matplotlib-users Mailing List for matplotlib

This was originally a much longer message with a great deal of context, 
but I'm going to make it a lot shorter as a series of questions in the 
hopes of getting a Socratic dialog going?
1. Is anyone else bothered by the fact that imshow(array) displays 
array[i,j] at Cartesian coordinates [j,shape(array)[0]-i] if origin is 
'upper' and at [j,i] if origin is 'lower'?
2. In light of the above, how do you handle overlaying contours on an 
image? I see by experiment that contour(array) also treats array[i,j] 
the same way as imshow.
3. Are the astronomers as confused by all of this in relation to the 
FITS WCS standard as I seem to be? How do I do the computation 
correctly so that x[i,j] is the first WCS coordinate of FITS pixel (i,j) 
(which is at array[j-1,i-1] after a PyFITS read)?

John Hunter wrote:
> Another option would be to use one of the precompiled matplotlib
> packages that have freetype statically compiled in. I think Charles
> Moad has been working on this.
Actually that's me. Charles' approach links matplotlib against a 
Framework build of freetype.
In either case, my concern is that if PYGTK and matplotlib use a 
different freetype, there could be problems. My goal ,in the past was to 
build an Apple-centric matplotlib, and I've kept a fink-free system, and 
never used PyGTK, so I don't know if there's a conflict there or not.
In general, GTK is kind of non-apple-y, so I tell folks that want to use 
it to go an all-fink or all darwinports route, which would mean a 
different python, and who knows what freetype lib, but I'm sure fink and 
darwinports have figured that out.
I know I couldn't figure out Apple's freetype, it seemed to have a 
totally different versioning system that what I found in sourceforge, 
and what the matplotlib expect.
>>E.g., perhaps I should install freetype into some location not on
>>the usual search paths, and direct matplotlib to look in that place. 
>>Is there a way to do this that doesn't require manually hacking
>>matplotlib every time I download a new version?
Well, what I'm doing is putting the static libs inside the matplotlib 
source tree.
> - 'darwin' : ['/sw/lib/freetype219', '/usr/local', '/usr', '/sw', '/usr/X11R6'],
> + 'darwin' : ['/sw/', '/usr'],
I'm hoping to be able to do is patch the setup.py so that it would build 
the statically linked libs by default, if they were there. It would be 
nice to have a whatever is in the official matplotlib source tarball 
just build properly out of the box. I"m open to suggestions as to how to 
do this.
One problem is that Python report the system as "darwin", but this could 
be Apple's Python, an Framework or non-framework build of the tarball 
python, fink python, darwinports python, etc. They're all darwin, but 
they all have different library and linking needs.
I'm going to plug away, and hopefully have a static build by the end of 
the day (Pacific Time), but it wont' include PYGTK. I'd love it if 
someone else would try building it my way, but adding PyGTK.
Another note: John suggested that we might want to do what he does on 
Windows and include the freetype and libpng code in the matplotlib 
source tree, and just have it automatically build and link static 
versions right there, with nothing else to download and install. Would 
this end up conflicting with the libs used by PyGTK (or wxPython or...)
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
 		
NOAA/OR&R/HAZMAT (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chr...@no...

Tom Loredo <lo...@as...> writes:
> E.g., perhaps I should install freetype into some location not on
> the usual search paths, and direct matplotlib to look in that place. 
> Is there a way to do this that doesn't require manually hacking
> matplotlib every time I download a new version?
The add_ft2font_flags function in setupext.py is quite enthusiastic
about using every copy of freetype it can find anywhere. I used to
have some build problems since I have one version of freetype from
fink in /sw, another from Gerben Wierda's TeX installer in /usr/local,
and of course one from Apple in /usr/X11R6; somehow a wrong header
file must have gotten included, since I got really strange errors in
the link phase. What I do now is apply the following patch before
building matplotlib, so this solution ranks just a notch above
"manually hacking". I suppose the right solution would be to hack
setup.py to call freetype-config at a configurable path, but this is
good enough for me...

John wrote:
> I use matplotlib with GTK on OSX 10.3 with freetype, gtk and mpl
> installed from src. I did this once a while ago and have had no
> trouble. Perhaps if you install freetype first, and then compile gtk
> against that it will work ok. I know this is easier said than done,
> since compiling gtk from src is a commitment.
Strange. Do you have pygtk working? I've been building gtk from
source. As I noted, I finally got it to build with freetype
in /usr/local, but only with certain CPP and LD flags set. But
I haven't been able to get pygtk to work. It builds fine, but
gives a bus error on import.
> Another option would be to use one of the precompiled matplotlib
> packages that have freetype statically compiled in. I think Charles
> Moad has been working on this.
I'm just a "use the source, Luke" kind of guy, I guess....
Thanks for the further input,
Tom

>>>>> "Tom" == Tom Loredo <lo...@as...> writes:
 Tom> Thanks for the quick feedback; I suspected as much. Can
 Tom> anyone suggest a way to use freetype to build matplotlib so
 Tom> that the freetype doesn't affect all the other stuff that
 Tom> likes to see Apple's X11 freetype? E.g., perhaps I should
 Tom> install freetype into some location not on the usual search
 Tom> paths, and direct matplotlib to look in that place. Is there
 Tom> a way to do this that doesn't require manually hacking
 Tom> matplotlib every time I download a new version? Surely I'm
 Tom> not the only person using both matplotlib and GTK stuff....
I use matplotlib with GTK on OSX 10.3 with freetype, gtk and mpl
installed from src. I did this once a while ago and have had no
trouble. Perhaps if you install freetype first, and then compile gtk
against that it will work ok. I know this is easier said than done,
since compiling gtk from src is a commitment.
Another option would be to use one of the precompiled matplotlib
packages that have freetype statically compiled in. I think Charles
Moad has been working on this.
JDH

Charlie noted:
> 	I don't know of anyone who has successfully compiled against Apple's
> freetype that is part of the X11SDK. I suggest that /usr/X11R6 be
> removed from the darwin list in setup.py.
Thanks for the quick feedback; I suspected as much. Can anyone
suggest a way to use freetype to build matplotlib so that the
freetype doesn't affect all the other stuff that likes to
see Apple's X11 freetype? E.g., perhaps I should install
freetype into some location not on the usual search paths, and
direct matplotlib to look in that place. Is there a way to 
do this that doesn't require manually hacking matplotlib
every time I download a new version? Surely I'm not the only
person using both matplotlib and GTK stuff....
-Tom

	I don't know of anyone who has successfully compiled against Apple's
freetype that is part of the X11SDK. I suggest that /usr/X11R6 be
removed from the darwin list in setup.py.
- Charlie
Tom Loredo wrote:
> Hi folks-
> 
> I've been building matplotlib from source for quite a while,
> and with no problem once I installed the required libs
> into /usr/local (first via the i-Installer, more recently
> from source). I'm currently using matplotlib-0.80.
> 
> Cutting to the chase: Is it possible to build matplotlib using
> Apple's freetype? Motivation/issues:
> 
> Recently I needed to install gtk+-2.4 on my Mac (to run gEDA). It
> looked easy---several sites describe the process (e.g., the GIMP
> site and the ApnaOpus site at apnaopus.var.cc), the usual
> series of ./configure-make-make install steps. But it proved
> a bit of a trial. After much poking around on the net and
> a lot of trial and error, I finally got gtk to install by
> removing freetype2 from its various /usr/local locations.
> Apparently a conflict between this freetype and Apple's
> (under /usr/X11R6/) led to my difficulties (things built fine,
> but running gtk-demo would give a Bus error).
> 
> Of course, this broke matplotplib, but this was fixed by
> reinstalling freetype into /usr/local and rebuilding matplotlib.
> 
> Yesterday I tried upgrading to gtk+-2.6 and building pygtk.
> I thought I'd try to get it to work *without* removing freetype
> from /usr/local. More googling and trial and error led me to
> build with these flags:
> 
> % setenv CPPFLAGS "-no-cpp-precomp"
> % setenv LDFLAGS "-bind_at_load"
> % setenv PKG_CONFIG_PATH /usr/local/geda/lib/pkgconfig:/usr/X11R6/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
> 
> This got gtk to build with freetype left in place; gtk-demo runs
> fine this way. However, pygtk won't run. It builds and installs
> (I have to manually copy the package and modules to /Library/...),
> but I get a bus error on import. I notice when it builds that
> it uses -I/usr/X11R6/include/freetype2. So I'm wondering if
> a freetype conflict is again the problem. Next I'll try moving
> the freetype stuff in /usr/local.
> 
> In the meantime---is it possible to build matplotlib using
> Apple's freetype? I'm guessing that if I could get rid of
> freetype in /usr/local, I'd be able to build gtk and pygtk
> as easily as the GIMP and ApnaOpus (etc.) people do....
> 
> Thanks,
> Tom
> 
> 
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>>>>> "William" == William Henney <wh...@gm...> writes:
 William> Hi, I was trying to install the latest matplotlib from
 William> source on an ancient RH9 system but I get the following
 William> compilation error:
 William> building 'matplotlib._na_cntr' extension gcc -DNDEBUG -O2
 William> -g -pipe -march=i386 -mcpu=i686 -D_GNU_SOURCE -fPIC -
 William> fPIC -I/usr/local/include -I/usr/include
 William> -I/usr/include/python2.2 -c src/_na_cntr.c -o
 William> build/temp.linux-i686-2.2/_na_cntr.o -DNUMARRAY=1
 William> src/_na_cntr.c:1698: parse error before "init_na_cntr"
 William> error: command 'gcc' failed with exit status 1
 William> Any advice would be greatly appreciated - I can't even
 William> find the file _na_cntr.c that triggers the error....
 William> The gcc version is 3.2.2 if that matters.
What is your python version? It looks like the macro PyMODINIT_FUNC
is not being found. This is defined in pyport.h in python2.4, but you
probably have a much older python installed. The reason you cannot
find _na_cntr.c is that it is autogenerated to support Numeric or
numarray at compile time. The src dile is src/cntr.c. In that file,
try replacing
PyMODINIT_FUNC 
 
 with 
extern "C" void
 or perhaps
DL_EXPORT(void)
and let me know if this helps
JDH

Hi folks-
I've been building matplotlib from source for quite a while,
and with no problem once I installed the required libs
into /usr/local (first via the i-Installer, more recently
from source). I'm currently using matplotlib-0.80.
Cutting to the chase: Is it possible to build matplotlib using
Apple's freetype? Motivation/issues:
Recently I needed to install gtk+-2.4 on my Mac (to run gEDA). It
looked easy---several sites describe the process (e.g., the GIMP
site and the ApnaOpus site at apnaopus.var.cc), the usual
series of ./configure-make-make install steps. But it proved
a bit of a trial. After much poking around on the net and
a lot of trial and error, I finally got gtk to install by
removing freetype2 from its various /usr/local locations.
Apparently a conflict between this freetype and Apple's
(under /usr/X11R6/) led to my difficulties (things built fine,
but running gtk-demo would give a Bus error).
Of course, this broke matplotplib, but this was fixed by
reinstalling freetype into /usr/local and rebuilding matplotlib.
Yesterday I tried upgrading to gtk+-2.6 and building pygtk.
I thought I'd try to get it to work *without* removing freetype
from /usr/local. More googling and trial and error led me to
build with these flags:
% setenv CPPFLAGS "-no-cpp-precomp"
% setenv LDFLAGS "-bind_at_load"
% setenv PKG_CONFIG_PATH /usr/local/geda/lib/pkgconfig:/usr/X11R6/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
This got gtk to build with freetype left in place; gtk-demo runs
fine this way. However, pygtk won't run. It builds and installs
(I have to manually copy the package and modules to /Library/...),
but I get a bus error on import. I notice when it builds that
it uses -I/usr/X11R6/include/freetype2. So I'm wondering if
a freetype conflict is again the problem. Next I'll try moving
the freetype stuff in /usr/local.
In the meantime---is it possible to build matplotlib using
Apple's freetype? I'm guessing that if I could get rid of
freetype in /usr/local, I'd be able to build gtk and pygtk
as easily as the GIMP and ApnaOpus (etc.) people do....
Thanks,
Tom

Hi,
I was trying to install the latest matplotlib from source on an 
ancient RH9 system but I get the following compilation error:
building 'matplotlib._na_cntr' extension
gcc -DNDEBUG -O2 -g -pipe -march=i386 -mcpu=i686 -D_GNU_SOURCE -fPIC - 
fPIC -I/usr/local/include -I/usr/include -I/usr/include/python2.2 -c 
src/_na_cntr.c -o build/temp.linux-i686-2.2/_na_cntr.o -DNUMARRAY=1
src/_na_cntr.c:1698: parse error before "init_na_cntr"
error: command 'gcc' failed with exit status 1
Any advice would be greatly appreciated - I can't even find the file 
_na_cntr.c that triggers the error....
The gcc version is 3.2.2 if that matters.
Cheers
Will

Michael Twomey wrote:
> AFAIK matplotlib will find fink's freetype automatically when
> building, if you install fink from http://fink.sourceforge.net/ and
> install freetype219 ("$ fink install freetype219"), then rebuild
> matplotlib all should be well.
You have a couple other options as well:
darwinports freetype ( I haven't used it, but it should exist)
the freetype tarball.
I ready-to-go binary installer. There is an older one at 
pythonmac.org/packages, and I'm in the process of building some newer 
ones. I've enclosed my instructions on how to build them here, if you 
want to do it yourself. If you find anything errors, or things that need 
clarifying, please let me know. It is a draft, so don't be too critical.
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
 		
NOAA/OR&R/HAZMAT (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chr...@no...

Hi,
I am using pylab to plot several graphs. One graph appears in one class where I
do the following:
plot_date(date, y, 'g-o')
savefig(path, dpi=75)
Later on, in a different class, I do the a similar call:
plot_date(d, z, 'b-')
savefig(path, dpi=75)
My problem is that the second call to plot_date simply appends the new line to
the original graph and I am not sure why since the new graph also has new axis
and a new label.
It seems that the problem can be solved by calling hold(False) after plotting
the first line. Yet, I would think that when I call the plot command in a
separate class and set up the axis labels, etc. that it would automatically
create a new set of axis, not append to the existing saved file.
Is there something I should know? I would appreciate any feedback on this matter.
Thanks,
Maria Khomenko
University of Toronto, Argon Team

Hi,
(I am assuming you've built your own copy of matplotlib)
This usually happens when matplotlib's ft2font.so links against OS X's
copy of freetype, instead of a newer copy (which you have to install).
The copy of freetype with OS X is too old to figure out some of the
newer fonts (especially asian ones) installed on OS X.
You can verify that it is linked against
/usr/X11R6/lib/libfreetype.6.dylib using:
$ otool -L /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/=
site-packages/matplotlib/ft2font.so
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag=
es/matplotlib/ft2font.so:
 /opt/local/lib/libfreetype.6.dylib (compatibility version
10.0.0, current version 10.7.0)
...
(In my case I've linked against darwinports' freetype)
AFAIK matplotlib will find fink's freetype automatically when
building, if you install fink from http://fink.sourceforge.net/ and
install freetype219 ("$ fink install freetype219"), then rebuild
matplotlib all should be well.
Michael
On 6/14/05, Brice Thurin <B.P...@ci...> wrote:
> I've just finished to install matplotlib on mac os X panther and when I
> try to import pylab, i have got the following error:
>=20
> Traceback (most recent call last):
> File "<stdin>", line 1, in ?
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/pylab.py", line 1, in ?
> from matplotlib.pylab import *
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/pylab.py", line 195, in ?
> from axes import Axes, PolarAxes
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/axes.py", line 14, in ?
> from axis import XAxis, YAxis
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/axis.py", line 21, in ?
> from font_manager import FontProperties
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/font_manager.py", line 982, in ?
> fontManager =3D FontManager()
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/font_manager.py", line 826, in __init__
> rebuild()
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/font_manager.py", line 819, in rebuild
> self.ttfdict =3D createFontDict(self.ttffiles)
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/font_manager.py", line 458, in createFontDict
> prop =3D ttfFontProperty(font)
> File
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/matplotlib/font_manager.py", line 271, in ttfFontProperty
> sfnt =3D font.get_sfnt()
> RuntimeError: No SFNT name table
>=20
>=20
> Could anyone help with this issue? Many thanks
>=20
> Brice
>=20
>=20
>=20
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>

I've just finished to install matplotlib on mac os X panther and when I 
try to import pylab, i have got the following error:
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/pylab.py", line 1, in ?
 from matplotlib.pylab import *
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/pylab.py", line 195, in ?
 from axes import Axes, PolarAxes
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/axes.py", line 14, in ?
 from axis import XAxis, YAxis
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/axis.py", line 21, in ?
 from font_manager import FontProperties
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 982, in ?
 fontManager = FontManager()
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 826, in __init__
 rebuild()
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 819, in rebuild
 self.ttfdict = createFontDict(self.ttffiles)
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 458, in createFontDict
 prop = ttfFontProperty(font)
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 271, in ttfFontProperty
 sfnt = font.get_sfnt()
RuntimeError: No SFNT name table
Could anyone help with this issue? Many thanks
Brice
Brice Thurin
Department of Optometry and Visual Science
City University, Northampton Square
London, EC1V 0HB, UK.
http://www.city.ac.uk/optometry/Luis/myresearch/Research/ 
scatteringproper.html
http://www.sharpeye.org/
Tel: +44 (0)20 7040 4157
Fax: +44(0)20 7040 8355
e-mail: B.P...@ci...

I've just finished to install matplotlib on mac os X panther and when I 
try to import pylab, i have got the following error:
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/pylab.py", line 1, in ?
 from matplotlib.pylab import *
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/pylab.py", line 195, in ?
 from axes import Axes, PolarAxes
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/axes.py", line 14, in ?
 from axis import XAxis, YAxis
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/axis.py", line 21, in ?
 from font_manager import FontProperties
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 982, in ?
 fontManager = FontManager()
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 826, in __init__
 rebuild()
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 819, in rebuild
 self.ttfdict = createFontDict(self.ttffiles)
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 458, in createFontDict
 prop = ttfFontProperty(font)
 File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/matplotlib/font_manager.py", line 271, in ttfFontProperty
 sfnt = font.get_sfnt()
RuntimeError: No SFNT name table
Could anyone help with this issue? Many thanks
Brice

On Tuesday 14 June 2005 00:56, Sebastian Haase wrote:
> Hi,
> using generators the fuction would go like this:
> def subplots(numRows,numCols):
> cnt = 0
> for i in range(numRows):
> for j in range(numCols):
> cnt+=1
> ax=subplot(numRows,numCols,cnt)
> yield ax
>
> right ?
>
> - Sebastian
Yes, exactly. I'd be interested in 
having your opinion on the convenience of this vs the standard use of 
subplot()...
cheers,
nicolas