py. But I'm  
getting this error:

building 'matplotlib.backends._tkagg' extension
g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g  
-bundle -undefined dynamic_lookup build/temp.macosx-10.3-fat-2.5/src/ 
_tkagg.o build/temp.macosx-10.3-fat-2.5/CXX/cxx_extensions.o build/ 
temp.macosx-10.3-fat-2.5/CXX/cxxsupport.o build/temp.macosx-10.3- 
fat-2.5/CXX/IndirectPythonInterface.o build/temp.macosx-10.3-fat-2.5/ 
CXX/cxxextensions.o -L/usr/local/lib -L/usr/lib -L/usr/local/lib -L/ 
usr/lib -lpng -lz -lstdc++ -lm -lfreetype -lz -lstdc++ -lm -o build/ 
lib.macosx-10.3-fat-2.5/matplotlib/backends/_tkagg.so -framework Tcl - 
framework Tk
/usr/bin/ld: for/usr/bin/ld: for architecture ppc
/usr/bin/ld: can't locate file for: -lpng
collect2: ld returned 1 exit status
architecture i386
/usr/bin/ld: can't locate file for: -lpng
collect2: ld returned 1 exit status
lipo: can't open input file: /var/tmp//ccl92wxW.out (No such file or  
directory)
error: command 'g++' failed with exit status 1
Computer:/Users/simsong/Desktop/matplotlib-0.90.0 root#


This basically says that it can't build the universal version on my  
mac because I only have intel binaries for libpng, and not universal  
binaries.

I don't need universal binaries; I'm only running on intel.

I'd rather not go down this path, it turns out. It would be a lot  
easier for me just to download binaries.

What I would like to know is:

1. What is the preferred way for installing matplotlib on Mac at this  
point?
2. How do I install an EGG file?

Thanks!

Thanks Jeff, that does what I want. It seems to be efficient, as long as 
you don't try to plot 10.000+ values on a small map (results in a 
colored rectangle anyway...). After thinning out my data

data = data.compress(maskX, axis=1)
data = data.compress(maskY, axis=0)

it seems to be only a little bit slower than contour / contourf.

Simon



Jeff Whitaker schrieb:
> Simon Kammerer wrote:
>> Hi list,
>>
>> what's the best (meaning most efficient/fastest) way to plot grid 
>> point values on a map created with basemap?
>>
>> I'd like to plot the raw values of my data-array to the correspondig 
>> gridpoints, instead of having it transformed to something like contour 
>> or contourf. The ne plus ultra would be the ability to assing a 
>> colormap, to control the font color of the plotted values...
>>
>> Regards
>> Simon
>>
>>   
> 
> Simon:  I don't know about efficiency, but this does what you want:
> 
> from pylab import show, title, arange, figure, title, arccos, pi, cm, 
> text, sqrt
> import random
> from matplotlib.colors import rgb2hex
> from matplotlib.toolkits.basemap import Basemap
> from matplotlib.numerix.random_array import uniform
> 
> # Plot a bunch of randomly distributed points on the earth.
> 
> # set up stereographic map centered on N. Pole.
> m = Basemap(lon_0=-105,boundinglat=30.,resolution='l',
>            area_thresh=10000.,projection='npstere')
> # number of points to plot.
> npts = 300
> # generate random points on a sphere,
> # so that every small area on the sphere is expected
> # to have the same number of points.
> # http://mathworld.wolfram.com/SpherePointPicking.html
> try: # this works for numpy
>    u = uniform(0.,1.,size=npts)
>    v = uniform(0.,1.,size=npts)
>    z = uniform(0,100,size=npts)
> except: # this works for Numeric/numarray
>    u = uniform(0.,1.,shape=npts)
>    v = uniform(0.,1.,shape=npts)
>    z = uniform(0,100,shape=npts)
> lons = 360.*u
> lats = (180./pi)*arccos(2*v-1) - 90.
> # transform lons and lats to map coordinates.
> x,y = m(lons,lats)
> # create a list of strings containing z values
> zn = [ '%2i' % zz for zz in z ]
> # plot numbers on map, colored by value.
> vmin = 0; vmax = 100
> cmap = cm.jet # use 'jet' colormap
> for name,zval,xpt,ypt in zip(zn,z,x,y):
>    # only plot values inside map region.
>    if xpt > m.xmin and xpt < m.xmax and ypt > m.ymin and ypt < m.ymax:
>        rgbcolor = cmap(1.-(zval-vmin)/(vmax-vmin))[:3]
>        hexcolor = rgb2hex(rgbcolor)
>        text(xpt,ypt,name,fontsize=9,weight='bold',color=hexcolor)
> # draw coasts and fill continents.
> m.drawcoastlines(linewidth=0.5)
> m.fillcontinents()
> # draw parallels and meridians.
> delat = 20.
> circles = arange(0.,90.,delat).tolist()+\
>          arange(-delat,-90,-delat).tolist()
> m.drawparallels(circles)
> delon = 45.
> meridians = arange(0,360,delon)
> m.drawmeridians(meridians,labels=[1,1,1,1])
> title('Random Data Value at Random Points',y=1.075)
> show()
> 
> 
> HTH,
> 
> -Jeff
> 
> 
> ------------------------------------------------------------------------
> 

Hi Giorgio,

Had a quick look at pylab based scripts and got an error on 
backend_tkagg when py2exe it.  It looks like one needs to force the 
backend to be included, I used tkagg but you would have to replace that 
with wxagg for your script.

Attached is a setup.py and from the examples the file simple_plot.py.

Werner

Giorgio Luciano ha scritto:
> At first I thought ... hey why people wat an interface, just use the 
> console, and then after listening  to their reason I have to agree.
> What do I generally do ? I have a matrix in txt, I apply my routines (a 
> SVD, a PCA, a filter etc etc  written in python), plot them (using 
> maplotlib) and then I want an output. that's it.
> I started looking at various Qt etc. etc. but for me it's overhelming, 
> because I think that the most important part should be dedicate to the 
> routines creation and not to making a gui, compiling, etc. etc. I need 
> simple command like people wants. grids, paste and copy, small working 
> plots :)
> I mean I can get crazy with setting my program, importing etc. etc. but 
> I also have to say that needs and claim about writing simple guis, 
> common paste and copy etc should be considered from someone there (we 
> wait for the help of some guru that makes things easier ;)

It's quite hard for me to understand what you mean.

Anyway, I solved the issue of usability vs code simplicity for my data 
analysis application by using a mixed CLI+GUI design. That is, I have a 
very simple GUI that just shows the plot and may have some button/menu 
for basic operations, and a custom command line to finely work with it. 
Think of RasMol, for example. The custom command line is done with the 
Python Cmd module that is included with Python, and it's a breeze to 
code with. The GUI uses Matplotlib embedded with wxMPL in a wxPython 
frame. The command line and the GUI are threaded (work on two different 
threads) that communicate by passing events (cli-->gui) and with a Queue 
(gui-->cli): easy.

Anyway, I'd advice you to learn wxPython basics. It's powerful, free, 
multiplatform and it's becoming the default Python GUI toolkit in the 
wild. Learning a GUI toolkit cannot harm. If you can, buy the Robin Dunn 
book "wxPython in Action", it's wonderful to say the least.

m.
-- 
Massimo Sandal
University of Bologna
Department of Biochemistry "G.Moruzzi"

snail mail:
Via Irnerio 48, 40126 Bologna, Italy

email:
mas...@un...

tel: +39-051-2094388
fax: +39-051-2094387

Hi Giorgio,

Giorgio Luciano wrote:
> Hello Werner,
> and thank for the reply I've tried to recompile everything. The file 
> you sent in the mailing list give me the problem of wxmsw26uh_vc.dll 
> (and also dll missing while compiling)
For the wxmsw26uh_vc.dll you need to rename the .pyd file as mentioned 
in the response to Daniel before you py2exe it.

The error output you get when running py2exe is normal, it just tells 
you that there are files not included by py2exe.  You need to decide if 
you need them, if you have the right to distribute them etc and then 
either include them with your installer or add them to the package 
include option for py2exe.
> but then it runs
> when I try to compile my file (nipals) it doesnt' start and give me as 
> error
Sorry, I don't understand why you get the error about backends, but I 
can't run your nipals.py as it contains/uses modules I don't have.

I'll see if I can do a setup.py for a simple matplotlib file using pylab.

Werner

Hi Daniel,

Daniel Stalder wrote:
> Hello
>
> I saw your thread and I have a related problem.
> I use matplotlib (0.90.0.win32-py2.5) with wxPython
> (2.8-win32-unicode-2.8.3.0-py25).
> I use matplotlib with WXAgg and got the following error msg:
> "This application has failed to start because wxmsw26uh_vc.dll was not
> found. Re-installing the application may fix this problem."
>   
Re-install will not help.  The problem is that matplotlib is 
compiled/linked against wxPython 2.6 Unicode.

A work around Andrea Gavana found is to do the following rename, before 
you py2exe the app.

matplotlib/backends/_wxagg.pyd

to

matplotlib/backends/_wxagg not used.pyd


Werner

Hello

I saw your thread and I have a related problem.
I use matplotlib (0.90.0.win32-py2.5) with wxPython
(2.8-win32-unicode-2.8.3.0-py25).
I use matplotlib with WXAgg and got the following error msg:
"This application has failed to start because wxmsw26uh_vc.dll was not
found. Re-installing the application may fix this problem."

The error msg appears on "import _wxagg" in the file backend_wxagg.py

# try to load the WXAgg accelerator
try:
    import _wxagg      >>> the msg appears here
except ImportError:
    _wxagg = None

I already had this problem with previous versions of both libraries.

Thanks for any help
Daniel


-----Original Message-----
From: Werner F. Bruhin [mailto:wer...@fr...] 
Sent: Wednesday, 4 April 2007 2:58 a.m.
To: lu...@di...; matplot
Subject: Re: [Matplotlib-users] matplotlib and py2exe

Hi Giorgio,

Giorgio Luciano wrote:
> Hello Werner,
> here is the file I try to compile.
> It gave an error of missing DLL when i try to launch :(
> no Idea why, since with you example everything works
> (I'm using maplotlib 0.87.7)
I assume the DLL not found is "wxmsw26uh_vc.dll" at least I believe that 
87.7 is already compiled against wxPython 2.6 Unicode (hopefully this 
dependency will go away with some future release of matplotlib), so you 
need to either use the Unicode version of wxPython 2.6 or do the 
following as mentioned earlier in this thread.

matplotlib/backends/_wxagg.pyd

to

matplotlib/backends/_wxagg not used.pyd

If it is another .dll missing it would help if you let us know the name 
and the exact exception.

Werner

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Hi there,

    A few months back, I complained about the slowness of the image 
function in matplotlib. One of the cullprit was a slow clip function; 
I've done a bit some work to improve the situation on numpy's side, 
efforts which were integrated in numpy 1.0.2. Now, when you clip a numpy 
array with scalar min and max values, you get a 5 to 30 fold speed-up; 
to get the maximum efficiency, you need inplace clipping (using the 
syntax a.clip(min, max, a) for a a numpy array). This makes image 
significantly faster (between 100 and 200 ms on recent computers), and I 
am sure in other functionalities of matplotlib as well.
    cheers,

    David

Hi Giorgio,

Giorgio Luciano wrote:
> Hello Werner,
> here is the file I try to compile.
> It gave an error of missing DLL when i try to launch :(
> no Idea why, since with you example everything works
> (I'm using maplotlib 0.87.7)
I assume the DLL not found is "wxmsw26uh_vc.dll" at least I believe that 
87.7 is already compiled against wxPython 2.6 Unicode (hopefully this 
dependency will go away with some future release of matplotlib), so you 
need to either use the Unicode version of wxPython 2.6 or do the 
following as mentioned earlier in this thread.

matplotlib/backends/_wxagg.pyd

to

matplotlib/backends/_wxagg not used.pyd

If it is another .dll missing it would help if you let us know the name 
and the exact exception.

Werner