Alan W. Irwin wrote:
> On 2009-04-08 19:33-0400 Hazen Babcock wrote:
>
>> Hello,
>>
>> Apologies if this has already been reported...
>>
>> While using Numpy and PLplot I've stumbled over a potential problem with
>> the interface. Numpy arrays are not necessarily contiguous in memory,
>> i.e. if I have a 2D array:
>>
>> p = [[1,2],[2,3],[3,4]]
>>
>> And I do:
>> plplot.plpoin(p[:,0], p[:,1], 9)
>>
>> Then I'll get a segmentation fault. Surprisingly, I have found that even
>> some 1D arrays are not be contiguous. Should we be trying to protect the
>> user by doing something like this to all the arrays that we get from numpy?
>> plplot.plpoin(numpy.ascontiguousarray(p[:,0]),
>> numpy.ascontiguousarray(p[:,1]), 9)
>
> Your report got me curious since I use plenty of two dimensional array
> in python/numpy without problems. So I just now tried the following:
>
>>>> from numpy import *
>>>> p = [[1,2],[2,3],[3,4]]
>>>> p
> [[1, 2], [2, 3], [3, 4]]
>>>> p[:,0]
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> TypeError: list indices must be integers
>
> However, if you put an array around it all is well.
>
>>>> p = array(p)
>>>> p
> array([[1, 2],
> [2, 3],
> [3, 4]])
>>>> p[:,0]
> array([1, 2, 3])
>>>> p[:,1]
> array([2, 3, 4])
>
> I haven't tried it, but I am virtually positive array([1, 2, 3]) and
> array([2, 3, 4]) would work fine as arguments to plpoin.
>
> Thus, is the problem that you forgot to turn the ordinary two-dimensional
> python array into a numpy one (with array) before you tried to create
> one-dimensional array results from two-dimensional ones?
When I ran into this issue I was using numpy arrays that I'd have saved
(and then reloaded) using Pytables. For some reason when I used slices
of these array in the call to plploin I would get a segfault, but if I
created an intermediate variable that stored a contiguous version of
each slice of interest from the array then everything was fine. I just
assumed that this was a numpy / plplot issue, but now in trying to write
a test case without using pytables I don't see any problem. This works
as expected for me either way:
import numpy
import plplot
plplot.plsdev("xcairo")
plplot.plspage(72, 72, 800, 800, 0, 0)
plplot.plinit()
plplot.plenv(0.0, 2.0, 0.0, 2.0, 0, 0)
for i in range(1000):
objs = numpy.random.random((200,6))
objs[:,2] += 1.0
if 0:
x = numpy.ascontiguousarray(objs[:,1])
y = numpy.ascontiguousarray(objs[:,2])
plplot.plpoin(x, y, 1)
else:
plplot.plpoin(objs[:,1], objs[:,2], 1)
plplot.pllab("X", "Y", "Spot Locations")
plplot.plend()
So it must be something unusual about arrays that have been stored and
reloaded using pytables.
-Hazen
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