matplotlib-users Mailing List for matplotlib

Well I have somewhat good news.  I was using an older machine (RedHat7) 
when I had these problems.  I went to a much newer redhat machine and 
everything works fine.  Same version of Python, gcc, etc - just a newer 
operating system.

I guess I'll just ignore this problem and stick with the newer machine.

Ted

At 01:47 PM 10/21/2004, Todd Miller wrote:
>On Thu, 2004-10-21 at 16:00, John Hunter wrote:
> > >>>>> "Ted" == Ted Drain <ted...@jp...> writes:
> >
> >     Ted> I'm trying to build matplotlib and I'm getting a segmentation
> >     Ted> fault when I do: from matplotlib import *
> >
> >     Ted> I've traced the fault down to the transforms module.
> >
> >     Ted> My first attempt used: gcc 3.3.2 Python 2.3.3 numarray 1.1
> >     Ted> gdmodule 0.52 gd 2.0.28 freetype 2.1.9 agg 22 matplotlib
> >     Ted> 0.63.4
> >
> > Standard issue stuff - very close to what most people are using w/o
> > incident.  Hmmmm....
> >
> >     Ted> In this version _na_transform segementation faults at this
> >     Ted> line: static _transforms_module* _transforms = new
> >     Ted> _transforms_module;
> >
> >     Ted> I traced the fault down to the ExtensionModuleBaseClass where
> >     Ted> it attempts to call: __Py_PackageContext()
> >
> >     Ted> It looks to me like this function is trying to access the
> >     Ted> variable (which it dereferences WITHOUT checking for a null
> >     Ted> pointer).  static char **ptr__Py_PackageContext = NULL;
> >
> > Could you try editing it an adding the NULL test; if this works can
> > you submit a patch pack to be and a bug report to the pycxx sf site?
> >
> >     Ted> This ptr gets init'ed in the function
> >     Ted> InitialisePythonIndirectInterface() but I can't find anywhere
> >     Ted> that function is being called.
> >
> >     Ted> FYI: I also tried matplotlib 0.62.4 and I get the same error.
> >
> > It couldn't be the exact same error, because _na_transforms did not
> > exist in 0.62.4.  Do you mean that you got a segfault on the same line
> > in _transform?
>
>Check for matplotlib/_transforms.so left over from prior installations
>and blow away your old matplotlib and re-install if you find it.  Before
>you re-install, also blow away matplotlib/build.
>
>Todd

On Thu, 2004-10-21 at 16:00, John Hunter wrote:
> >>>>> "Ted" == Ted Drain <ted...@jp...> writes:
> 
>     Ted> I'm trying to build matplotlib and I'm getting a segmentation
>     Ted> fault when I do: from matplotlib import *
> 
>     Ted> I've traced the fault down to the transforms module.
> 
>     Ted> My first attempt used: gcc 3.3.2 Python 2.3.3 numarray 1.1
>     Ted> gdmodule 0.52 gd 2.0.28 freetype 2.1.9 agg 22 matplotlib
>     Ted> 0.63.4
> 
> Standard issue stuff - very close to what most people are using w/o
> incident.  Hmmmm....
> 
>     Ted> In this version _na_transform segementation faults at this
>     Ted> line: static _transforms_module* _transforms = new
>     Ted> _transforms_module;
> 
>     Ted> I traced the fault down to the ExtensionModuleBaseClass where
>     Ted> it attempts to call: __Py_PackageContext()
> 
>     Ted> It looks to me like this function is trying to access the
>     Ted> variable (which it dereferences WITHOUT checking for a null
>     Ted> pointer).  static char **ptr__Py_PackageContext = NULL;
> 
> Could you try editing it an adding the NULL test; if this works can
> you submit a patch pack to be and a bug report to the pycxx sf site?
> 
>     Ted> This ptr gets init'ed in the function
>     Ted> InitialisePythonIndirectInterface() but I can't find anywhere
>     Ted> that function is being called.
> 
>     Ted> FYI: I also tried matplotlib 0.62.4 and I get the same error.
> 
> It couldn't be the exact same error, because _na_transforms did not
> exist in 0.62.4.  Do you mean that you got a segfault on the same line
> in _transform?

Check for matplotlib/_transforms.so left over from prior installations
and blow away your old matplotlib and re-install if you find it.  Before
you re-install, also blow away matplotlib/build.

Todd

>It couldn't be the exact same error, because _na_transforms did not
>exist in 0.62.4.  Do you mean that you got a segfault on the same line
>in _transform?

Sorry - that's what I meant.  It looks like I was a little mistaken.  I 
didn't realize that there are 2 versions of __Py_PackageContext() in the 
same file.  I was orginally looking at the Windows version (I'm building on 
linux).

However, if the linux version looks like this (unmodified):

char *__Py_PackageContext()     { return _Py_PackageContext; }

I get a segmentation fault at the return line.

I then added a print statement to it:

char *__Py_PackageContext()
{
    std::cerr << "context 0\n";
    return _Py_PackageContext;
}

and then everything works!  Off the top of my head, it might be a case of 
C++ static object initialization problems but I can't find any obvious 
places that might be happening.

Ted

At 01:00 PM 10/21/2004, John Hunter wrote:
> >>>>> "Ted" == Ted Drain <ted...@jp...> writes:
>
>     Ted> I'm trying to build matplotlib and I'm getting a segmentation
>     Ted> fault when I do: from matplotlib import *
>
>     Ted> I've traced the fault down to the transforms module.
>
>     Ted> My first attempt used: gcc 3.3.2 Python 2.3.3 numarray 1.1
>     Ted> gdmodule 0.52 gd 2.0.28 freetype 2.1.9 agg 22 matplotlib
>     Ted> 0.63.4
>
>Standard issue stuff - very close to what most people are using w/o
>incident.  Hmmmm....
>
>     Ted> In this version _na_transform segementation faults at this
>     Ted> line: static _transforms_module* _transforms = new
>     Ted> _transforms_module;
>
>     Ted> I traced the fault down to the ExtensionModuleBaseClass where
>     Ted> it attempts to call: __Py_PackageContext()
>
>     Ted> It looks to me like this function is trying to access the
>     Ted> variable (which it dereferences WITHOUT checking for a null
>     Ted> pointer).  static char **ptr__Py_PackageContext = NULL;
>
>Could you try editing it an adding the NULL test; if this works can
>you submit a patch pack to be and a bug report to the pycxx sf site?
>
>     Ted> This ptr gets init'ed in the function
>     Ted> InitialisePythonIndirectInterface() but I can't find anywhere
>     Ted> that function is being called.
>
>     Ted> FYI: I also tried matplotlib 0.62.4 and I get the same error.
>
>It couldn't be the exact same error, because _na_transforms did not
>exist in 0.62.4.  Do you mean that you got a segfault on the same line
>in _transform?
>
>Thanks,
>JDH

At long last, I finally have a prototype version of polar plots / axes
/ transforms in CVS (mirrors may lag). 

I don't use polar plots a lot in my own work, so those of you who do
should provide some feedback on the implementation, appearance and
functionality.  

See examples/polar_demo.py (included below)

Here is a snapshot of the src distribution if you have CVS problems

  http://nitace.bsd.uchicago.edu:8080/files/share/matplotlib-0.64.0a.tar.gz

In particular, I need some feedback on how setting axis limits should
work and what, if anything, the navigation controls are expected to
do.  These issues are discussed a bit more in the polar_demo.py
example file.

Let me know....
JDH

#!/usr/bin/env python
#
# matplotlib now has a PolarAxes class and a polar function in the
# matplotlib interface.  This is considered alpha and the interface
# may change as we work out how polar axes should best be integrated
#
# The only function that has been tested on polar axes is "plot" (the
# matlab interface function "polar" calls ax.plot where ax is a
# PolarAxes) -- other axes plotting functions may work on PolarAxes
# but haven't been tested and may need tweaking.
#
# you can get get a PolarSubplot instance by doing, for example
#
#   subplot(211, polar=True)
#
# or a PolarAxes instance by doing
#   axes([left, bottom, width, height], polar=True)
#
# The view limits (eg xlim and ylim) apply to the lower left and upper
# right of the rectangular box that surrounds to polar axes.  Eg if
# you have
#
#  r = arange(0,1,0.01)
#  theta = 2*pi*r
#
# the lower left corner is 5/4pi, sqrt(2) and the
# upper right corner is 1/4pi, sqrt(2)
#
# you could change the radial bounding box (zoom out) by setting the
# ylim (radial coordinate is the second argument to the plot command,
# as in matlab, though this is not advised currently because it is not
# clear to me how the axes should behave in the change of view limits.
# Please advise me if you have opinions.  Likewise, the pan/zoom
# controls probably do not do what you think they do and are better
# left alone on polar axes.  Perhaps I will disable them for polar
# axes unless we come up with a meaningful, useful and functional
# implementation for them.
#
# Note that polar axes are sufficiently different that regular axes
# that I haven't stived for a consistent interface to the gridlines,
# labels, etc.  To set the properties of the gridlines and labels,
# access the attributes directly from the polar axes, as in
#
#   ax = gca()
#   set(ax.rgridlines, color='r')
#
# The following attributes are defined
#
#      thetagridlines  : a list of Line2D for the theta grids
#      rgridlines      : a list of Line2D for the radial grids
#      thetagridlabels : a list of Text for the theta grid labels
#      rgridlabels     : a list of Text for the theta grid labels                  

from matplotlib.matlab import *

r = arange(0,4,0.001)
theta = 6*pi*r
polar(theta, r)
title("It's about time!")
savefig('polar_demo')
ax = gca()

show()

>>>>> "Ted" == Ted Drain <ted...@jp...> writes:

    Ted> I'm trying to build matplotlib and I'm getting a segmentation
    Ted> fault when I do: from matplotlib import *

    Ted> I've traced the fault down to the transforms module.

    Ted> My first attempt used: gcc 3.3.2 Python 2.3.3 numarray 1.1
    Ted> gdmodule 0.52 gd 2.0.28 freetype 2.1.9 agg 22 matplotlib
    Ted> 0.63.4

Standard issue stuff - very close to what most people are using w/o
incident.  Hmmmm....

    Ted> In this version _na_transform segementation faults at this
    Ted> line: static _transforms_module* _transforms = new
    Ted> _transforms_module;

    Ted> I traced the fault down to the ExtensionModuleBaseClass where
    Ted> it attempts to call: __Py_PackageContext()

    Ted> It looks to me like this function is trying to access the
    Ted> variable (which it dereferences WITHOUT checking for a null
    Ted> pointer).  static char **ptr__Py_PackageContext = NULL;

Could you try editing it an adding the NULL test; if this works can
you submit a patch pack to be and a bug report to the pycxx sf site?

    Ted> This ptr gets init'ed in the function
    Ted> InitialisePythonIndirectInterface() but I can't find anywhere
    Ted> that function is being called.

    Ted> FYI: I also tried matplotlib 0.62.4 and I get the same error.

It couldn't be the exact same error, because _na_transforms did not
exist in 0.62.4.  Do you mean that you got a segfault on the same line
in _transform?

Thanks,
JDH

I'm trying to build matplotlib and I'm getting a segmentation fault when I do:

from matplotlib import *

I've traced the fault down to the transforms module.

My first attempt used:
gcc 3.3.2
Python 2.3.3
numarray 1.1
gdmodule 0.52
gd 2.0.28
freetype 2.1.9
agg 22
matplotlib 0.63.4

In this version _na_transform segementation faults at this line:
   static _transforms_module* _transforms = new _transforms_module;

I traced the fault down to the ExtensionModuleBaseClass where it attempts 
to call:  __Py_PackageContext()

It looks to me like this function is trying to access the variable (which 
it dereferences WITHOUT checking for a null pointer).
static char **ptr__Py_PackageContext = NULL;

This ptr gets init'ed in the function InitialisePythonIndirectInterface() 
but I can't find anywhere that function is being called.

FYI: I also tried matplotlib 0.62.4 and I get the same error.

Can anybody figure out what's happening to me?
Thanks,
Ted

Thank you, this works fine.


On Wednesday 20 October 2004 22:47, John Hunter wrote:
> Hmm, I don't know how this slipped in untested.  corrcoef definitely
> works for corrcoeff(x,y), but is obviously broken for matrices.
>
> Here is a fixed implementation, tested against matlab for MxN matrices
> with 5 significant digits of agreement in the correlation matrix
> output with Numeric and numarray.

-- 
Sebastian Stark -- http://www.kyb.tuebingen.mpg.de/~stark
Max Planck Institute for Biological Cybernetics
Spemannstr. 38, 72076 Tuebingen
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