[Numpy-discussion] Runtime error in numpy.polyfit

[josef.pktd at gmail.com]

On Wed, May 19, 2010 at 3:51 PM, William Carithers <wccarithers at lbl.gov> wrote:
> Thanks David and Josef. Replies interspersed below.
>
>
> On 5/19/10 12:24 PM, "josef.pktd at gmail.com" <josef.pktd at gmail.com> wrote:
>
>> On Wed, May 19, 2010 at 3:18 PM, David Goldsmith
>> <d.l.goldsmith at gmail.com> wrote:
>>> Charles H.: is this happening because he's calling the old version of
>>> polyfit?
>>>
>>> William: try using numpy.polynomial.polyfit instead, see if that works.
>
> It says  ypoly = n.polynomial.polyfit(yvalues, avalues, 2)
> AttributeError: 'module' object has no attribute 'polynomial'
>
> Is this because I'm using a relatively old (numpy-1.2.1) version?
>>>
>>> DG
>>>
>>> On Wed, May 19, 2010 at 11:03 AM, William Carithers <wccarithers at lbl.gov>
>>> wrote:
>>>>
>>>> I'm trying to do a simple 2nd degree polynomial fit to two arrays of 5
>>>> entries. I get a runtime error:
>>>> RuntimeError: more argument specifiers than keyword list entries
>>>> (remaining
>>>> format:'|:calc_lwork.gelss')  in the lstsq module inside numpy.polyfit.
>>>>
>>>> Here's the code snippet:
>>>> def findPeak(self, ydex, xdex):
>>>>        # take a vertical slice
>>>>        vslice = []
>>>>        for i in range(-1,10,1) :
>>>>            vslice.append(arcImage[ydex+i][xdex])
>>>>        vdex = n.where(vslice == max(vslice))
>>>>        ymax = ydex -1 + vdex[0][0]
>>>>        # approximate gaussian fit by parabolic fit to logs
>>>>        yvalues = n.array([ymax-2, ymax-1, ymax, ymax+1, ymax+2])
>>>>
>>>>
>>>> svalues=n.array([arcImage[ymax-2][xdex],arcImage[ymax-1][xdex],arcImage[ymax
>>>> ][xdex],arcImage[ymax+1][xdex], arcImage[ymax+2][xdex]])
>>>>        avalues = n.log(svalues)
>>>>        ypoly = n.polyfit(yvalues, avalues, 2)
>>>>
>>>> And the traceback:
>>>> File "/Users/williamcarithers/BOSS/src/calibrationModel.py", line 345, in
>>>> findPeak
>>>>    ypoly = n.polyfit(yvalues, avalues, 2)
>>>>  File
>>>>
>>>> "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/
>>>> numpy/lib/polynomial.py", line 503, in polyfit
>>>>    c, resids, rank, s = _lstsq(v, y, rcond)
>>>>  File
>>>>
>>>> "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/
>>>> numpy/lib/polynomial.py", line 46, in _lstsq
>>>>    return lstsq(X, y, rcond)
>>>>  File
>>>>
>>>> "/Library/Python/2.6/site-packages/scipy-0.7.1-py2.6-macosx-10.6-universal.e
>>>> gg/scipy/linalg/basic.py", line 545, in lstsq
>>>>    lwork = calc_lwork.gelss(gelss.prefix,m,n,nrhs)[1]
>>>> RuntimeError: more argument specifiers than keyword list entries
>>>> (remaining
>>>> format:'|:calc_lwork.gelss')
>>>>
>>>> This is such a simple application of polyfit and the error occurs in the
>>>> guts of lstsq, so I'm completely stumped. Any help would be greatly
>>>> appreciated.
>>
>> which version of numpy and the arguments to polyfit would be useful
>> information,e.g.
>>
>> print repr(yvalues)
>> print repr(avalues)
>>
>> before the call to polyfit
>
> Hi Josef,
>
> I'm using numpy-1.2.1

I don't remember whether 1.2.1 was fully python 2.6 compatible. I
would recommend upgrading if possible.

I don't have any problems with more recent versions of scipy and numpy

>>> import numpy as np
>>> y = np.array([ 864.,  865.,  866.,  867.,  868.])
>>> x = np.array([ 5.24860191,  6.0217514 ,  6.11434555,  6.09198856,  5.73753977],dtype=np.float32)
>>> np.polyfit(y, x, 2)
array([ -1.69296265e-01,   2.93325942e+02,  -1.27049335e+05])


I didn't know numpy will use the scipy version of linalg for this.
Do the scipy.test() pass?

My guess would be that there are some incompatibilities with your
python/numpy/scipy versions.

Josef


>
> Here are the arrays
> array([ 864.,  865.,  866.,  867.,  868.])
> array([ 5.24860191,  6.0217514 ,  6.11434555,  6.09198856,  5.73753977],
> dtype=float32)
>
> thanks
>>
>> Josef
>>
>>
>>>>
>>>> Thanks,
>>>> Bill Carithers
>>>>
>>>>
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>>>
>>>
>>>
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