[SciPy-dev] Subtle fitpack2 bug: resize (but only in doctest)

Michael McNeil Forbes mforbes@physics.ubc...
Sat Mar 1 08:53:09 CST 2008


Hi,

I have been running into a very strange and hard to track down bug  
with fitpack2.py.  When I run certain tests as doctests, then I get  
the following error:

       File "/data/apps/Python-2.5.1/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ 
interpolate/fitpack2.py", line 91, in __init__
         data = self._reset_nest(data)
       File "/data/apps/Python-2.5.1/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ 
interpolate/fitpack2.py", line 128, in _reset_nest
         t.resize(nest)
     ValueError: cannot resize an array that has been referenced or  
is referencing
     another array in this way.  Use the resize function

I am doing a simple 1d interpolation, but the tricky part is that  
this only occurs when I am running under the doctest module: if I  
import the file at an interpreter prompt and then run the doctests,  
there is no problem.

The problem is at line 128 in fitpack2.py which occurs in this context:

128        t,c,fpint,nrdata = data[8].copy(),data[9].copy(),\
129                           data[11].copy(),data[12].copy()
130        t.resize(nest)
131        c.resize(nest)
132        fpint.resize(nest)
133        nrdata.resize(nest)

...

Thus, t should be a fresh copy and should be resizable, but somehow,  
when running the code under a doctest, there is a reference created  
that messes up the call to resize.

I have no idea what is causing this problem - it also seems to be  
very fickle: I can cause the problem on my macbook pro (Core Duo)  
with the following program:

err.py:
"""
 >>> x = [-1.,-0.65016502,-0.58856235,-0.26903553,-0.17370892,
...      -0.10011001,0.,0.10011001,0.17370892,0.26903553,0.58856235,
...       0.65016502,1.]
 >>> y = [ 1.,0.62928599,0.5797223, 0.39965815,0.36322694,0.3508061,
...      0.35214793,0.3508061, 0.36322694,0.39965815,0.5797223,
...      0.62928599,1.]
 >>> w = [1.00000000e+12, 6.88875973e+02, 4.89314737e+02, 4.26864807e 
+02,
...      6.07746770e+02, 4.51341444e+02, 3.17480210e+02, 4.51341444e+02,
...      6.07746770e+02, 4.26864807e+02, 4.89314737e+02, 6.88875973e+02,
...      1.00000000e+12]
 >>> from scipy.interpolate import UnivariateSpline
 >>> sp = UnivariateSpline(x=x,y=y,w=w,s=None)
"""
import doctest
doctest.testmod()

But when I run it on my linux box (64 bit), it runs fine.

In any case, there is an easy patch.  Just replace the lines above with

128        t,c,fpint,nrdata = [resize(data[n],nest) for n in
129                            [8,9,11,12]]

and add resize to the numpy imports

21 from numpy import ... resize

The bug is so strange, though, that I though it should be  
investigated a bit more.  Any ideas what could be causing this?

Michael.



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