matplotlib-users Mailing List for matplotlib (Page 2)

>>>>> "JUAN" == JUAN ERNESTO FLORES BELTRAN <jua...@ho...> writes:

    JUAN> Hi you all, I am trying to get the mouse location in
    JUAN> coordenates, i have been able to get the X and Y position in
    JUAN> pixels however getting the location in coordinates has not
    JUAN> been possible. My code as follows:

    JUAN> self.figura = Figure(figsize=(8,4), facecolor=0.99, dpi=70,
    JUAN> frameon=True) self.vista=self.figura.add_subplot(111)
    JUAN> self.canvas = FigureCanvasGTK(self.figura)
    JUAN> self.canvas.connect("button_press_event", self.location)

You want matplotlib events, not gtk events

self.canvas.mpl_connect("button_press_event", self.location)
            ^^^^

JDH

Hi you all,

I am trying to get the mouse location in coordenates, i have been able to 
get the X and Y position in pixels however getting the location in 
coordinates has not been possible. My code as follows:

-----------------------------------------------------------------------------------------------------------
self.figura = Figure(figsize=(8,4), facecolor=0.99, dpi=70, frameon=True)
self.vista=self.figura.add_subplot(111)
self.canvas = FigureCanvasGTK(self.figura)
self.canvas.connect("button_press_event", self.location)
-----------------------------------------------------------------------------------------------------------
def location(self,widget, event):
   print event.x, event.y
-----------------------------------------------------------------------------------------------------------


however when i try:
-----------------------------------------------------------------------------------------------------------
def location(self,widget, event):
   print event.x, event.y
-----------------------------------------------------------------------------------------------------------

i do get the folowing:

AttributeError: xdata

Any sugestion to get the xdata value??

Thanks for your answers, any help highly appretiated

Juan

Seems the last email didn't deliver the attachement (even though I =20
received it back?)

The attachment is here again but just in case, here's the code as =20
plain text:

#!/usr/bin/env python

#
# ported fnnls.m to fnnls.py
#
# gjok - 20050816
#

import sys, math
import numpy, numpy.linalg.linalg as la

def any(X)     : return len(numpy.nonzero(X)) !=3D 0
def find(X)    : return numpy.nonzero(X)
def norm(X, d) : return max(numpy.sum(abs(X)))

#
# x, w =3D fnnls(XtX, Xty, tol)
#
def fnnls(XtX, Xty, tol =3D 0) :
#FNNLS	Non-negative least-squares.
#
# 	Adapted from NNLS of Mathworks, Inc.
#          [x,w] =3D nnls(X, y)
#
#	x, w =3D fnnls(XtX,Xty) returns the vector X that solves x =3D =
pinv(XtX)=20
*Xty
#	in a least squares sense, subject to x >=3D 0.
#	Differently stated it solves the problem min ||y - Xx|| if
#	XtX =3D X'*X and Xty =3D X'*y.
#
#	A default tolerance of TOL =3D MAX(SIZE(XtX)) * NORM(XtX,1) * =
EPS
#	is used for deciding when elements of x are less than zero.
#	This can be overridden with x =3D fnnls(XtX,Xty,TOL).
#
#	[x,w] =3D fnnls(XtX,Xty) also returns dual vector w where
#	w(i) < 0 where x(i) =3D 0 and w(i) =3D 0 where x(i) > 0.
#
#	See also NNLS and FNNLSb

#	L. Shure 5-8-87
#	Revised, 12-15-88,8-31-89 LS.
#	(Partly) Copyright (c) 1984-94 by The MathWorks, Inc.

#	Modified by R. Bro 5-7-96 according to
#       Bro R., de Jong S., Journal of Chemometrics, 1997, 11, 393-401
# 	Corresponds to the FNNLSa algorithm in the paper
#=09
#	Rasmus bro
#	Chemometrics Group, Food Technology
#	Dept. Dairy and Food Science
#	Royal Vet. & Agricultural
#	DK-1958 Frederiksberg C
#	Denmark
#	rb...@kv...
#	http://newton.foodsci.kvl.dk/users/rasmus.html
#  Reference:
#  Lawson and Hanson, "Solving Least Squares Problems", Prentice-=20
Hall, 1974.
#

# initialize variables
     m =3D XtX.shape[0]
     n =3D XtX.shape[1]

     if tol =3D=3D 0 :
         eps =3D 2.2204e-16
         tol =3D 10 * eps * norm(XtX,1)*max(m, n);
     #end

     P =3D numpy.zeros(n, numpy.Int16)
     P[:] =3D -1
     Z =3D numpy.arange(0,n)

     z =3D numpy.zeros(m, numpy.Float)
     x =3D numpy.array(P)
     ZZ =3D numpy.array(Z)

     w =3D Xty - numpy.dot(XtX, x)

   # set up iteration criterion
     iter =3D 0
     itmax =3D 30 * n

   # outer loop to put variables into set to hold positive coefficients
     while any(Z) and any(w[ZZ] > tol) :
         wt =3D w[ZZ].max()
         t =3D find(w[ZZ] =3D=3D wt)
         t =3D t[-1:][0]
         t =3D ZZ[t]
         P[t] =3D t
         Z[t] =3D -1
         PP =3D find(P !=3D -1)

         ZZ =3D find(Z !=3D -1)
         if len(PP) =3D=3D 1 :
             XtyPP =3D Xty[PP]
             XtXPP =3D XtX[PP, PP]
             z[PP] =3D XtyPP / XtXPP
         else :
             XtyPP =3D numpy.array(Xty[PP])
             XtXPP =3D numpy.array(XtX[PP, numpy.array(PP)[:, =20
numpy.NewAxis]])
             z[PP] =3D numpy.dot(XtyPP, la.generalized_inverse(XtXPP))
         #end
         z[ZZ] =3D 0

# inner loop to remove elements from the positive set which no longer =20=

belong
         while any(z[PP] <=3D tol) and (iter < itmax) :
             iter +=3D 1
             iztol =3D find(z <=3D tol)
             ip =3D find(P[iztol] !=3D -1)
             QQ =3D iztol[ip]

             if len(QQ) =3D=3D 1 : alpha =3D x[QQ] / (x[QQ] - z[QQ])
             else :
                 x_xz =3D x[QQ] / (x[QQ] - z[QQ])
                 alpha =3D x_xz.min()
             #end

             x +=3D alpha * (z - x)
             iabs =3D find(abs(x) < tol)
             ip =3D find(P[iabs] !=3D -1)
             ij =3D iabs[ip]

             Z[ij] =3D numpy.array(ij)
             P[ij] =3D -1
             PP =3D find(P !=3D -1)
             ZZ =3D find(Z !=3D -1)

             if len(PP) =3D=3D 1 :
                 XtyPP =3D Xty[PP]
                 XtXPP =3D XtX[PP, PP]
                 z[PP] =3D XtyPP / XtXPP
             else :
                 XtyPP =3D numpy.array(Xty[PP])
                 XtXPP =3D numpy.array(XtX[PP, numpy.array(PP)[:, =20
numpy.NewAxis]])
                 z[PP] =3D numpy.dot(XtyPP, =
la.generalized_inverse(XtXPP))
             #endif
             z[ZZ] =3D 0
         #end while
         x =3D numpy.array(z)
         w =3D Xty - numpy.dot(XtX, x)
     #end while

     return x, w

#end def

if __name__ =3D=3D '__main__' :
#
# test [x, w] =3D fnnls(Xt.X, Xt.y, tol)
# to solve min ||y - X.x|| s.t. x >=3D 0
#
# matlab:lsqnonneg
#   X =3D [1, 10, 4, 10; 4, 5, 1, 12; 5, 1, 9, 20];
#   y =3D [4; 7; 4]
#   x =3D lsqnonneg(X, y) =3D> x =3D [0.9312; 0.3683; 0; 0];
#

     X =3D numpy.array([[1, 10, 4, 10], [4, 5, 1, 12], [5, 1, 9, 20]], =20=

numpy.Float)
     y =3D numpy.array([4, 7, 4], numpy.Float)

     if False :
         X =3D numpy.array([[1, 10, 4, 10],
                          [4, 5, 1, 12],
                          [5, 1, 9, 20],
                          [4, 3, 2, 1]], numpy.Float)
         y =3D numpy.array([4, 7, 4, 1], numpy.Float)
     #end

     if False :
         X =3D numpy.zeros((20, 20), numpy.Float)
         for n in range(20) : X[n,:] =3D numpy.arange(0.0, 400.0, step =20=

=3D 20)
         y =3D numpy.arange(0.0, 20.0)
     #end
     Xt =3D numpy.transpose(numpy.array(X))
     x, w =3D fnnls(numpy.dot(Xt, X), numpy.dot(Xt, y))

     print 'X =3D ', X
     print 'y =3D ', y
     print 'x =3D ', x
#end if __name__ =3D=3D '__main__'


Begin forwarded message:

> From: Graeme O'Keefe <gj...@ne...>
> Date: 25 May 2006 8:46:07 PM
> To: matplotlib user list <mat...@li...>
> Subject: [Matplotlib-users] Fwd: python version of nnls/fnnls
>
>
> Dear matplotlibers,
>
> I seem to use Non Negative Least Squares every couple of months and =20=

> the most recent problem I solved reminded me that I meant to post =20
> this last November.
>
> fnnls.py is a port of fnnls.m which was written by Rasmus Bro =20
> (http://newton.foodsci.kvl.dk/users/rasmus.html, code available at =20
> http://www.ub.es/gesq/mcr/als/fnnls.m, and also available on Matlab =20=

> Central).
>
> I've retained Rasmus' comments and translated the matlab to python/=20
> numpy.
>
=EF=BF=BC
>
> I've used this to linearise problems such as:
> 	fitting Neutron TOF data with a E0 energy spectrum of gaussians =20=

> (with energy-resolutions a function of TOF =3D> E): exp(-((E - E0) / =20=

> deltaE)^2)
> 	fitting Cerebral Blood Flow data with a k-spectrum set of =20
> exponentials: exp(-kt)
> 	fitting BGO detector pulses (to detect/correct pile-up) with =20
> Tdelay-spectrum of exponentials: exp(-(t - Tdelay) / tau)
>
> Hope others find it as useful as I have.
>
> regards,
>
>
> Graeme
>
>
>
> Graeme O'Keefe, PhD, MACPSEM
> Principal Medical Physicist
> Centre for PET
> Austin Hospital
> Tel: (613)-9496-5767
> Fax: (613) 9458-5023
>
>

On Thu, 25 May 2006, Graeme O'Keefe apparently wrote: 
> fnnls.py 

And it is ... where?

Cheers,
Alan Isaac

Dear matplotlibers,

I seem to use Non Negative Least Squares every couple of months and =20
the most recent problem I solved reminded me that I meant to post =20
this last November.

fnnls.py is a port of fnnls.m which was written by Rasmus Bro (http://=20=

newton.foodsci.kvl.dk/users/rasmus.html, code available at http://=20
www.ub.es/gesq/mcr/als/fnnls.m, and also available on Matlab Central).

I've retained Rasmus' comments and translated the matlab to python/=20
numpy.

=EF=BF=BC

I've used this to linearise problems such as:
	fitting Neutron TOF data with a E0 energy spectrum of gaussians =20=

(with energy-resolutions a function of TOF =3D> E): exp(-((E - E0) / =20
deltaE)^2)
	fitting Cerebral Blood Flow data with a k-spectrum set of =20
exponentials: exp(-kt)
	fitting BGO detector pulses (to detect/correct pile-up) with =
Tdelay-=20
spectrum of exponentials: exp(-(t - Tdelay) / tau)

Hope others find it as useful as I have.

regards,


Graeme



Graeme O'Keefe, PhD, MACPSEM
Principal Medical Physicist
Centre for PET
Austin Hospital
Tel: (613)-9496-5767
Fax: (613) 9458-5023

On Wed, 2006-05-24 at 17:39 +0800, Allan Noriel Estrella wrote:
> is there a way to modify the toolbars in matplotlib and add more
> functions, like a button for averaging the data displayed then display
> it; draw threshold levels and have a spin up button to change the
> level while drawing it?

To accomplish similar goals, I embed a matplotlib panel (including
toolbar) in a wxPython application (and use the 'WXAgg' backend).
Additional GUI elements (menus, controls etc.) can be added around the
matplotlib panel for all the additional functionality you might need. 

With wxPython, the NavigationalToolbar object could easily be subclassed
and additional elements added, if need be.

You could equally well do this using an alternative toolkit-of-choice
(Tk, gtk, Qt etc.). 

See the "embedding_in_*.py" files from the matplotlib examples set.

Bryan

Dear matplotlibers,

I seem to use Non Negative Least Squares every couple of months and =20
the most recent problem I solved reminded me that I meant to post =20
this last November.

fnnls.py is a port of fnnls.m which was written by Rasmus Bro (http://=20=

newton.foodsci.kvl.dk/users/rasmus.html, code available at http://=20
www.ub.es/gesq/mcr/als/fnnls.m, and also available on Matlab Central).

I've retained Rasmus' comments and translated the matlab to python/=20
numpy.

=EF=BF=BC

I've used this to linearise problems such as:
	fitting Neutron TOF data with a E0 energy spectrum of gaussians =20=

(with energy-resolutions a function of TOF =3D> E): exp(-((E - E0) / =20
deltaE)^2)
	fitting Cerebral Blood Flow data with a k-spectrum set of =20
exponentials: exp(-kt)
	fitting BGO detector pulses (to detect/correct pile-up) with =
Tdelay-=20
spectrum of exponentials: exp(-(t - Tdelay) / tau)

Hope others find it as useful as I have.

regards,


Graeme



Graeme O'Keefe, PhD, MACPSEM
Principal Medical Physicist
Centre for PET
Austin Hospital
Tel: (613)-9496-5767
Fax: (613) 9458-5023

Hi --

I'm trying to create a scatter plot that represents a matrix
cross-referencing two categorical lists. For example, given the
following:

Joe	San Francisco
Sam	Seattle
Frank	New York
Frank	Boston
Frank	Miami
Andrew	Miami

I would like a scatter plot with names on one axis and cities on the
other, with a plot mark at the axis intersections where there is a
match. Is there a way to map directly from such categories to matplotlib
datasets, or do I first need to map this to a numerical indexing scheme
and then visualize it? Is there a simple way to at least have the
categories used as value labels on the axes?

I'm new to matplotlib, so if this turns out to be a poor fit for this
tool, any pointers to better tools (preferrably python-based) would be
appreciated.

Thank you in advance for your time,

Ramon



----+----
This email message (and any attached document) contains information from =
Ingenuity Systems Inc. which may be considered confidential by =
Ingenuity, or which may be privileged or otherwise exempt from =
disclosure under law, and is for the sole use of the individual or =
entity to whom it is addressed.  Any other dissemination, distribution =
or copying of this message is strictly prohibited.  If you receive this =
message in error, please notify me and destroy the attached message (and =
all attached documents) immediately.=20

Dear Sam,

Could you please try the following patch? I think it will fix the issue, 
but I'm not sure -- I don't have this problem on my linux system. If it 
works, I'll commit it to svn.

(Robert Kern suggested modifying the setup.py to include a compiler 
command-line directive. IMO this is better because it will be in the 
source file and is thus more visible to anyone who wants to re-use the 
code. Additionally, it will modify the file, triggering a re-build.)

Samuel M. Smith wrote:

>Well, I gave up. I regressed and installed numpy 0.9.6 from the  
>package installer and looks like matplotlib works now.
>It sure blows my confidence when two months go by and there are  
>enough changes that I can't install from source anymore.
>I would like to try again but it would be nice to know what you did  
>to get it to work since what I did last time no longer works.
>
>Sam
>
>_______________________________________________
>Pythonmac-SIG maillist  -  Pyt...@py...
>http://mail.python.org/mailman/listinfo/pythonmac-sig
>  
>

>>>>> "Stefan" == Stefan van der Walt <st...@su...> writes:

    Stefan> But, after fixing all these problems, I still can't get it
    Stefan> to plot.  It might be worth including surface.py in the
    Stefan> examples directory, as a test, to guarantee that the 3D
    Stefan> code gets updated with the rest.

    Stefan> It could be that I am missing something completely obvious
    Stefan> -- I'd appreciate any help in getting it running!

This code is known to be broken (and never worked).  John Porter's
code originally worked as an add-on module to matplotlib.  Since then
TextWithDash has been refactored which broke mplot3d.  I've been
planning to refactor the code to make it work internally, eg like the
rest of pylab, but haven't gotten it done yet.

JDH

Hi all,

I am trying to get the examples from
http://www.scipy.org/Cookbook/Matplotlib/mplot3D
to work.

I found that the 3D code is already included in matplotlib (SVN
version), but that it does not work:

- axes3d.py makes use of pylab, but it is not imported.

- text_update_coords in axis3d.py refers to self._mytext.foo, but
  TextWithDash has been updated to use the form Text.foo(self,...)
  instead.

- The TextWithDash class's doesn't have a_twd_window_extent
  property. Instead of assigning it in update_coords, it should be
  assigned in __init__.

- When working with matrices, the following occurs:

  def bar(self,M=3DNone):
	M =3D somematrix or M

  which is not allowed.  It should be

        if nx.any(somematrix): M =3D somematrix

But, after fixing all these problems, I still can't get it to plot.
It might be worth including surface.py in the examples directory, as a
test, to guarantee that the 3D code gets updated with the rest.

It could be that I am missing something completely obvious -- I'd
appreciate any help in getting it running!

Cheers
St=E9fan

is there a way to modify the toolbars in matplotlib and add more functions,
like a button for averaging the data displayed then display it; draw
threshold levels and have a spin up button to change the level while drawin=
g
it?

Hi,

Thanks for all the replies, It helped me finding the the cause of the 
problem rather quickly. I did a special trick with the title, that is 
not accepted by the PS backend:

pylab.title("\begin{center} First line \\ Next line \end{center}")

I poked a bit in the code, and it seems that the version 0.87.2 does not 
offer real good alternative for this trick. When making the following 
modification in text.py, one can obtain the intended double title:

         if self.is_math_text():
             tmp = self._text.split("\n\n")
             lines = []
             for line1 in tmp:
                 if len(line1.strip()) > 0:
                     for line2 in line1.split(r"\\"):
                         lines.append(line2.strip())

Using this patch, I just have to use this code for a centered double title:

pylab.title("First line \\ Next line")

This works well and gives the same result independent of the backend 
that is being used. Is the proposed patch a good idea?

regards,

Toon

Jouni K Seppanen wrote:
> Toon Verstraelen <Too...@UG...> writes:
> 
>> I tried to use the PS backend of matplotlib 0.87.2 to create EPS
>> figures, but I got the error at the bottom of this email. 
> [...]
>> ! LaTeX Error: Something's wrong--perhaps a missing \item.
> 
> There is probably something in the text strings you are plotting that
> LaTeX doesn't like. You need to post an example of the script that
> produces the error so we can debug it.
> 

[snipping cross-posts]

Samuel M. Smith wrote:
> So I could either regress numpy or build Matplotlib from source.  Since
> I like being able to get
> the latest bug fixes for Matplotlib and the last time I build it from 
> svn it went without a hitch, I
> decided to try to build Matplotlib from source. Unfortunately it  didn't
> work this time. I get the error shown below.
> I have a powerbook g4 with 10.4.6 and Universal Python 
> 2.4.3-2006-04-07.dmg. What am I missing?

> gcc: src/_ns_cntr.c
> In file included from /usr/include/math.h:26,
>                  from /Library/Frameworks/Python.framework/Versions/
> 2.4/include/python2.4/pyport.h:90,
>                  from /Library/Frameworks/Python.framework/Versions/
> 2.4/include/python2.4/Python.h:55,
>                  from src/_ns_cntr.c:17:
> /usr/include/architecture/ppc/math.h:477: warning: conflicting types 
> for built-in function 'scalb'
> In file included from src/_ns_cntr.c:28:
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-
> packages/numpy/core/include/numpy/arrayobject.h:139: error: 
> redefinition of typedef 'ushort'
> /usr/include/sys/types.h:85: error: previous declaration of 'ushort' 
> was here

It looks like matplotlib should be building all of the _ns_*.c modules with
-DPY_ARRAY_TYPES_PREFIX=something_or_other .

-- 
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

Well, I gave up. I regressed and installed numpy 0.9.6 from the  
package installer and looks like matplotlib works now.
It sure blows my confidence when two months go by and there are  
enough changes that I can't install from source anymore.
I would like to try again but it would be nice to know what you did  
to get it to work since what I did last time no longer works.

Sam

So I could either regress numpy or build Matplotlib from source. =20
Since I like being able to get
the latest bug fixes for Matplotlib and the last time I build it from =20=

svn it went without a hitch, I
decided to try to build Matplotlib from source. Unfortunately it =20
didn't work this time. I get the error shown below.
I have a powerbook g4 with 10.4.6 and Universal Python =20
2.4.3-2006-04-07.dmg. What am I missing?

svn co https://svn.sourceforge.net/svnroot/matplotlib/trunk/=20
matplotlib matplotlib
Checked out revision 2411.

edit darwin path in setupext.py

basedir =3D {
     'win32'  : ['win32_static',],
     'linux2' : ['/usr/local', '/usr',],
     'linux'  : ['/usr/local', '/usr',],
     'cygwin' : ['/usr/local', '/usr',],
     'darwin' : ['/usr/local','/opt/local','/usr'],
     'freebsd4' : ['/usr/local', '/usr'],
     'freebsd5' : ['/usr/local', '/usr'],
     'freebsd6' : ['/usr/local', '/usr'],
     'sunos5' : [os.getenv('MPLIB_BASE') or '/usr/local',],
     'gnukfreebsd5' : ['/usr/local', '/usr'],
     'gnukfreebsd6' : ['/usr/local', '/usr'],
}

from terminal

export WX_CONFIG=3D"usr/local/lib/wxPython-ansi-2.6.3.2rc2/bin/wx-config"

cd matplotlib


python setup.py build



gcc: src/_ns_cntr.c
In file included from /usr/include/math.h:26,
                  from /Library/Frameworks/Python.framework/Versions/=20
2.4/include/python2.4/pyport.h:90,
                  from /Library/Frameworks/Python.framework/Versions/=20
2.4/include/python2.4/Python.h:55,
                  from src/_ns_cntr.c:17:
/usr/include/architecture/ppc/math.h:477: warning: conflicting types =20
for built-in function 'scalb'
In file included from src/_ns_cntr.c:28:
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:139: error: =20
redefinition of typedef 'ushort'
/usr/include/sys/types.h:85: error: previous declaration of 'ushort' =20
was here
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:140: error: =20
redefinition of typedef 'uint'
/usr/include/sys/types.h:86: error: previous declaration of 'uint' =20
was here
In file included from src/_ns_cntr.c:28:
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:139: error: =20
redefinition of typedef 'ushort'
/usr/include/sys/types.h:85: error: previous declaration of 'ushort' =20
was here
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:140: error: =20
redefinition of typedef 'uint'
/usr/include/sys/types.h:86: error: previous declaration of 'uint' =20
was here
lipo: can't figure out the architecture type of: /var/tmp//ccR0VtyV.out
In file included from /usr/include/math.h:26,
                  from /Library/Frameworks/Python.framework/Versions/=20
2.4/include/python2.4/pyport.h:90,
                  from /Library/Frameworks/Python.framework/Versions/=20
2.4/include/python2.4/Python.h:55,
                  from src/_ns_cntr.c:17:
/usr/include/architecture/ppc/math.h:477: warning: conflicting types =20
for built-in function 'scalb'
In file included from src/_ns_cntr.c:28:
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:139: error: =20
redefinition of typedef 'ushort'
/usr/include/sys/types.h:85: error: previous declaration of 'ushort' =20
was here
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:140: error: =20
redefinition of typedef 'uint'
/usr/include/sys/types.h:86: error: previous declaration of 'uint' =20
was here
In file included from src/_ns_cntr.c:28:
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:139: error: =20
redefinition of typedef 'ushort'
/usr/include/sys/types.h:85: error: previous declaration of 'ushort' =20
was here
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-=20
packages/numpy/core/include/numpy/arrayobject.h:140: error: =20
redefinition of typedef 'uint'
/usr/include/sys/types.h:86: error: previous declaration of 'uint' =20
was here
lipo: can't figure out the architecture type of: /var/tmp//ccR0VtyV.out
error: Command "gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/=20
MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp =20=

-mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -I/Library/=20
Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/=20
numpy/core/include -I/usr/local/include -I/opt/local/include -I/usr/=20
include -I. -I/Library/Frameworks/Python.framework/Versions/2.4/=20
include/python2.4 -c src/_ns_cntr.c -o build/temp.macosx-10.4-fat-2.4/=20=

src/_ns_cntr.o -DSCIPY=3D1" failed with exit status 1
albook:smithsm$

On 23 May, 2006, at 11:52, Charlie Moad wrote:

> Yeah, mpl 0.87.2 was built with numpy 0.9.6.  I don't think a new
> matplotlib release is in the near future unless the new numpy warrants
> a minor bump.
>
> - Charlie
>
> On 5/23/06, Samuel M. Smith <sm...@sa...> wrote:
>> Charlie,
>>
>> I finally had some time to update my python matplotlib installation.
>>
>> I installed
>> Universal Python 2.4.3-2006-04-07.dmg
>> numpy 0.9.8 from source
>> wxPython2.6-osx-unicode-2.6.3.2rc2-universal10.4-py.2.4.dmg
>> wxPython2.6-osx-ansi-2.6.3.2rc2-universal10.4.py2.4.dmg
>>
>> Iipython 0.7.1.fix1 was already installed
>>
>> I tried a test of  matplotlib using ipython and get a segmentation
>> fault.
>>
>> ipython -pylab
>> loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
>> matplotlib version 0.87.2
>> verbose.level helpful
>> interactive is False
>> platform is darwin
>> numerix numpy 0.9.8
>> Segmentation fault
>>
>> I am guessing that you used a different version of numpy?
>>
>> If I just do python from terminal and import matplotlob then no
>> segmentation fault
>>
>>  >>> import matplotlib
>> loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
>> matplotlib version 0.87.2
>> verbose.level helpful
>> interactive is False
>> platform is darwin
>>
>> Anybody have any ideas what is happening?
>>
>> On 03 May, 2006, at 20:09, Charlie Moad wrote:
>>
>> >     I posted a universal build of matplotlib 0.87.2 on =20
>> sourceforge in
>> > egg and mpkg format.  It is compiled against the latest numarray,
>> > numpy, and Numeric as well as Tk and the new wxPython-rc2
>> > universal. Libpng and freetype2 are statically linked in.  Please
>> > post or link to
>> > either/both at "http://pythonmac.org/packages/py24-fat/".
>> >
>> > http://sourceforge.net/project/showfiles.php?
>> > group_id=3D80706&package_id=3D82474
>> >
>>
>
>
> -------------------------------------------------------
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2966 Fort Hill Road
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801-768-2768 voice
801-768-2769 fax
**********************************************************************
"The greatest source of failure and unhappiness in the world is
giving up what we want most for what we want at the moment"
**********************************************************************

Yeah, mpl 0.87.2 was built with numpy 0.9.6.  I don't think a new
matplotlib release is in the near future unless the new numpy warrants
a minor bump.

- Charlie

On 5/23/06, Samuel M. Smith <sm...@sa...> wrote:
> Charlie,
>
> I finally had some time to update my python matplotlib installation.
>
> I installed
> Universal Python 2.4.3-2006-04-07.dmg
> numpy 0.9.8 from source
> wxPython2.6-osx-unicode-2.6.3.2rc2-universal10.4-py.2.4.dmg
> wxPython2.6-osx-ansi-2.6.3.2rc2-universal10.4.py2.4.dmg
>
> Iipython 0.7.1.fix1 was already installed
>
> I tried a test of  matplotlib using ipython and get a segmentation
> fault.
>
> ipython -pylab
> loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
> matplotlib version 0.87.2
> verbose.level helpful
> interactive is False
> platform is darwin
> numerix numpy 0.9.8
> Segmentation fault
>
> I am guessing that you used a different version of numpy?
>
> If I just do python from terminal and import matplotlob then no
> segmentation fault
>
>  >>> import matplotlib
> loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
> matplotlib version 0.87.2
> verbose.level helpful
> interactive is False
> platform is darwin
>
> Anybody have any ideas what is happening?
>
> On 03 May, 2006, at 20:09, Charlie Moad wrote:
>
> >     I posted a universal build of matplotlib 0.87.2 on sourceforge in
> > egg and mpkg format.  It is compiled against the latest numarray,
> > numpy, and Numeric as well as Tk and the new wxPython-rc2
> > universal. Libpng and freetype2 are statically linked in.  Please
> > post or link to
> > either/both at "http://pythonmac.org/packages/py24-fat/".
> >
> > http://sourceforge.net/project/showfiles.php?
> > group_id=3D80706&package_id=3D82474
> >
>

Charlie,

I finally had some time to update my python matplotlib installation.

I installed
Universal Python 2.4.3-2006-04-07.dmg
numpy 0.9.8 from source
wxPython2.6-osx-unicode-2.6.3.2rc2-universal10.4-py.2.4.dmg
wxPython2.6-osx-ansi-2.6.3.2rc2-universal10.4.py2.4.dmg

Iipython 0.7.1.fix1 was already installed

I tried a test of  matplotlib using ipython and get a segmentation  
fault.

ipython -pylab
loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
matplotlib version 0.87.2
verbose.level helpful
interactive is False
platform is darwin
numerix numpy 0.9.8
Segmentation fault

I am guessing that you used a different version of numpy?

If I just do python from terminal and import matplotlob then no  
segmentation fault

 >>> import matplotlib
loaded rc file /Users/smithsm/.matplotlib/matplotlibrc
matplotlib version 0.87.2
verbose.level helpful
interactive is False
platform is darwin

Anybody have any ideas what is happening?

On 03 May, 2006, at 20:09, Charlie Moad wrote:

>     I posted a universal build of matplotlib 0.87.2 on sourceforge in
> egg and mpkg format.  It is compiled against the latest numarray,
> numpy, and Numeric as well as Tk and the new wxPython-rc2  
> universal. Libpng and freetype2 are statically linked in.  Please  
> post or link to
> either/both at "http://pythonmac.org/packages/py24-fat/".
>
> http://sourceforge.net/project/showfiles.php? 
> group_id=80706&package_id=82474
>

Toon Verstraelen <Too...@UG...> writes:

> I tried to use the PS backend of matplotlib 0.87.2 to create EPS
> figures, but I got the error at the bottom of this email. 
[...]
> ! LaTeX Error: Something's wrong--perhaps a missing \item.

There is probably something in the text strings you are plotting that
LaTeX doesn't like. You need to post an example of the script that
produces the error so we can debug it.

-- 
Jouni

On Tuesday 23 May 2006 12:23, Toon Verstraelen wrote:
> Hi,
>
> I tried to use the PS backend of matplotlib 0.87.2 to create EPS
> figures, but I got the error at the bottom of this email. I'm using
> tetex-2.0.2. These are my modified matplotlibrc settings:
>
> matplotlib.rcParams["backend"] = "PS"
> matplotlib.rcParams["font.family"] = "serif"
> matplotlib.rcParams["font.size"] = 7.0
> matplotlib.rcParams["text.usetex"] = True
> matplotlib.rcParams["axes.titlesize"] = 8.0
> matplotlib.rcParams["axes.labelsize"] = 7.0
> matplotlib.rcParams["xtick.labelsize"] = 7.0
> matplotlib.rcParams["ytick.labelsize"] = 7.0
> matplotlib.rcParams["legend.fontsize"] = 7.0
> matplotlib.rcParams["legend.markerscale"] = 0.7
> matplotlib.rcParams["figure.dpi"] = 72
> matplotlib.rcParams["figure.facecolor"] = "white"
> matplotlib.rcParams["savefig.dpi"] = 72
> matplotlib.rcParams["ps.papersize"] = "A4"
>
> What could be the problem? Which versions of tetex are known to work?

Its difficult to say what the problem might be without seeing a script that 
reproduces the problem. The svn version works well, but I dont know when the 
next release might occur.

Darren

Is there a cookbook or reference that is about using matplotlib for data
analysis? I will be using it to plot a waveform from the data samples. Then
have some several clickable options/ tools so that some data manipulation
can occur (e.g. averaging, placing a threshold line in the plot where the
threshold levels can be change dynamically in the plot).

Hi,

I tried to use the PS backend of matplotlib 0.87.2 to create EPS 
figures, but I got the error at the bottom of this email. I'm using 
tetex-2.0.2. These are my modified matplotlibrc settings:

matplotlib.rcParams["backend"] = "PS"
matplotlib.rcParams["font.family"] = "serif"
matplotlib.rcParams["font.size"] = 7.0
matplotlib.rcParams["text.usetex"] = True
matplotlib.rcParams["axes.titlesize"] = 8.0
matplotlib.rcParams["axes.labelsize"] = 7.0
matplotlib.rcParams["xtick.labelsize"] = 7.0
matplotlib.rcParams["ytick.labelsize"] = 7.0
matplotlib.rcParams["legend.fontsize"] = 7.0
matplotlib.rcParams["legend.markerscale"] = 0.7
matplotlib.rcParams["figure.dpi"] = 72
matplotlib.rcParams["figure.facecolor"] = "white"
matplotlib.rcParams["savefig.dpi"] = 72
matplotlib.rcParams["ps.papersize"] = "A4"

What could be the problem? Which versions of tetex are known to work?

Any help is greatly appreciated.

regards,

Toon

Writing water_cr_chi_eta_degeneracy_plot_npa_h.eps
Traceback (most recent call last):
   File "/usr/bin/tp-default-transform", line 146, in ?
     projectlog.express(body, doc)
   File "/usr/lib/python2.4/site-packages/task_projects/logs.py", line 
101, in express
     content.express(div_el, doc, depth+1)
   File "/usr/lib/python2.4/site-packages/task_projects/logs.py", line 
101, in express
     content.express(div_el, doc, depth+1)
   File "/usr/lib/python2.4/site-packages/task_projects/logs.py", line 
103, in express
     content.express(div_el, doc)
   File "/usr/lib/python2.4/site-packages/ffaudit/logs.py", line 176, in 
express
     pylab.savefig("%s.eps" % filename, dpi=self.dpi)
   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 
839, in savefig
     return fig.savefig(*args, **kwargs)
   File "/usr/lib/python2.4/site-packages/matplotlib/figure.py", line 
658, in savefig
     self.canvas.print_figure(*args, **kwargs)
   File 
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gtkagg.py", 
line 112, in print_figure
     orientation, **kwargs)
   File 
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py", 
line 493, in print_figure
     orientation, **kwargs)
   File 
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py", 
line 987, in print_figure
     orientation, papertype)
   File 
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py", 
line 1205, in _print_figure_tex
     orientation)
   File 
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py", 
line 1262, in convert_psfrags
     if exit_status: raise RuntimeError('LaTeX was not able to process \
RuntimeError: LaTeX was not able to process your image.
Here is the full report generated by LaTeX:

This is TeX, Version 3.14159 (Web2C 7.4.5)
(/tmp/ce5a2910205804a7f7b68a822d15a84d.tex
LaTeX2e <2001/06/01>
Babel <v3.7h> and hyphenation patterns for american, french, german, 
ngerman, n
ohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/article.cls
Document Class: article 2001/04/21 v1.4e Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
(/usr/share/texmf/tex/latex/misc/type1cm.sty)
(/usr/share/texmf/tex/latex/psnfss/helvet.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/psnfss/courier.sty)
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/misc/geometry.sty
(/usr/share/texmf/tex/latex/config/geometry.cfg)

Package geometry Warning: Over-specification in `h'-direction.
     `width' (411.93877pt) is ignored.


Package geometry Warning: Over-specification in `v'-direction.
     `height' (411.93877pt) is ignored.

) (/usr/share/texmf/tex/latex/misc/psfrag.sty
(/usr/share/texmf/tex/latex/graphics/graphics.sty
(/usr/share/texmf/tex/latex/graphics/trig.sty)
(/usr/share/texmf/tex/latex/config/graphics.cfg)
(/usr/share/texmf/tex/latex/graphics/dvips.def)))
(/usr/share/texmf/tex/latex/graphics/graphicx.sty)
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf/tex/latex/graphics/dvipsnam.def))
(./ce5a2910205804a7f7b68a822d15a84d.aux)
(/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/ot1pnc.fd)
<ce5a2910205804a7f7b68a822d15a84d.eps>

! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}


! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
  ...

l.33 ...e=0]{ce5a2910205804a7f7b68a822d15a84d.eps}

[1] (./ce5a2910205804a7f7b68a822d15a84d.aux) )
(see the transcript file for additional information)
Output written on ce5a2910205804a7f7b68a822d15a84d.dvi (1 page, 3940 bytes).
Transcript written on ce5a2910205804a7f7b68a822d15a84d.log.

Those of you who are PSF mentors for the summer of code, could I ask
you to take a look at Edin's resubmitted proposal for enhancing
mathtext


http://code.google.com/soc/psf/app.html?csaid=edin.salkovic%40gmail.com%3A048a69f9%3A96f5f65b

Google will be funding 25 PSF projects, and this one will need a
higher score to make the cut.  I think the work he is proposing will
be a nice enhancement to the mathtext facility which is used by both
matplotlib and chaco, and since one of Edin's goals is to refactor
mathtext into a standalone project, it should see some usage beyond
those two projects.

Thanks!
JDH

Hello,

I am trying to generate a short movie using matplotlib.
The core of my code looks like

    for i in range(1,len(t)):
        U0,U1x,U1y,H1 =3D list(sig[i,:])

        for x in arange(0,1.001,0.05):
            for y in arange(0,1.001,0.05):
                xx,yy=3Dtrace(U0,U1x,U1y,H1,x,y)
                ts[(x,y)].set_data(xx,yy)

        for j in range(0,nobs):
            tr[j].center =3D (obs[i,2*j],obs[i,2*j+1])

        savefig("f%04d.png"%i)

where the entries of the dictionary 'ts' are lines and the entries of
the dictionary 'tr' a patches (circles).  Moving the lines around with
set_data works quite fine, but moving the patches by setting 'center'
does not.

My question: how do I move a patch?

Many thanks,
Jochen
--=20
http://seehuhn.de/

After waiting for some days for some suggestion, I would like to ask if
there is some suggestion or "starting-point" for solving this issue.
Sincerely yours,
clovis

John Hunter wrote:

>>>>>>"clovis" == clovis  <cl...@pe...> writes:
>>>>>>            
>>>>>>
>
>    clovis> All, I followed up the 'memory leak' discussion in the
>    clovis> sourceforge list and I know the Matplotlib-FAQ entry about
>    clovis> this subject. I've also seen John Hunter's post about the
>    clovis> need of matching figure/close pairs.  Anyway, I still feel
>    clovis> that there are problems in this subject, which can be
>    clovis> exposed by the following script (for Windows, but can
>    clovis> easily be adapted to Unix).
>
>    clovis> As can be seen by the results (also given below), there is
>    clovis> a steady increase in memory usage which is not recovered!
>
>If I recall correctly, there is a known leak in tkagg when you create
>multiple canvases, and this is in Tk and not matplotlib proper.  Todd
>may have something to add here.  
>
>JDH
>
>
>-------------------------------------------------------
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>Mat...@li...
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>
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>  
>