Mailman 3 February 2008 - NumPy-Discussion

numpyx.pyx (recent svn) works?
by Neal Becker 09 Apr '08

09 Apr '08

I tried numpyx.pyx with cython-0.9.6.12. Here's what I got: In [2]: import numpyx In [3]: numpyx.test() -=-=-=-=-=-=-=-=-=-= printing array info for ndarray at 0x0 print number of dimensions: 0 address of strides: 0x0 strides: memory dump: -1e-30 -=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-=-=-= --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /home/nbecker/cython/<ipython console> in <module>() /home/nbecker/cython/numpyx.pyx in numpyx.test() 94 95 for arr in [arr1,arr2,arr3,arr4,arr5]: ---> 96 print arr 97 print_array_info(arr) 98 /home/nbecker/cython/numpyx.pyx in numpyx.print_array_info() 12 13 print '-='*10 ---> 14 print 'printing array info for ndarray at 0x%0lx'%(<c_python.Py_intptr_t>arr,) 15 print 'print number of dimensions:',arr.nd 16 print 'address of strides: 0x%0lx'%(<c_python.Py_intptr_t>arr.strides,) TypeError: only length-1 arrays can be converted to Python scalars

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Problem with numpy.linalg.eig?
by Peter Creasey 04 Apr '08

04 Apr '08

Hi all, The following code calling numpy v1.0.4 fails to terminate on my machine, which was not the case with v1.0.3.1 from numpy import arange, float64 from numpy.linalg import eig a = arange(13*13, dtype = float64) a.shape = (13,13) a = a%17 eig(a) Regards, Peter

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planet.scipy.org
by Jarrod Millman 01 Apr '08

01 Apr '08

Hey, I just wanted to announce that we now have a NumPy/SciPy blog aggregator thanks to Gaël Varoquaux: http://planet.scipy.org/ Feel free to contact me if you have a blog that you would like included. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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confusion about eigenvector
by devnew＠gmail.com 29 Mar '08

29 Mar '08

i all I am learning PCA method by reading up Turk&Petland papers etc while trying out PCA on a set of greyscale images using python, and numpy I tried to create eigenvectors and facespace. i have facesarray--- an NXP numpy.ndarray that contains data of images N=numof images,P=pixels in an image avgarray --1XP array containing avg value for each pixel adjustedfaces=facesarray-avgarray adjustedmatrix=matrix(adjustedfaces) adjustedmatrix_trans=adjustedmatrix.transpose() covariancematrix =adjustedmatrix*adjustedmatrix_trans evalues,evect=eigh(covariancematrix) after sorting such that most significant eigenvectors are selected. evectmatrix is now my eigenvectors matrix here is a sample using 4X3 greyscale images evalues [ -1.85852801e-13 6.31143639e+02 3.31182765e+03 5.29077871e+03] evect [[ 0.5 -0.06727772 0.6496399 -0.56871936] [ 0.5 -0.77317718 -0.37697426 0.10043632] [ 0.5 0.27108233 0.31014514 0.76179023] [ 0.5 0.56937257 -0.58281078 -0.29350719]] evectmatrix (sorted according to largest evalue first) [[-0.56871936 0.6496399 -0.06727772 0.5 ] [ 0.10043632 -0.37697426 -0.77317718 0.5 ] [ 0.76179023 0.31014514 0.27108233 0.5 ] [-0.29350719 -0.58281078 0.56937257 0.5 ]] then i can create facespace by facespace=evectmat*adjustedfaces till now i 've been following the steps as mentioned in the PCA tutorial(by Lindsay smith & others) what i want to know is that in the above evectmatrix is each row ([-0.56871936 0.6496399 -0.06727772 0.5 ] etc) an eigenvector? or does a column in the above matrix represent an eigenvector? to put it differently, should i represent an eigenvector by evectmatrix[i] or by (get_column_i_of(evectmatrix)).transpose() if someone can make this clear please do D

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Problems with long
by Tom Johnson 12 Mar '08

12 Mar '08

Hi, I'm having some troubles with long. >>> from numpy import log >>> log(8463186938969424928L) 43.5822574833 >>> log(10454852688145851272L) <type 'exceptions.AttributeError'>: 'long' object has no attribute 'log' Thoughts?

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Rename record array fields (with object arrays)
by Sameer DCosta 06 Mar '08

06 Mar '08

Hi, I'm having trouble renaming record array fields if they contain object arrays in them. I followed the solutions posted by Robert Kern and Stefan van der Walt (Thanks again) but it doesn't look like this method works in all cases. For reference: http://projects.scipy.org/pipermail/numpy-discussion/2008-February/031509.h… In [1]: from numpy import * In [2]: olddt = dtype([('foo', '|O4'), ('bar', float)]) In [3]: a = zeros(10, olddt) In [4]: a Out[4]: array([(0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0), (0, 0.0)], dtype=[('foo', '|O4'), ('bar', '<f8')]) In [5]: newdt = dtype([('notfoo', '|O4'), ('notbar', float)]) In [6]: b = a.view(newdt) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /home/titan/sameer/projects/<ipython console> TypeError: Cannot change data-type for object array. -- Sameer

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f2py compiled module not found by python
by Chris 05 Mar '08

05 Mar '08

Hello, I'm trying to build a package on Linux (Ubuntu) that contains a fortran module, built using f2py. However, despite the module building and installing without error, python cannot seem to see it (see log below). This works fine on Windows and Mac; the problem only seems to happen on Linux: In [1]: import PyMC ----------------------------------------------- exceptions.ImportError Traceback (most recent call last) /home/tianhuil/≤ipython console> /usr/lib/python2.4/site-packages/PyMC/__init__.py /home/tianhuil/≤string> /usr/lib/python2.4/site-packages/PyMC/MCMC.py ImportError: No module named flib /usr/lib/python2.4/site-packages/PyMC/MCMC.py Notice that the module exists in the site-packages directory: tianhuil <at> tianhuil:/usr/lib/python2.4/site-packages/PyMC$ ll total 432 drwxr-xr-x 2 root root 4096 2008-02-03 17:24 Backends -rwxrwx--- 1 root root 195890 2008-02-03 17:24 flib.so -rwxrwx--- 1 root root 259 2008-02-03 17:14 __init__.py -rw-r--r-- 1 root root 473 2008-02-03 17:24 __init__.pyc -rwxrwx--- 1 root root 10250 2008-02-03 17:14 Matplot.py -rw-r--r-- 1 root root 7516 2008-02-03 17:24 Matplot.pyc -rwxrwx--- 1 root root 98274 2008-02-03 17:14 MCMC.py -rw-r--r-- 1 root root 79039 2008-02-03 17:24 MCMC.pyc drwxr-xr-x 2 root root 4096 2008-02-03 17:24 Tests -rwxrwx--- 1 root root 6631 2008-02-03 17:14 TimeSeries.py -rw-r--r-- 1 root root 5043 2008-02-03 17:24 TimeSeries.pyc

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A little help please?
by Neal Becker 03 Mar '08

03 Mar '08

My user-defined type project has mostly gone well, but I'm stuck on mixed-type arithmetic. I have 2 types: cmplx_int32 and cmplx_int64. I have added basic arithmetic for those types, and for mix of those arrays and their respective scalars. But mixed arithmetic only partly works. In [2]: a Out[2]: array([(0,0), (1,0), (2,0), (3,0), (4,0), (5,0), (6,0), (7,0), (8,0), (9,0)], dtype=cmplx_int32) In [3]: b Out[3]: array([(0,0), (1,0), (2,0), (3,0), (4,0), (5,0), (6,0), (7,0), (8,0), (9,0)], dtype=cmplx_int64) In [4]: a+b --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /home/nbecker/numpy/<ipython console> in <module>() TypeError: function not supported for these types, and can't coerce safely to supported types In [5]: b+a Out[5]: array([(0,0), (2,0), (4,0), (6,0), (8,0), (10,0), (12,0), (14,0), (16,0), (18,0)], dtype=cmplx_int64) What I did: d1 is dtype cmplx_int32, d2 is dtype cmplx_int64. 1. PyArray_RegisterCastFunc (d1, d2->type_num, &cmplx_to_cmplx<cmplx_int64_t,cmplx_int32_t>); That registers a conversion from cmplx_int32->cmplx_int64. (Docs never explain when this conversion is used, BTW) 2. PyArray_RegisterCanCast (d1, d2->type_num, PyArray_NOSCALAR); 3. d1->f->castdict = PyDict_New(); PyObject *key = PyInt_FromLong (d2->type_num); PyObject *cobj = PyCObject_FromVoidPtr ((void*)(void(* (void*,void*,npy_intp,void*,void*))&cmplx_to_cmplx<cmplx_int64_t,cmplx_int32_t>, 0); PyDict_SetItem (d1->f->castdict, key, cobj); So now add (cmplx_int64, cmplx_int32) is OK, the 2nd arg is converted, but no attempt is made at radd. Obviously, I don't want to convert 64->32. Any clues what's missing here?

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contiguous true
by John Hunter 01 Mar '08

01 Mar '08

[apologies if this is a resend, my mail just flaked out] I have a boolean array and would like to find the lowest index "ind" where N contiguous elements are all True. Eg, if x is In [101]: x = np.random.rand(20)>.4 In [102]: x Out[102]: array([False, True, True, False, False, True, True, False, False, True, False, True, False, True, True, True, False, True, False, True], dtype=bool) I would like to find ind=1 for N=2 and ind=13 for N=2. I assume with the right cumsum, diff and maybe repeat magic, this can be vectorized, but the proper incantation is escaping me. for N==3, I thought of In [110]: x = x.astype(int) In [112]: y = x[:-2] + x[1:-1] + x[2:] In [125]: ind = (y==3).nonzero()[0] In [126]: if len(ind): ind = ind[0] In [128]: ind Out[128]: 13 Thanks, JDH

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image to array doubt
by Ray Schumacher 29 Feb '08

29 Feb '08

At 10:00 AM 2/29/2008, you wrote: > > Robin wrote > > I'm not sure why they would be doing this - to me it looks they might > > be using Image as a convenient way to store some other kind of data... > >thanks Robin, >I am wondering if there is a more straightforward way to do these.. >especially the vector to image function I would normally suggest PIL, as it contains most all of these types of array<>image functions See: http://www.pythonware.com/library/pil/handbook/imagemath.htm http://www.pythonware.com/library/pil/handbook/imageops.htm etc... as well as the built-ins for numpy array objects http://effbot.org/zone/pil-changes-116.htm frombuffer, fromstring, fromarray, tostring etc. http://www.pythonware.com/library/pil/handbook/image.htm (I've used them for home astronomy projects, myself.) Ray Schumacher Blue Cove Interactive No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.516 / Virus Database: 269.21.2/1304 - Release Date: 2/29/2008 8:18 AM

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