[Matplotlib-users] basemap-0.9.8 failure, linux
Hi all, Just updated basemap from 0.9.4 to 0.9.8 on Mandriva Linux 2008. I also installed basemap-data-fullres-0.9.7. I've noticed there's a couple of recent posts about problems (on Macs) with 0.9.8, the solution being to install setuptools until 0.9.9 comes along; the problem I have is similar to the posts but not the same, so I'd like to check here before proceeding with setuptools. I installed the included geos-2.2.3, then basemap-0.9.8, then basemap-data-fullres-0.9.7. However when I now import basemap I get: In [1]: from matplotlib.toolkits.basemap import Basemap --- Traceback (most recent call last) /home/emason/python/tools/ in () /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/__init__.py in () > 1 from basemap import __doc__, __version__ 2 from basemap import * /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/basemap.py in () 29 from matplotlib.cbook import is_scalar, dedent 30 from shapelib import ShapeFile ---> 31 import _geos, pupynere 32 33 # basemap data files now installed in lib/matplotlib/toolkits/basemap/data : libgeos_c.so.1: cannot open shared object file: No such file or directory Yet the file, in fact a link, libgeos_c.so.1, does exist at the location (/usr/local/lib) where it is supposed to be: [EMAIL PROTECTED] lib]# ll total 44230 -rw-r--r-- 1 root root 28107924 2007-12-28 16:31 libgeos.a -rw-r--r-- 1 root root 581806 2007-12-28 16:31 libgeos_c.a -rwxr-xr-x 1 root root 830 2007-12-28 16:31 libgeos_c.la* lrwxrwxrwx 1 root root 18 2007-12-28 16:31 libgeos_c.so -> libgeos_c.so.1.1.1* lrwxrwxrwx 1 root root 18 2007-12-28 16:31 libgeos_c.so.1 -> libgeos_c.so.1.1.1* -rwxr-xr-x 1 root root 452162 2007-12-28 16:31 libgeos_c.so.1.1.1* -rwxr-xr-x 1 root root 790 2007-12-28 16:31 libgeos.la* lrwxrwxrwx 1 root root 16 2007-12-28 16:31 libgeos.so -> libgeos.so.2.2.3* lrwxrwxrwx 1 root root 16 2007-12-28 16:31 libgeos.so.2 -> libgeos.so.2.2.3* -rwxr-xr-x 1 root root 13443604 2007-12-28 16:31 libgeos.so.2.2.3* I'd appreciate any help with this. Thanks, Evan - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] power law fitting of data
Hi Johann, I believe the scipy optimization package gives a variety of optimization algorithms but you would have to implement your own codes to fix/thaw parameters. That being said, there is a lot there and I haven't dug into all of it into detail. I would suggest posting a message to the scipy mailing list after the holidays and you may get a better response. Cheers, Jessica On Dec 26, 2007, at 3:52 PM, Johann Cohen-Tanugi wrote: > hi jessica, thanks So scipy.optmizer as it stands cannot do > that? I gues I should move the issue to the scipy list then. Yes > there is mpfit, there is also pyminuit in google.code that is > wrapper of the high energy physics standard package MINUIT, etc > but I would think that fitting data, with fixed/thawed parameters, > is a basic feature of a scientific package. As there seems to be a > snergy between matplotlib and scipy, I would expect the latter to > take care of optimization > thanks for the replies, > Johann > > Jessica Lu wrote: >> Hi Johann, >> >> I would recommend using the python mpfit module: >> >> http://cars9.uchicago.edu/software/python/mpfit.html >> >> Cheers, >> Jessica >> >> On Dec 22, 2007, at 8:57 PM, Johann Cohen-Tanugi wrote: >> >>> hi jessica, >>> This FittingData tutorial is very nice. Could you illustrate how to >>> fix/thaw parameters? >>> I did not find any such attribute and when I try some kludges >>> they fail >>> with a msg saying >>> : shape mismatch: objects cannot be >>> broadcast to a single shape >>> >>> >>> thanks, >>> Johann >>> >>> >>> - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>> http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ >>> ___ >>> Matplotlib-users mailing list >>> Matplotlib-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >>> >> > - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] basemap-0.9.8 failure, linux
Evan Mason wrote:
> Hi all,
>
> Just updated basemap from 0.9.4 to 0.9.8 on Mandriva Linux 2008. I
> also installed basemap-data-fullres-0.9.7. I've noticed there's a
> couple of recent posts about problems (on Macs) with 0.9.8, the
> solution being to install setuptools until 0.9.9 comes along; the
> problem I have is similar to the posts but not the same, so I'd like
> to check here before proceeding with setuptools.
>
> I installed the included geos-2.2.3, then basemap-0.9.8, then
> basemap-data-fullres-0.9.7 . However when I now import basemap I get:
>
> In [1]: from matplotlib.toolkits.basemap import Basemap
> ---
>Traceback (most recent call
> last)
>
> /home/emason/python/tools/ in ()
>
> /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/__init__.py
> in ()
> > 1 from basemap import __doc__, __version__
> 2 from basemap import *
>
> /usr/lib/python2.5/site-packages/matplotlib/toolkits/basemap/basemap.py
> in ()
> 29 from matplotlib.cbook import is_scalar, dedent
> 30 from shapelib import ShapeFile
> ---> 31 import _geos, pupynere
> 32
> 33 # basemap data files now installed in
> lib/matplotlib/toolkits/basemap/data
>
> : libgeos_c.so.1: cannot open shared
> object file: No such file or directory
>
> Yet the file, in fact a link, libgeos_c.so.1, does exist at the
> location (/usr/local/lib) where it is supposed to be:
>
> [EMAIL PROTECTED] lib]# ll
> total 44230
> -rw-r--r-- 1 root root 28107924 2007-12-28 16:31 libgeos.a
> -rw-r--r-- 1 root root 581806 2007-12-28 16:31 libgeos_c.a
> -rwxr-xr-x 1 root root 830 2007-12-28 16:31 libgeos_c.la*
> lrwxrwxrwx 1 root root 18 2007-12-28 16:31 libgeos_c.so ->
> libgeos_c.so.1.1.1*
> lrwxrwxrwx 1 root root 18 2007-12-28 16:31 libgeos_c.so.1 ->
> libgeos_c.so.1.1.1*
> -rwxr-xr-x 1 root root 452162 2007-12-28 16:31 libgeos_c.so.1.1.1*
> -rwxr-xr-x 1 root root 790 2007-12-28 16:31 libgeos.la*
> lrwxrwxrwx 1 root root 16 2007-12-28 16:31 libgeos.so ->
> libgeos.so.2.2.3*
> lrwxrwxrwx 1 root root 16 2007-12-28 16:31 libgeos.so.2 ->
> libgeos.so.2.2.3*
> -rwxr-xr-x 1 root root 13443604 2007-12-28 16:31 libgeos.so.2.2.3*
>
> I'd appreciate any help with this.
>
> Thanks, Evan
Evan: I think this is a LD_LIBRARY_PATH problem. There are two
possible workarounds:
1) set the LD_LIBRARY_PATH environment variable to include
/usr/local/lib, i.e.
export LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"
2) edit setup.py and make the following change
currents_nbp:(basemap_svn)$ svn diff
Index: setup.py
===
--- setup.py(revision 4791)
+++ setup.py(working copy)
@@ -90,7 +90,11 @@
extensions.append(Extension("matplotlib.toolkits.basemap._geod",deps+['src/_geod.c'],include_dirs
= ['src'],))
# for some reason, pickling won't work if this extension is installed
# as "matplotlib.toolkits.basemap._geos"
-extensions.append(Extension("_geos",['src/_geos.c'],library_dirs=geos_library_dirs,include_dirs=geos_include_dirs,libraries=['geos_c','geos']))
+extensions.append(Extension("_geos",['src/_geos.c'],
+library_dirs=geos_library_dirs,
+runtime_library_dirs=geos_library_dirs,
+include_dirs=geos_include_dirs,
+libraries=['geos_c','geos']))
then rebuild. As Eric Firing pointed out to me, adding
runtime_library_dirs negates the need to set LD_LIBRARY_PATH manually.
This is already done in svn, and so 0.9.9 will not require manually
setting LD_LIBRARY_PATH.
HTH,
-Jeff
--
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX: (303)497-6449
NOAA/OAR/PSD R/PSD1Email : [EMAIL PROTECTED]
325 BroadwayOffice : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web: http://tinyurl.com/5telg
-
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Re: [Matplotlib-users] basemap-0.9.8 failure, linux
Thank you Jeff. Setting LD_LIBRARY_PATH works fine as a quick test, though that leads me to the "ImportError: No module named pkg_resources" problem that the other recent posters had. I'll either try setuptools or wait for 0.9.9 to come out - will it be long? -Evan - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] basemap-0.9.8 failure, linux
Evan Mason wrote: > Thank you Jeff. Setting LD_LIBRARY_PATH works fine as a quick test, > though that leads me to the "ImportError: No module named > pkg_resources" problem that the other recent posters had. I'll either > try setuptools or wait for 0.9.9 to come out - will it be long? > > -Evan Evan: Sometime next week probably, If you have svn installed, you can get the latest version that way. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX: (303)497-6449 NOAA/OAR/PSD R/PSD1Email : [EMAIL PROTECTED] 325 BroadwayOffice : Skaggs Research Cntr 1D-124 Boulder, CO, USA 80303-3328 Web: http://tinyurl.com/5telg - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Problems adding arrow to plot
Dear matplotlib colleagues,
I am very new to matplotlib but I have been able to generate the plots I need;
however, I am having trouble annotating a plot with an arrow. Could you help me
with the syntax? Here is the code I am using:
ax.annotate('sol
9',xy=(xMinorLocs[9],0.5),xytext=(xMinorLocs[9],0.8),arrowprops=dict(width=1,
frac=0.1, headwidth=5, facecolor='black'))
when I do that, I get a 'ZeroDivisionError: float division'
As a test, I tried the command without the arrowprops:
ax.annotate('sol 9',xy=(xMinorLocs[9],0.5),xytext=(xMinorLocs[9],0.8))
and I didn't get any errors and the label was plotted (no arrow) at the right
location. How can I get the arrow to show up?
Any help you can provide would be really appreciated.
Thanks and happy Holidays!
Fernando
-
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