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Re: Memory error with quadratic interpolation

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Date Wed, 23 Jan 2013 16:51:43 +0000
Subject Re: Memory error with quadratic interpolation
From Oscar Benjamin <oscar.j.benjamin@gmail.com>
To Isaac Won <winefrog@gmail.com>
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Cc Python List <python-list@python.org>, Ulrich Eckhardt <ulrich.eckhardt@dominolaser.com>
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On 23 January 2013 14:57, Isaac Won <winefrog@gmail.com> wrote:
> On Wednesday, January 23, 2013 8:40:54 AM UTC-6, Oscar Benjamin wrote:
>> On 23 January 2013 14:28, Isaac Won <winefrog@gmail.com> wrote:
>>
[SNIP]
>
> Following is full error message after I adjusted following Ulich's advice:
>
> interp = interp1d(indices[not_nan], x[not_nan], kind = 'quadratic')
> File "/lustre/work/apps/python-2.7.1/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 311, in __init__
>      self._spline = splmake(x,oriented_y,order=order)
>   File "/lustre/work/apps/python-2.7.1/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 809, in splmake
>      coefs = func(xk, yk, order, conds, B)
>   File "/lustre/work/apps/python-2.7.1/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 530, in _find_smoothest
>      u,s,vh = np.dual.svd(B)
>   File "/lustre/work/apps/python-2.7.1/lib/python2.7/site-packages/scipy/linalg/decomp_svd.py", line 91, in svd
>      full_matrices=full_matrices, overwrite_a = overwrite_a)
> MemoryError

Where is the new code? You should show full working code (with the
import statements) and the full error that is generated by exactly
that code. If possible you should also write code that someone else
could run even without having access to your data files. If you did
that in your first post, you'd probably have an answer to your problem
by now.

Here is a version of your code that many people on this list can test
straight away:

import numpy as np
from scipy.interpolate import interp1d
x = np.array(31747 * [0.0], float)
indices = np.arange(len(x))
interp = interp1d(indices, x, kind='quadratic')

Running this gives the following error:

~$ python tmp.py
Traceback (most recent call last):
  File "tmp.py", line 5, in <module>
    interp = interp1d(indices, x, kind='quadratic')
  File "/usr/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
line 308, in __init__
    self._spline = splmake(x,oriented_y,order=order)
  File "/usr/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
line 805, in splmake
    B = _fitpack._bsplmat(order, xk)
MemoryError

Unless I've misunderstood how this function is supposed to be used, it
just doesn't really seem to work for arrays of much more than a few
hundred elements.


Oscar

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Thread

Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-22 20:06 -0800
  Re: Memory error with quadratic interpolation Ulrich Eckhardt <ulrich.eckhardt@dominolaser.com> - 2013-01-23 09:55 +0100
    Re: Memory error with quadratic interpolation Oscar Benjamin <oscar.j.benjamin@gmail.com> - 2013-01-23 10:08 +0000
      Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:26 -0800
      Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:26 -0800
      Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:28 -0800
        Re: Memory error with quadratic interpolation Oscar Benjamin <oscar.j.benjamin@gmail.com> - 2013-01-23 14:40 +0000
          Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:57 -0800
            Re: Memory error with quadratic interpolation Oscar Benjamin <oscar.j.benjamin@gmail.com> - 2013-01-23 16:51 +0000
              Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 09:33 -0800
                Re: Memory error with quadratic interpolation Oscar Benjamin <oscar.j.benjamin@gmail.com> - 2013-01-24 10:30 +0000
              Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 09:33 -0800
          Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:57 -0800
      Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:28 -0800
    Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:47 -0800
  Re: Memory error with quadratic interpolation Isaac Won <winefrog@gmail.com> - 2013-01-23 06:24 -0800

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