Mailman 3 March 2009 - NumPy-Discussion

Apropos ticked #913
by Charles R Harris March 5, 2009

March 5, 2009

Hi David, It isn't clear to me that trac is mailing out the ticket reponses, so I'm posting to the list. > #913: max is bogus if nan is in the array > --------------------+------------------------------------------------------- > Reporter: cdavid | Owner: somebody > Type: defect | Status: closed > Priority: normal | Milestone: 1.3.0 > Component: Other | Version: none > Severity: major | Resolution: fixed > Keywords: | > --------------------+------------------------------------------------------- > > Comment(by cdavid): > > What's the status on this, Chuck ? What do max/min and amax/amin do ? There are python max/min and their behaviour depends on the scalar type. I haven't looked at the numpy scalars to see precisely what they do. Numpy max/min are aliases for amax/amin defined when the core is imported. The functions amax/amin in turn map to the array methods max/min which call the maximum.reduce/minimum.reduce ufuncs, so they all propagate nans, i.e., if the array contains a nan, nan will be the return value. The nonpropagating comparisons are the ufuncs fmax/fmin and there are no corresponding array methods. I think fmax/fmin should be renamed fmaximum/fminimum before the release of 1.3 and the names fmax/fmin reserved for the reduced versions to match the names amax/amin. I'll do that if there are no objections. Chuck

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Faster way to generate a rotation matrix?
by Jonathan Taylor March 5, 2009

March 5, 2009

Hi, I am doing optimization on a vector of rotation angles tx,ty and tz using scipy.optimize.fmin. Unfortunately the function that I am optimizing needs the rotation matrix corresponding to this vector so it is getting constructed once for each iteration with new values. >From profiling I can Hi, I am doing optimization on a vector of rotation angles tx,ty and tz using scipy.optimize.fmin. Unfortunately the function that I am optimizing needs the rotation matrix corresponding to this vector so it is getting constructed once for each iteration with new values. >From profiling I can see that the function I am using to construct this rotation matrix is a bottleneck. I am currently using: def rotation(theta): tx,ty,tz = theta Rx = np.array([[1,0,0], [0, cos(tx), -sin(tx)], [0, sin(tx), cos(tx)]]) Ry = np.array([[cos(ty), 0, -sin(ty)], [0, 1, 0], [sin(ty), 0, cos(ty)]]) Rz = np.array([[cos(tz), -sin(tz), 0], [sin(tz), cos(tz), 0], [0,0,1]]) return np.dot(Rx, np.dot(Ry, Rz)) Is there a faster way to do this? Perhaps I can do this faster with a small cython module, but this might be overkill? Thanks for any help, Jonathan.see that the function I am using to construct this rotation matrix is a bottleneck. I am currently using: def rotation(theta): tx,ty,tz = theta Rx = np.array([[1,0,0], [0, cos(tx), -sin(tx)], [0, sin(tx), cos(tx)]]) Ry = np.array([[cos(ty), 0, -sin(ty)], [0, 1, 0], [sin(ty), 0, cos(ty)]]) Rz = np.array([[cos(tz), -sin(tz), 0], [sin(tz), cos(tz), 0], [0,0,1]]) return np.dot(Rx, np.dot(Ry, Rz)) Is there a faster way to do this? Perhaps I can do this faster with a small cython module, but this might be overkill? Thanks for any help, Jonathan.

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Re: [Numpy-discussion] numpy and python 2.6 on windows: please test
by James Watson March 5, 2009

March 5, 2009

> I would appreciate if people would test building numpy > (trunk); in particular since some issues are moderately complex and > system dependent On Vista with VS2008, numpy rev r6535, I get the following behaviour: 1. Building and installing numpy on python 2.6.1 compiled in debug mode succeeds, but 'import numpy' returns 'ImportError: No module named multiarray'. 2. Building and installing numpy using python compiled in release mode succeeds, 'import numpy' succeeds, but 'numpy.test()' crashes the interpreter. When running in a debug version of python, 'from numpy.core import multiarray' raises an ImportError, but this does not happen with the release version, where multiarray functions seem to work. Could this be related to the PyImport_Import and PyImport_ImportModule changes made in 2.6 (bottom of http://docs.python.org/whatsnew/2.6.html)? James.

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how to multiply the rows of a matrix by a different number?
by Jose Borreguero March 4, 2009

March 4, 2009

I guess there has to be an easy way for this. I have: M.shape=(10000,3) N.shape=(10000,) I want to do this: for i in range(10000): M[i]*=N[i] without the explicit loop -Jose

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NumPy SVN?
by Travis E. Oliphant March 4, 2009

March 4, 2009

Is commit to NumPy SVN still turned off? How do I get a working SVN again? -Travis

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loadtxt issues
by A B March 4, 2009

March 4, 2009

Hi, How do I write a loadtxt command to read in the following file and store each data point as the appropriate data type: 12|h|34.5|44.5 14552|bbb|34.5|42.5 Do the strings have to be read in separately from the numbers? Why would anyone use 'S10' instead of 'string'? dt = {'names': ('gender','age','weight','bal'), 'formats': ('i4', 'S4','f4', 'f4')} a = loadtxt("sample_data.txt", dtype=dt) gives ValueError: need more than 1 value to unpack I can do a = loadtxt("sample_data.txt", dtype="string") but can't use 'string' instead of S4 and all my data is read into strings. Seems like all the examples on-line use either numeric or textual input, but not both. Thanks.

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PyArray_SETITEM with object arrays in Cython
by Wes McKinney March 4, 2009

March 4, 2009

Hello, I am writing some Cython code and have noted that the buffer interface offers very little speedup for PyObject arrays. In trying to rewrite the same code using the C API in Cython, I find I can't get PyArray_SETITEM to work, in a call like: PyArray_SETITEM(result, <void *> iterresult.dataptr, obj) where result is an ndarray of dtype object, and obj is a PyObject*. Anyone have some experience with this can offer pointers (no pun intended!)? Thanks, Wes

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Question on lstsq and correlation coeff
by Anthony Kong March 4, 2009

March 4, 2009

Hi, all, It is probably a newbie question. I trying to use scipy/numpy in a finanical context. I want to compute the correlation coeff of two series (returns vs index returns). I tried two appoarches Firstly, from scipy.linalg import lstsq coeffs,a,b,c = lstsq(matrix, returns) # matrix contains index returns then I tried, import numpy as np cov = np.cov(idx1, returns) print cov.tolist() stddev_x = np.std(returns, ddof=1) stddev_y = np.std(idx1, ddof=1) print "cor = %s" % (cov.tolist()[:-1] /(stddev_x * stddev_y)) They differ from each other. As you can see from the numpy example, I am trying to find cor coeff for a sample. (ddof=1) So, my question is: is the discrepency caused by the fact that I am trying to use lstsq() on a 'sample popluation' (i.e. I am not regressing a full return series)? Is it correct to use lstsq() this way? Cheers, Anthony NOTICE This e-mail and any attachments are confidential and may contain copyright material of Macquarie Group Limited or third parties. If you are not the intended recipient of this email you should not read, print, re-transmit, store or act in reliance on this e-mail or any attachments, and should destroy all copies of them. Macquarie Group Limited does not guarantee the integrity of any emails or any attached files. The views or opinions expressed are the author's own and may not reflect the views or opinions of Macquarie Group Limited.

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[Fwd: Issue 113 in sphinx: nodes.py KeyError "entries" in numpy doc build]
by Eric Firing March 3, 2009

March 3, 2009

I have been trying to build numpy docs from the svn doc subdirectory, and I have been notifying the sphinx people when things don't work. They have made several fixes, but here is one that will require a change on the numpy side. I know zip about sphinx extensions, so I don't expect to be able to suggest a fix myself. (I am assuming that the doc subdirectory in svn *should* be buildable--am I correct?) Eric

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SVN and TRAC migrations starting NOW
by David Cournapeau March 3, 2009

March 3, 2009

Dear Numpy and Scipy developers, We are now starting the svn and trac migrations to new servers: - The svn repositories of both numpy and scipy are now unavailable, and should be available around 16:00 UTC (3rd March 2009). You will then be able to update/commit again. - Trac for numpy and scipy are also unavailable. We will send an email when everything will be backed up, The Scipy website administrators

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