matplotlib-users Mailing List for matplotlib (Page 13)

per freem <perfreem@...> writes:
> 
> hi all,
> 
> i have a 3x2 subplot figure, and i would like to adjust the relative
> width of the second column. in other words, if i have:
> 
I set the axes positions by hand in these situations using add_axes(). So:
fig = plt.figure()
width1 = 0.3
width2 = 0.2
height = 0.75 / 3
left = 0.1
bottom = 0.15
axes_column0 = []
for i in range(3):
 axes_column0.append(fig.add_axes([left, bottom + i*height, width1, 
 height]))
axes_column1 = []
for i in range(3):
 axes_column1.append(fig.add_axes([left+width1, bottom + i*height, 
 width2, height]))
axes_column2 = []
for i in range(3):
 axes_column2.append(fig.add_axes([left+width1+width2, bottom + i*height, 
 width1, height]))
You can adjust this slightly if you want to put gaps between the subplots, 
or otherwise use axes.set_yticklabels([]) (for example) to get rid of 
unwanted tick labels.
Plot to each of the subplots using something like:
axes_column0[1].plot(x,y)
Neil

Thanks,
I thougth that this could be the problem. Actually i fixed it by myself.
Thanks anyway.
Cheers
Davide

Hi Per,
You need 2*N, not N*2 arrays here. I think you're also trying to use 
absolute values so you probably need something like this:
plt.errorbar([1,2,3],[1,2,3],yerr=np.abs(a.T-[1,2,3]))
I hope this is what you're after,
Gary R.
per freem wrote:
> hi all,
> 
> i am trying to plot asymmetric yaxis error bars. i have the following code:
> 
> import matplotlib.pyplot as plt
> a = array([[ 0.5, 1.5],
> [ 0.7, 2.2],
> [ 2.8, 3.1]])
> plt.errorbar([1,2,3],[1,2,3],yerr=a)
<snip>

I was able to get it working on my home machine, but can't get it installed
on my webhost. I get this error when I try to import the module:
--------------------------------------
Python 2.6 (r26:66714, Apr 30 2009, 20:04:43) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
(InteractiveConsole)
>>> from mpl_toolkits.basemap import Basemap
/home/nbv4/lib/python2.6/dbflib/dbflib.py:2: RuntimeWarning: Python C API
version mismatch for module dbflibc: This Python has API version 1013,
module dbflibc has version 1012.
 import dbflibc
/home/nbv4/lib/python2.6/shapelib/shapelib.py:2: RuntimeWarning: Python C
API version mismatch for module shapelibc: This Python has API version 1013,
module shapelibc has version 1012.
 import shapelibc
Traceback (most recent call last):
 File "<console>", line 1, in <module>
 File "/home/nbv4/lib/python2.6/mpl_toolkits/basemap/__init__.py", line 43,
in <module>
 import _geoslib, netcdftime
ImportError: /home/nbv4/lib/python2.6/_geoslib.so: undefined symbol:
PyUnicodeUCS4_DecodeUTF8
---------------------------------------
Any ideas as to what may be causing this?
-- 
View this message in context: http://www.nabble.com/can%27t-get-basemap-working%3A-undefined-symbol%3A-PyUnicodeUCS4_DecodeUTF8-tp25420971p25420971.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

hi all,
i am trying to plot asymmetric yaxis error bars. i have the following code:
import matplotlib.pyplot as plt
a = array([[ 0.5, 1.5],
 [ 0.7, 2.2],
 [ 2.8, 3.1]])
plt.errorbar([1,2,3],[1,2,3],yerr=a)
where each element in the list represents the -yerror, +yerror, like
the documentation for plt.errorbar asks for. when i try to plot this,
i get the following error:
/Library/Python/2.5/site-packages/matplotlib/axes.pyc in vlines(self,
x, ymin, ymax, colors, linestyles, label, **kwargs)
 3271
 3272 verts = [ ((thisx, thisymin), (thisx, thisymax))
-> 3273 for thisx, (thisymin,
thisymax) in zip(x,Y)]
 3274 #print 'creating line collection'
 3275 coll = mcoll.LineCollection(verts, colors=colors,
ValueError: too many values to unpack
any idea what's causing this?
the only way it lets me plot is if i do:
plt.errorbar([1,2,3],[1,2,3],yerr=[a[:, 0], a[:, 1]])
which is not the intended result, since the first column in a is the
-yerror and the second is +yerror. does anyone know how to fix this?
thank you.

On 09/11/2009 10:51 PM, Michael Droettboom wrote:
> The log doesn't show any actual plotting. Did you run the same example
> with debug-annoying turned on? Turning debugging on shouldn't change
> any behavior -- only output more debugging information to the console.
There seems to be something really, really wrong here. As running the
_same_ example with debug-annoying turned on just terminates the
execution at:
backend Agg version v2.2
backend_agg.new_figure_manager
-- 
Regards,
Kamran Riaz Khan.
http://inspirated.com/

davide lasagna <las...@gm...> writes:
> gcc: error trying to exec 'cc1plus': execvp: No such file or directory
Sounds like you don't have a complete g++ install. Since you mentioned
Ubuntu, I suppose the command you need to run is
 sudo apt-get install build-essential g++
and perhaps also
 sudo apt-get build-dep python-matplotlib
to install all the dependencies.
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Hi everybody,
I have a problem in building matplotlib from svn sources. Here is the output
of the build process.
#######################################################################################
smif1984@ubuntu [14:11:05] ~/cvs/matplotlib :sudo python setupegg.py develop
============================================================================
BUILDING MATPLOTLIB
 matplotlib: 1.0.svn
 python: 2.6.2 (release26-maint, Apr 19 2009, 01:56:41) [GCC
 4.3.3]
 platform: linux2
REQUIRED DEPENDENCIES
 numpy: 1.2.1
 freetype2: 9.20.3
OPTIONAL BACKEND DEPENDENCIES
 libpng: 1.2.27
 Tkinter: no
 * TKAgg requires Tkinter
 wxPython: 2.8.9.1
 * WxAgg extension not required for wxPython >= 2.8
 pkg-config: looking for pygtk-2.0 gtk+-2.0
 * Package pygtk-2.0 was not found in the pkg-config
 * search path. Perhaps you should add the directory
 * containing `pygtk-2.0.pc' to the PKG_CONFIG_PATH
 * environment variable No package 'pygtk-2.0' found
 * You may need to install 'dev' package(s) to
 * provide header files.
 Gtk+: no
 * Could not find Gtk+ headers in any of
 * '/usr/local/include', '/usr/include', '.'
 Mac OS X native: no
 Qt: no
 Qt4: no
 Cairo: 1.4.12
OPTIONAL DATE/TIMEZONE DEPENDENCIES
 datetime: present, version unknown
 dateutil: matplotlib will provide
 pytz: 2008c
OPTIONAL USETEX DEPENDENCIES
 dvipng: 1.11
 ghostscript: 8.64
 latex: 3.141592
 pdftops: 0.10.5
[Edit setup.cfg to suppress the above messages]
============================================================================
pymods ['pylab']
packages ['matplotlib', 'matplotlib.backends', 'matplotlib.projections',
'matplotlib.testing', 'matplotlib.testing.jpl_units', 'matplotlib.tests',
'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid',
'matplotlib.sphinxext', 'matplotlib.numerix', 'matplotlib.numerix.mlab', '
matplotlib.numerix.ma', 'matplotlib.numerix.linear_algebra',
'matplotlib.numerix.random_array', 'matplotlib.numerix.fft',
'matplotlib.delaunay', 'dateutil', 'dateutil/zoneinfo']
running develop
running egg_info
writing lib/matplotlib.egg-info/PKG-INFO
writing namespace_packages to lib/matplotlib.egg-info/namespace_packages.txt
writing top-level names to lib/matplotlib.egg-info/top_level.txt
writing dependency_links to lib/matplotlib.egg-info/dependency_links.txt
writing entry points to lib/matplotlib.egg-info/entry_points.txt
reading manifest template 'MANIFEST.in'
warning: no files found matching 'MANIFEST'
warning: no files found matching 'examples/data/*'
warning: no files found matching 'lib/mpl_toolkits'
writing manifest file 'lib/matplotlib.egg-info/SOURCES.txt'
running build_ext
building 'matplotlib.ft2font' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -DPY_ARRAYAUNIQUE_SYMBOL=MPL_ARRAY_API
-I/usr/lib/python2.6/dist-packages/numpy/core/include
-I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I.
-I/usr/include/python2.6 -c src/ft2font.cpp -o
build/temp.linux-i686-2.6/src/ft2font.o
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
#############################################################################################
Any help is appreciated.
Cheers
Davide

Thanks, work like a charm.
On Sat, Sep 12, 2009 at 4:06 PM, Gary Ruben <gr...@bi...> wrote:
> gray() sets the default colormap for raster-based plot commands like
> imshow(), matshow() and figimage(). For scatter(), you need to set the
> colors of plot elements invidually. Setting the facecolor in the scatter()
> command will work for the example you tried:
>
> scatter(x,y,s=area, marker='^', facecolor=(.7,.7,.7), c='r')
>
> Gary R.
>
>
> lotrpy wrote:
>
>> Hello, Sorry for my broken english. I copy the source code from
>>
>> http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_demo.html
>> Just Insert one line "gray()" before the last line "show()".
>> But the picture is sitll colorful. not a gray picture.
>> It there somethig I missed. Thanks in advance.
>>
>

gray() sets the default colormap for raster-based plot commands like 
imshow(), matshow() and figimage(). For scatter(), you need to set the 
colors of plot elements invidually. Setting the facecolor in the 
scatter() command will work for the example you tried:
scatter(x,y,s=area, marker='^', facecolor=(.7,.7,.7), c='r')
Gary R.
lotrpy wrote:
> Hello, Sorry for my broken english. I copy the source code from
> http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_demo.html
> 
> Just Insert one line "gray()" before the last line "show()".
> But the picture is sitll colorful. not a gray picture.
> It there somethig I missed. Thanks in advance.

I think this was fixed in 0.99 by the removal of a call to
processEvents, which was causing segfaults in other contexts.
On Fri, Sep 11, 2009 at 6:32 PM, <lau...@gm...> wrote:
> Hi Darren,
>
> Thanks for your answer.
> ... I've updated to matplotlib 0.99 since the last email... and the bug
> disappeared :)
> Must be a bug of previous version since I had ever added a layout to the
> central widget!
>
> Thanks anyway for your help!
>
>> On Fri, Sep 11, 2009 at 5:52 PM, Laurent Dufrechou
>>
>> lau...@gm...> wrote:
>>
>> > Hello,
>>
>> >
>>
>> > I face a very boring problem.
>>
>> > Here is a little modified pyqt widget example found on matplotlib
>> > website.
>>
>> > Basicaly I've just added a tab widget and inside it a matplotlib widget.
>>
>> >
>>
>> > Sadly, on creation the widget don't get the full size of the PA_tab
>> > widget
>>
>> > :(
>>
>> > BUT once I resize manually the app all became OK...
>>
>> >
>>
>> > To be honest I've got NO idea of what is the problem :(
>>
>> >
>>
>> > Any direction highly appreciated!
>>
>>
>>
>> Try adding a layout to the central widget and adding your tab widget
>>
>> to that layout.
>>
>>
>>
>> Darren
>>
> ------------------------------------------------------------------------------
> 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
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> _______________________________________________
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>
-- 
"In our description of nature, the purpose is not to disclose the real
essence of the phenomena but only to track down, so far as it is
possible, relations between the manifold aspects of our experience" -
Niels Bohr
"It is a bad habit of physicists to take their most successful
abstractions to be real properties of our world." - N. David Mermin
"Once we have granted that any physical theory is essentially only a
model for the world of experience, we must renounce all hope of
finding anything like the correct theory ... simply because the
totality of experience is never accessible to us." - Hugh Everett III

Hi Darren,
Thanks for your answer.
... I've updated to matplotlib 0.99 since the last email... and the bug 
disappeared :)
Must be a bug of previous version since I had ever added a layout to the 
central widget!
Thanks anyway for your help!
> On Fri, Sep 11, 2009 at 5:52 PM, Laurent Dufrechou
> lau...@gm...> wrote:
> > Hello,
> >
> > I face a very boring problem.
> > Here is a little modified pyqt widget example found on matplotlib 
> website.
> > Basicaly I've just added a tab widget and inside it a matplotlib widget.
> >
> > Sadly, on creation the widget don't get the full size of the PA_tab 
> widget
> > :(
> > BUT once I resize manually the app all became OK...
> >
> > To be honest I've got NO idea of what is the problem :(
> >
> > Any direction highly appreciated!
> Try adding a layout to the central widget and adding your tab widget
> to that layout.
> Darren

Hello,
I face a very boring problem.
Here is a little modified pyqt widget example found on matplotlib website.
Basicaly I've just added a tab widget and inside it a matplotlib widget.
Sadly, on creation the widget don't get the full size of the PA_tab widget
:(
BUT once I resize manually the app all became OK...
To be honest I've got NO idea of what is the problem :(
Any direction highly appreciated!
Laurent
matplotlib:
__version__ = '0.98.5.2'
And pyqt: 4.4.3.6

n.l.o wrote:
> Im a bit confused of how I should use the "quiver" plotting function.
> 
> My data is 2D, a 512x512 data array, where every entry is an angle
> (polarimetry).
> I also have an array with the degree of polarization which would be nice to
> colour-code in to the arrows.
> So:
> How do I use my angles to control the direction of the arrows, and how do I
> get values to control the colour of the arrows?
> 
> Cheers,
> Magnus
> 
Example with ipython -pylab:
x = arange(4)
y = arange(5)
X, Y = meshgrid(x, y)
u = ones_like(X)
v = zeros_like(X)
c = arange(u.size) # values mapped to colors
angles = (X * 20 + Y * 20).ravel()
quiver(X, Y, u, v, c, angles=angles)
axis([-1, 4, -1, 5])
The .ravel() of the angles is to get around a bug that I fixed a few 
minutes ago in svn.
Eric

hi all,
i have the following simple plot using the 'errorbars' function. when
i plot it, one of the error bars is cut off:
from numpy import *
from scipy import *
from mpl_toolkits.axes_grid.axislines import SubplotZero
fig = plt.figure()
ax = SubplotZero(fig, 3, 2, 1)
fig.add_subplot(ax)
ax.axis["xzero"].set_visible(True)
for k in ["bottom", "top", "right"]:
 ax.axis[k].set_visible(False)
m = array([0.8382035000000001, 0.81685835000000007])
sd = array([0.18543833, 0.12603507])
lw = 1.2
msize = 3
plt.errorbar([1, 2], m, yerr=sd, fmt='-s', markersize=msize, linewidth=lw)
tm = .8
lower_y = max(tm-.2, 0)
upper_y = min(tm+.4, 1)
ytickvals = arange(lower_y, upper_y + .1, .1)
plt.xlim([0, 3])
plt.yticks(ytickvals)
plt.ylim([lower_y, upper_y])
plt.savefig('test.pdf')
when i plot it, the top error bar of the first data point gets cut
off. this error bar should be at location:
0.8382035000000001+0.18543833 which slightly exceeds the ylimit of 1.
since the y value here is a probability, i dont want the plot to have
labels on it that exceed 1, since that does not make sense. is there
any way to allow more room for the y axis without plotting values
greater than 1? this is only for the purpose of errorbars. again,
these data were just various probabilities, and so they never exceed
1.
thanks.

hi all,
i have a 3x2 subplot figure, and i would like to adjust the relative
width of the second column. in other words, if i have:
import matplotlib.pyplot as plt
plt.subplot(3, 2, 1)
# plot stuff
plt.subplot(3, 2, 2)
# plot, etc...
i want to make it so the second column occupies less width in the
figure than the first column. for example, i want the series of
subplots in the first column to take up 70% of the figure, and the
subplots in the second column to take up only 30%. is there a way to
do this?
i looked into plt.subplots_adjust but i do not know how to use that
function to get this desired effect.
thanks.

The log doesn't show any actual plotting. Did you run the same example 
with debug-annoying turned on? Turning debugging on shouldn't change 
any behavior -- only output more debugging information to the console.
Cheers,
Mike
Kamran Riaz Khan wrote:
> On 09/11/2009 07:28 PM, Michael Droettboom wrote:
> 
>> Can you add
>>
>> "verbose.level : debug-annoying"
>>
>> to your ~/.matplotlib/matplotlibrc file and send us the output produced?
>>
>> FWIW, I just tested the matplotlib package on FC11 and it seems to work
>> fine on my system, so it's possibly a configuration issue.
>>
>> You might want to try removing for font cache file in:
>>
>> ~/.matplotlib/fontList.cache
>> 
>
> Thanks for the quick reply. I deleted the fontList.cache file and added
> verbose.level : debug-annoying to my matplobrc file. The next run of
> pyplot example gave me:
>
> http://pastebin.com/f6d783aec
>
> The plot didn't appear but I guess that's the default behavior of
> verbose level option. I removed the debug-annoying and reran the example
> which in turn gave me the same image output as before.
>
> 
>> Kamran Riaz Khan wrote:
>> 
>>> Matplotlib's built-in mathematical expression parser produces garbage
>>> output for math text:
>>>
>>> http://img3.imageshack.us/img3/8194/matplotlibmathtext.png
>>>
>>> I'm using the distribution packages from Fedora 11. I guess there's an
>>> issue with the fonts on my system but I can't figure out how to proceed
>>> with pinpointing the issue.
>>>
>>> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Dave wrote:
>
> I resolved the issue by compiling matplotlib from source on my windows box 
> which I'm happy to report wasn't too difficult! It seems to work for my usual
> interactive use however it segfaults when running the tests :|
>
> http://pastebin.com/m5ee30885
> 
Thanks for running this. To my knowledge, you're the first one to run 
the new test infrastructure on Windows, so congratulations. :)
(I presume you erased the MPL/build directory before compiling to clear 
out any cruft in there.)
Anyhow, I have no clue what's going on. Is there any way you can get a 
stack trace? And why do you say segfault -- did Windows pop up a dialog? 
What did it say?
One of these days I will try to get a Windows buildslave for the MPL 
buildbot,
-Andrew

Hi
Where can I download current mpl documentation in HTML format? Because
there is now way to build it under win32

On 09/11/2009 07:28 PM, Michael Droettboom wrote:
> Can you add
> 
> "verbose.level : debug-annoying"
> 
> to your ~/.matplotlib/matplotlibrc file and send us the output produced?
> 
> FWIW, I just tested the matplotlib package on FC11 and it seems to work
> fine on my system, so it's possibly a configuration issue.
> 
> You might want to try removing for font cache file in:
> 
> ~/.matplotlib/fontList.cache
Thanks for the quick reply. I deleted the fontList.cache file and added
verbose.level : debug-annoying to my matplobrc file. The next run of
pyplot example gave me:
http://pastebin.com/f6d783aec
The plot didn't appear but I guess that's the default behavior of
verbose level option. I removed the debug-annoying and reran the example
which in turn gave me the same image output as before.
> Kamran Riaz Khan wrote:
>> Matplotlib's built-in mathematical expression parser produces garbage
>> output for math text:
>>
>> http://img3.imageshack.us/img3/8194/matplotlibmathtext.png
>>
>> I'm using the distribution packages from Fedora 11. I guess there's an
>> issue with the fonts on my system but I can't figure out how to proceed
>> with pinpointing the issue.
>>
-- 
Kamran Riaz Khan.
http://inspirated.com/

Can you add
"verbose.level : debug-annoying"
to your ~/.matplotlib/matplotlibrc file and send us the output produced?
FWIW, I just tested the matplotlib package on FC11 and it seems to work 
fine on my system, so it's possibly a configuration issue.
You might want to try removing for font cache file in:
~/.matplotlib/fontList.cache
Mike
Kamran Riaz Khan wrote:
> Matplotlib's built-in mathematical expression parser produces garbage
> output for math text:
>
> http://img3.imageshack.us/img3/8194/matplotlibmathtext.png
>
> I'm using the distribution packages from Fedora 11. I guess there's an
> issue with the fonts on my system but I can't figure out how to proceed
> with pinpointing the issue.
>
> Regards,
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi list,
I need to plot a barchart with dates on X-axis and values on Y-axis. This barchart must show the presence or absence of some factors in a some time. I try to use the "barchart_demo.py" as example, but in my case (X-values are dates in datetime format) this not quite fit.
I want to get something like attached example. Is this possible? Which type of graphs (hist, bar...) and how I need to use?
Thanks,
 Alexander
-- 
Alexander Bruy
mailto: ale...@gm...

Must be something about asking the right question... 
This works perfectly.
For those interested, my code is now as: 
 dmn = 0.00001
 dmx = 1000000
 logspace = 10.**np.linspace(dmn, dmx, 100) 
 clevs = logspace
 colmap = pyplot.get_cmap('gist_ncar')
 im =
m.imshow(topodat,cmap=colmap,norm=LogNorm(vmin=clevs[0],vmax=clevs[-1]))
 ## CREATE COLORBAR 
 ## make a copy of the image object
 ## use non normalized colormap 
 im2 = copy.copy(im)
 im2.set_cmap(colmap)
 ## create new axis for colorbar.
 cax = pyplot.axes([l+w+0.025, b, 0.025, h]) # setup colorbar axes
 ## using im2, not im (hack to prevent colors from being
 ## too compressed at the low end on the colorbar - results
 ## from highly nonuniform colormap)
 pyplot.colorbar(im2, cax, format='%3.2g') # draw colorbar
 ## reset colorbar tick labels
 clabels = clevs[::10]
 clabels.append(clevs[-1])
 cax.set_yticks(np.linspace(0,1,len(clabels)))
 cax.set_yticklabels(['%3.2g' % cl for cl in clabels])
 ## make the original axes current again
 pyplot.axes(ax) 
-- 
View this message in context: http://www.nabble.com/logarithmic-colormaps-for-imshow-tp25392480p25397260.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Eric Firing <efiring@...> writes:
> 
> Dave wrote:
> > I upgraded my numpy to 1.4.0.dev7375 and scipy to 0.8.0.dev5920. After 
> > doing so I get a segfault upon calling the plot command (see below)
> 
> What happens if you simply do
> 
> x = randn(100) 
>
> or
>
> plot([1,2,3,2,1])
> 
> 
> My guess is that you are seeing a numpy installation problem, not a 
> matplotlib problem (that is, I expect the first trial above to fail and 
> the second to succeed), and that the problem may be that you did not 
> delete the build directory before rebuilding numpy from source. 
> Distutils often fails to rebuild components that need to be recompiled 
> after a change to the source, so the build and install appear to work, 
> but the resulting numpy (or matplotlib, for that matter) does not.
> 
> Eric
> 
I initially had problems with numpy/scipy as I forgot to delete the build
directories. After doing so & recompiling they both passed all tests (barring
some known issues with windows & arctan -
http://article.gmane.org/gmane.comp.python.numeric.general/31967)
x = randn(100) worked fine and returned expected results for .mean() and .std()
the segfault only occurred upon calling the plot(x).
I resolved the issue by compiling matplotlib from source on my windows box 
which I'm happy to report wasn't too difficult! It seems to work for my usual
interactive use however it segfaults when running the tests :|
http://pastebin.com/m5ee30885
HTH,
Dave

Im a bit confused of how I should use the "quiver" plotting function.
My data is 2D, a 512x512 data array, where every entry is an angle
(polarimetry).
I also have an array with the degree of polarization which would be nice to
colour-code in to the arrows.
So:
How do I use my angles to control the direction of the arrows, and how do I
get values to control the colour of the arrows?
Cheers,
Magnus
-- 
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