matplotlib-users Mailing List for matplotlib

Thanks for all the suggestions,
for future reference here's a summary of my results producing
various kinds of quicktime compatible videos from matplotlib.
I used Ubuntu Jaunty and had the medibuntu codecs installed.
The target audience is undergraduates, so straightforward is
good.

Executive summary:
either MOV or mjpeg work with quicktime 7.6.2 as-is.  Ogg-vorbis
is the compression winner, so requiring that students
install vlc is another option for large animations.

1) MOV

ffmpeg -r 60 -i shum%05d.png -vcodec libx264 -b 2000k out.mov

http://clouds.eos.ubc.ca/~phil/video/samples/out.mov
size: 0.9 Mbytes
note: works with my (patient) colleague's stock QT 7.6.2

2) FLV

ffmpeg -r 60 -i shum%05d.png -vcodec libx264 -b 2000k out.flv

http://clouds.eos.ubc.ca/~phil/video/samples/out.flv
size: 0.9 Mbytes
note: Safari tried to open this as a text file

3) WMV2:

ffmpeg -r 60 -i shum%05d.png -vcodec wmv2 -b 2000k out.avi
http://clouds.eos.ubc.ca/~phil/video/samples/out.avi
size: 1.1 Mbytes
note:  no luck getting quicktime to recognize this, even
        after we installed the codecs from
 
http://www.microsoft.com/windows/windowsmedia/player/wmcomponents.mspx

4) jpeg:

mencoder -nosound -ovc lavc \
         -lavcopts vbitrate=5000:vcodec=mjpeg \
         -mf type=png:fps=15 -o  moviejpeg.avi mf://\*.png -v
http://clouds.eos.ubc.ca/~phil/video/samples/moviejpeg.avi
size: 5.7 Mbytes
note: works, although not svelt

5) ogv

ffmpeg2theora --nosound --optimize --width 800 --height 600 
--inputfps=15 --aspect 4:3 shum%05d.png -o movie.ogv

http://clouds.eos.ubc.ca/~phil/video/samples/movie.ogv
size: 0.33 Mbytes (!)
note: we followed the install instructions at 
http://www.theora.org/downloads/
       but Safari didn't recognize the ogv suffix, and didn't
       offer to associate it with a player

On Fri, Sep 4, 2009 at 10:11 AM, Westly Ward<son...@gm...> wrote:
> Hi. I need some help creating a 3d wireframe in matplotlib in python. Here
> is my code.
>
> Code:
> from __future__ import division
> import matplotlib.pyplot as plt
> from numpy import *
>
> fig = plt.figure()
> from mpl_toolkits.mplot3d import Axes3D
> ax = Axes3D(fig)
> xlist = []
> ylist = []
> zlist = []
> for x in range(1, 100) :
>    for y in range(1, 100) :
>        xlist.append(x)
>        ylist.append(y)
>        zlist.append(x/y)
> numpyx = array(xlist)
> numpyy = array(ylist)
> numpyz = array(zlist)
> ax.plot_wireframe(numpyx, numpyy, numpyz)
> ax.set_xlabel('X Label')
> ax.set_ylabel('Y Label')
> ax.set_zlabel('Z Label')
> plt.show()
>
>
> Traceback (most recent call last):
>  File "C:\Users\Westly\Desktop\3dimage.py", line 19, in <module>
>    ax.plot_wireframe(numpyx, numpyy, numpyz)
>  File "C:\Python25\Lib\site-packages\mpl_toolkits\mplot3d\axes3d.py", line
> 684, in plot_wireframe
>    rows, cols = Z.shape
> ValueError: need more than 1 value to unpack
>
> How exactly do I give it my arrays?
> Thanks in advance for any help.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
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> _______________________________________________
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>
>

how about:

from __future__ import division
import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
from mpl_toolkits.mplot3d import Axes3D
ax = Axes3D(fig)

ys, xs = np.mgrid[1:100, 1:100]

ax.plot_wireframe(xs, ys, xs/ys)
plt.show()

Hi. I need some help creating a 3d wireframe in matplotlib in python. Here
is my code.

Code:
from __future__ import division
import matplotlib.pyplot as plt
from numpy import *

fig = plt.figure()
from mpl_toolkits.mplot3d import Axes3D
ax = Axes3D(fig)
xlist = []
ylist = []
zlist = []
for x in range(1, 100) :
   for y in range(1, 100) :
       xlist.append(x)
       ylist.append(y)
       zlist.append(x/y)
numpyx = array(xlist)
numpyy = array(ylist)
numpyz = array(zlist)
ax.plot_wireframe(numpyx, numpyy, numpyz)
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
plt.show()


Traceback (most recent call last):
 File "C:\Users\Westly\Desktop\3dimage.py", line 19, in <module>
   ax.plot_wireframe(numpyx, numpyy, numpyz)
 File "C:\Python25\Lib\site-packages\mpl_toolkits\mplot3d\axes3d.py", line
684, in plot_wireframe
   rows, cols = Z.shape
ValueError: need more than 1 value to unpack

How exactly do I give it my arrays?
Thanks in advance for any help.

In [162]: print "$\beta$"
eta$

In [163]: print r"$\beta$"
$\beta$

use the raw sting for math expression.
Regards,

-JJ


On Fri, Sep 4, 2009 at 12:06 PM, Nicolas
Chopin<nic...@br...> wrote:
>  Hi list,
> when I do:
> hist(randn(100)); xlabel('$\gamma$')
> things work as expected.
> However, if I try:
> hist(randn(100)); xlabel('$\beta$')
> then either I get an error, or I get the label "eta" under the plot.
> Other letters seem to trigger this: tau, alpha, rho, maybe others.
> This problems wether text.usetex is set to True or not (in matplolibrc file).
>
> Version: 0.98.5.2 (Ubuntu Jaunty, ipython 0.9.1 shell).
>
> Has anyone had the same problem, and is there any fix?
> Sorry if this has been reported before, I tried to find it, but
> nothing came out.
>
> Thanks in advance
>
> --
> ________________________________________________________
> Nicolas Chopin
> ENSAE
> 3, Avenue Pierre Larousse
> 92245 Malakoff CEDEX
> FRANCE
> tel +33 1 41 17 65 22 | fax +33 1 41 17 38 52
> http://www.crest.fr/pageperso/Nicolas.Chopin/Nicolas.Chopin.htm
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

  Hi list,
when I do:
hist(randn(100)); xlabel('$\gamma$')
things work as expected.
However, if I try:
hist(randn(100)); xlabel('$\beta$')
then either I get an error, or I get the label "eta" under the plot.
Other letters seem to trigger this: tau, alpha, rho, maybe others.
This problems wether text.usetex is set to True or not (in matplolibrc file).

Version: 0.98.5.2 (Ubuntu Jaunty, ipython 0.9.1 shell).

Has anyone had the same problem, and is there any fix?
Sorry if this has been reported before, I tried to find it, but
nothing came out.

Thanks in advance

-- 
________________________________________________________
Nicolas Chopin
ENSAE
3, Avenue Pierre Larousse
92245 Malakoff CEDEX
FRANCE
tel +33 1 41 17 65 22 | fax +33 1 41 17 38 52
http://www.crest.fr/pageperso/Nicolas.Chopin/Nicolas.Chopin.htm

Hi,

I have found a bug that might or might not be related to my setup,  
when building matplotlib from svn:
When building I get the following error:
In file included from src/ft2font.h:13,
                  from src/ft2font.cpp:1:
/usr/local/include/ft2build.h:56:38: error: freetype/config/ 
ftheader.h: No such file or directory
--------
I can solve this problem by making a soft link from /usr/local/include/ 
freetype2/freetype to /usr/local/include/. It doesnt seem to know that  
there is a freetype2 directory and then a freetype directory.

I hope that helps
      Wolfgang

Le jeudi 03 septembre 2009 à 20:16 -0500, John Hunter a écrit :
> On Thu, Sep 3, 2009 at 8:04 PM, Alan G Isaac<ala...@gm...> wrote:
> > The default download from the Matplotlib page
> > link to http://sourceforge.net/projects/matplotlib/
> > which once again highlights basemap.  (I think
> > this was fixed at one point.)
> 
> I'm not seeng this, nor am I seeing basemap settings in the File
> Manager which would trigger this.  Of course, the default download is
> platform specific, which may be why I am not seeing this, so please
> give us as much info as possible about your platform (mainly the OS)
> 
> When I click on the green download button at
> http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
> redirected to the mpl 0.99 OSX download::
> 
>   https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx10.5.dmg/download

Strangely, the green button points to
http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx-10.3-i386.egg/download
when I browse on a linux (debian) machine with epiphany (which uses
gecko, the firefox engine). Why macosx ?

-- 
Fabrice Silva
Laboratory of Mechanics and Acoustics - CNRS
31 chemin Joseph Aiguier, 13402 Marseille, France.

Dear all,

I recently cried for help (see below) but sadly didn't get any answer... This problem is really a bottleneck for me and if I must find a solution... Can anyone PLEAAAAAAAAASE point me in the right direction ? 

I recently bumped into a problem while trying to display
imshow images (2048x2048 pix) in a GUI based on TkAgg (matplotib0.91.2,
python 2..4..4, numpy1.0.4). In brief, building the image with imshow is
Ok, but the call to show() or draw() takes about 1.2 s on my system
(XP, 2.8Ghz, 2Go ram). After reading a lot of posts and trying out a
few things, I turned to the Animation_blit_tk.py example and modified
it accordingly (code attached below). In the end, the display is still
not much faster using this method (still in the order of 1.2 s as
indicated by the result below).
Could any one tel me whether I'm doing something wrong ? 

As
far as I understand, at least in my Tk GUI, the limiting step using the
ImageTk.FigureCanvasTkAgg is the call to draw() or draw_artist(). I
read some comments from John regarding TkAgg being slow in some cases
but couldn't find a definite answer.

Any hint would be much appreciated....

Cheers,

Aure


--------
# For detailed comments on animation and the techniqes used here, see
# the wiki entry http://www.scipy.org/Cookbook/Matplotlib/Animations

import matplotlib
matplotlib.use('TkAgg')

import sys
import pylab as p
#import matplotlib.numerix as nx
import time

from FileUtils10 import fileHandling

# for profiling
tstart = time.time()
tprevious = time.time()

fnamelist = ['fname1','fname2','fname3']

ax = p.subplot(111)
canvas = ax.figure.canvas

print 't1 ',time.time()-tprevious
tprevious = time.time()

# create the initial line
dataarr = fileHandling(fnamelist[0]).readSpecial()
#print dataarr.dtype        =>   numpy dtype uint16
#dataarr = dataarr.astype('uint8')
print 't2 ',time.time()-tprevious
tprevious = time.time()

image = p.imshow(dataarr, animated=True)
print 't3 ',time.time()-tprevious
tprevious = time.time()

def run(*args):
    tprevious = time.time()
    background = canvas.copy_from_bbox(ax.bbox)
    print 't4 ',time.time()-tprevious
    tprevious = time.time()
    while 1:
        #print fnamelist[run.cnt]
        # restore the clean slate background
        canvas.restore_region(background)
        print 't5 ',time.time()-tprevious
        tprevious = time.time()
        # update the data
        dataarr = fileHandling(fnamelist[run.cnt]).readSpecial()
        print 't6 ',time.time()-tprevious
        tprevious = time.time()
        image.set_data(dataarr)
        print 't7 ',time.time()-tprevious
        tprevious = time.time()
        # just draw the animated artist
        ax.draw_artist(image)
        print 't8 ',time.time()-tprevious
        tprevious = time.time()
        # just redraw the axes rectangle
        canvas.blit(ax.bbox)
        print 't9 ',time.time()-tprevious
        tprevious = time.time()

        if fnamelist[run.cnt] == fnamelist[-1]:
            # print the timing info and quit
            print 'total time:' , time.time()-tstart
            print 'FPS:' , 1000./(time.time()-tstart)
            p.close('all')
            sys.exit()

        run.cnt += 1
run.cnt = 0


p.subplots_adjust(left=0.3, bottom=0.3) # check for flipy bugs
p.grid() # to ensure proper background restore
manager = p.get_current_fig_manager()
manager.window.after(100, run)

p.show()


====
Results in:

t1  0.858999967575
t2  0.0320000648499
t3  1.31299996376
t4  0.0
t5  0.0
t6  0.0310001373291
t7  0.0
t8  1.18700003624
t9  0.0160000324249
t5  0.0
t6  0.0469999313354
t7  0.0
t8  1.17200016975
t9  0.0149998664856
t5  0.0
t6  0.047000169754
t7  0.0
t8  1.21899986267
t9  0.0
t5  0.0
t6  0.0460000038147
t7  0.0
t8  1.17199993134
t9  0.0
t5  0.0
t6  0.0469999313354
t7  0.0
t8  1.18700003624
t9  0.0160000324249
total time: 8.75
FPS: 114.285714286


      

Hi,

I have the following code:

    pylab.pcolormesh(data, multialignment='center')
    xlocs, xlabels = pylab.xticks(range(0, data.shape[1]+1), xlabels)
    pylab.setp(xlabels, 'rotation', 70)
    pylab.colorbar()
    pylab.show()

where data is a 2D numpy array containing some masked values and
'xlabels' is - originally - a list of strings for the xlabels.

This gives me two problems:
- The "column" on the right is shown as blank, although this column has
valid data and
- the labels aren't placed below the center of a field, but below the
xticks. I would like to have them centered, below a field, as the ticks
are merely separators and not associated with any unit.

TIA
Christian

Phil Austin wrote:
> Andrew Straw wrote:
>   
>> I use::
>>
>>  ffmpeg -r 60 -i frame%05d.png -vcodec wmv2 -b 2000k out.avi
>>
>>     
>
> That's encouraging, thanks.  I tried this and produced
>
> http://clouds.eos.ubc.ca/~phil/video/out.avi
>
> Just to confirm: the two OSX users down the hall get a "missing
> components" message from quicktime when they click on this file in
> firefox or safari, and
> are sent to a page that gives an undifferentiated list of extra codecs
> (divx, etc.).
Hmm. It plays fine on QuickTime 7.6.2 on Mac OS X 10.5.7 using Firefox 
3.5.2 for me. I don't remember installing any extra codecs for wmv, but 
I do remember installing the Theora codec.
>   Do I need to tell them to install something like
> http://www.microsoft.com/windows/windowsmedia/player/wmcomponents.mspx
> or am I still missing some proprietary codec on my end?  I'm happy to
> post the detailed ffmpeg output if it would provide any clues.
>   
Hmm, come to this of it, that does look familiar. I think I installed it 
at one point.

A colleague of mine managed to get .avi files with an mpeg4 codec 
variant encoded using ffmpeg or mencoder on linux that played in Mac and 
Windows versions of Adobe Reader and in the linux video players. I don't 
know whether this also required an additional codec.

Apple seems to push the h264 codec, so maybe that would be the best bet 
on Mac?


-Andrew

Hi Matthias ,

thanks a lot for your explanations. They were very useful.

Vicent

-- 
Share what you know, learn what you don't.

> 2009/9/3 Dave Draper <dd...@wi...>:
> Scott,
>
> Have you done any plots using boxplot?
>
> I am having an issue with the xaxis and trying to change the Date Formatter…
>
> Thanks,
>
> David

Hi David,

Please post questions to the mailing list, if you can clarify what
issues you are having (with a stand alone example) then I'm sure
you'll get help.

I guess you can specify the labels directly using something like:

import matplotlib.pyplot as plt
from matplotlib.dates import date2num

# dates is a sequence of datetime.datetime objects
# x is as per boxplot docstring

fig = plt.figure()
ax = fig.add_subplot(111)
ax.boxplot(x, positions=date2num(dates))

xlabels = []
for dt in dates:
    xlabels.append(dt.strftime('%Y/%m/%d/%H:00'))

ax.xaxis.set_ticklabels(xlabels)

If you want to use date formatters it looks like you might need to add
a second axis using twinx. Perhaps there is a better way?

Cheers,
Scott

I should mention that I tested 32 bit

On Thu, Sep 3, 2009 at 11:59 PM, Alan G Isaac <ala...@gm...> wrote:

> John Hunter wrote:
> > I'm not seeng this, nor am I seeing basemap settings in the File
> > Manager which would trigger this.  Of course, the default download is
> > platform specific, which may be why I am not seeing this, so please
> > give us as much info as possible about your platform (mainly the OS)
> >
> > When I click on the green download button at
> > http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
> > redirected to the mpl 0.99 OSX download:
>
>
> Windows Vista 64bit.
> I see
>
> http://sourceforge.net/projects/matplotlib/files/matplotlib-toolkits/basemap-0.99.4/basemap-0.99.4.win32-py2.6.exe/download
>
> Alan Isaac
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

John Hunter wrote:
> I'm not seeng this, nor am I seeing basemap settings in the File
> Manager which would trigger this.  Of course, the default download is
> platform specific, which may be why I am not seeing this, so please
> give us as much info as possible about your platform (mainly the OS)
>
> When I click on the green download button at
> http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
> redirected to the mpl 0.99 OSX download:


Windows Vista 64bit.
I see
http://sourceforge.net/projects/matplotlib/files/matplotlib-toolkits/basemap-0.99.4/basemap-0.99.4.win32-py2.6.exe/download

Alan Isaac

I saw this for windows when I was downloading .99.  I just checked again in
Vista--I believe it did the same thing in XP
Cheers,
William

On Thu, Sep 3, 2009 at 9:16 PM, John Hunter <jd...@gm...> wrote:

> On Thu, Sep 3, 2009 at 8:04 PM, Alan G Isaac<ala...@gm...> wrote:
> > The default download from the Matplotlib page
> > link to http://sourceforge.net/projects/matplotlib/
> > which once again highlights basemap.  (I think
> > this was fixed at one point.)
>
> I'm not seeng this, nor am I seeing basemap settings in the File
> Manager which would trigger this.  Of course, the default download is
> platform specific, which may be why I am not seeing this, so please
> give us as much info as possible about your platform (mainly the OS)
>
> When I click on the green download button at
> http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
> redirected to the mpl 0.99 OSX download::
>
>
> https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx10.5.dmg/download
>
> JDH
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Thu, Sep 3, 2009 at 8:04 PM, Alan G Isaac<ala...@gm...> wrote:
> The default download from the Matplotlib page
> link to http://sourceforge.net/projects/matplotlib/
> which once again highlights basemap.  (I think
> this was fixed at one point.)

I'm not seeng this, nor am I seeing basemap settings in the File
Manager which would trigger this.  Of course, the default download is
platform specific, which may be why I am not seeing this, so please
give us as much info as possible about your platform (mainly the OS)

When I click on the green download button at
http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
redirected to the mpl 0.99 OSX download::

  https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx10.5.dmg/download

JDH

The default download from the Matplotlib page
link to http://sourceforge.net/projects/matplotlib/
which once again highlights basemap.  (I think
this was fixed at one point.)

fwiw,
Alan Isaac