Mailman 3 June 2007 - NumPy-Discussion

PCA - Principal Component Analysis
by Alex Torquato S. Carneiro June 25, 2007

June 25, 2007

I'm doing some projects in Python (system GNU / Linux - Ubuntu 7.0) about image processing. I'm needing a implementation of PCA, prefer to library for apt-get. Thanks. Alex. ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso

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qr decomposition with column pivoting/qr decomposition with householder reflections
by traveller3141 June 24, 2007

June 24, 2007

I'm in the process of trying to convert some Matlab code into Python. There's a statement of the form: [q,r,e] = qr(A) which performs a qr-decomposition of A, but then also returns a 'permutation' matrix. The purpose of this is to ensure that the values along r's diagonal are decreasing. I believe this technique is called "qr decomposition with column pivoting" or (equivalently) "qr decomposition with householder reflections". I have not been able to find an implementation of this within numpy. Does one exist? Or should I come to truly understand this algorithm (prob'ly a good idea regardless) and implement it? Thanks, Steven

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Help installing numpy 1.0.2 on LINUX
by John Pruce June 24, 2007

June 24, 2007

I am trying to install nunpy 1.0.2 on aMandrake Linux system kernel 2.6.17mdk. I have followed the Install instructions in numpy. I am including a small portion of the python setup.py install command: Running from numpy source directory. F2PY Version 2_3649 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib/atlas NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib/atlas NOT AVAILABLE atlas_blas_info: FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = c Could not locate executable g77 Could not locate executable f95 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc -pthread _configtest.o -L/usr/local/lib/atlas -lf77blas -lcblas -latlas -o _configtest ATLAS version 3.6.0 built by root on Fri Jun 15 18:59:04 EDT 2007: UNAME : Linux localhost 2.6.17-5mdv #1 SMP Wed Sep 13 14:32:31 EDT 2006 i686 Celeron (Mendocino) GNU/Linux INSTFLG : MMDEF : ARCHDEF : F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 131072 F77 : /usr/local//gcc2.95.3/bin/g77, version GNU Fortran 0.5.25 20010315 (release) F77FLAGS : -fomit-frame-pointer -O CC : /usr/local/gcc2.95.3/bin/gcc, version 2.95.3 CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops MCC : /usr/local/gcc2.95.3/bin/gcc, version 2.95.3 MCCFLAGS : -fomit-frame-pointer -O success! removing: _configtest.c _configtest.o _configtest FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = c define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/lib/atlas NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib/atlas libraries lapack_atlas not found in /usr/local/lib/atlas numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries lapack_atlas not found in /usr/local/lib/atlas numpy.distutils.system_info.atlas_info FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = f77 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc -pthread _configtest.o -L/usr/local/lib/atlas -llapack -lf77blas -lcblas -latlas -o _configtest ATLAS version 3.6.0 built by root on Fri Jun 15 18:59:04 EDT 2007: UNAME : Linux localhost 2.6.17-5mdv #1 SMP Wed Sep 13 14:32:31 EDT 2006 i686 Celeron (Mendocino) GNU/Linux INSTFLG : MMDEF : ARCHDEF : F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 131072 F77 : /usr/local//gcc2.95.3/bin/g77, version GNU Fortran 0.5.25 20010315 (release) F77FLAGS : -fomit-frame-pointer -O CC : /usr/local/gcc2.95.3/bin/gcc, version 2.95.3 CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops MCC : /usr/local/gcc2.95.3/bin/gcc, version 2.95.3 MCCFLAGS : -fomit-frame-pointer -O success! removing: _configtest.c _configtest.o _configtest FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] running install running build running config_fc running build_src building py_modules sources creating build/src.linux-i686-2.5 creating build/src.linux-i686-2.5/numpy creating build/src.linux-i686-2.5/numpy/distutils building extension "numpy.core.multiarray" sources creating build/src.linux-i686-2.5/numpy/core Generating build/src.linux-i686-2.5/numpy/core/config.h customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC When I try to run numpy.test(level=1) I get: >>> import numpy >>> numpy.test(level=1) Traceback (most recent call last) File "<stdln>". line 1, in <module> AttributeError: 'module' has no attribute 'test' >>> Thank you for your help or suggestions. John -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 9 at http://www.opera.com Powered by Outblaze

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Re: [Numpy-discussion] Help installing numpy 1.0.2 on LINUX
by John Pruce June 24, 2007

June 24, 2007

> ----- Original Message ----- > From: "Stefan van der Walt" <stefan(a)sun.ac.za> > To: numpy-discussion(a)scipy.org > Subject: Re: [Numpy-discussion] Help installing numpy 1.0.2 on LINUX > Date: Sun, 24 Jun 2007 19:48:14 +0200 > > > On Sun, Jun 24, 2007 at 05:58:33PM +0100, John Pruce wrote: > > When I try to run numpy.test(level=1) I get: > > > > >>> import numpy > > >>> numpy.test(level=1) > > Traceback (most recent call last) > > File "<stdln>". line 1, in <module> > > AttributeError: 'module' has no attribute 'test' > > >>> > > > > Thank you for your help or suggestions. > > Are you running from the numpy source directory? If so, change out of > it and try again. > > Stéfan > _______________________________________________ > Numpy-discussion mailing list > Numpy-discussion(a)scipy.org > http://projects.scipy.org/mailman/listinfo/numpy-discussion Thank you That was the problem John -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 9 at http://www.opera.com Powered by Outblaze

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Unhandled floating point exception running test in numpy-1.0.3 and svn 3875
by John Ollinger June 24, 2007

June 24, 2007

I have just been updating our version of Python, numpy and scipy and have run into a floating point exception that crashes Python when I test the release. I am running gcc 3.3.1 on SuSe Linux 2.4.21-144-smp4G. The error first occurred with numpy-1.0.3. I downloaded svn 3875 when I then read the scipy web page and installed the latest subversion. The test command I am using is python -c 'import numpy; numpy.test(level=1,verbosity==2)' and occurs during the matvec test. This test uses rand to generate 10x8 and 8x1 matrices. The test that multiplies the first matrix by its transpose works; the second test that multiplies the first matrix times the second causes the floating point exception. The code does not crash if the matrices are created with "zero()" but crashes any random matrix generated by rand. It works fine with all of my applications (ones that only multiply 4x4 and 4x1 matrices. Does anyone know if this is a known problem? I can't find any mention of it on the web. It is cold comfort to know that my applications will fail catastrophically rather than by being inaccurate. Thanks. John

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Re: [Numpy-discussion] How to create a boolean sub-array from a larger string array?
by Andriy Basilisk June 23, 2007

June 23, 2007

> You can always use something like > > mdat[[2,4]] == '*' > > to get the boolean array you want. This scheme can work with any string > representation of True and False. > Dang! I keep forgetting that a conditional test can return an array like that - thanks for the reminder, this will clean up my ugly code from before :) Back to the drawing board, -Basilisk96

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How to create a boolean sub-array from a larger string array?
by Andriy Basilisk June 23, 2007

June 23, 2007

Hello all, My challenge is this: I'm working on an application that parses numerical data from a text report using regular expressions, and then places the results in Numpy matrices for processing. The data contains integers, floats, and boolean values. The boolean values are represented in the text file by either an empty string '', or by a star '*'. The regex parser creates a sequence of nested lists that is readily converted to a MxN string-type matrix. Then, the necessary rows of that matrix are sliced to create the necessary new sub-matrices. Here is a simplified sample of my solution so far: import numpy as _N data = [['1', '5.30', '', '3.44', '*'], ['2', '-4.12', '*', '-1.24', ''], ['3', '0.45', '', '3.22', '*']] mdat = _N.mat(data).T # mdat.shape is now (5,3) ids = mdat[0,].astype(_N.int) #this works for str->int noms = mdat[(1,3),].astype(_N.float64) #same idea also works for str->float64 ## The following technique would be nice, but ## it causes a ValueError: invalid literal for int() with base 10: '' outs = mdat[(2,4),].astype(_N.bool) ## Instead, I have to convert the strings to '0' or '1' ## explicitly, then cast them to a bool matrix: for i, b in enumerate(mdat[(2,4),].T): mdat[2, i] = 1 if mdat[2, i] else 0 mdat[4, i] = 1 if mdat[4, i] else 0 outs = mdat[(2,4),].astype(_N.bool) I was expecting the above to behave similar to the Python bool() function on strings: >>> bool(''), bool('*') (False, True) but it doesn't work that way. Can anyone enlighten me as to why slices of my string matrix cannot be cast to boolean matrices? I'd rather not have to resort to the 'for' loop if there is a smarter way to do this. If an intermediate numpy.array is required instead of numpy.matrix as I have shown here, it's acceptable. I am using the matrix class in this case because the application thrives on it. I'm using Python 2.5 and NumPy 1.0.1 on WinXP. Any help and useful comments will be appreciated, -Basilisk96

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alter_code1 and "from Numeric import *"
by Trevor Law June 22, 2007

June 22, 2007

Hello, I have just tried using alter_code1 on a code tree, and it appears to ignore "from Numeric import *" statements (does not change them to "from numpy.oldnumeric import *"). I looked at the alter_code1.py and it says that the script should warn about importing *. Although the script may not be behaving absolutely correctly, I am more concerned as to whether or not using "from numpy.oldnumeric import *" is likely to result in undetected (non-syntactic) errors. Any feedback would be welcome. Thank you for your time, Trevor Law

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handling of inf
by Kilian Koepsell June 22, 2007

June 22, 2007

Hi, I was wondering if the numpy function 'isinf' should return True for complex infinity. I encountered the following behavior that could be considered a bug: >>> import numpy as N >>> N.isinf(1j*N.inf) True >>> 1j/(N.array(1)-1) (nannanj) >>> N.isinf(1j/(N.array(1)-1)) False >>> 1j/(N.array([1])-1) array([ nan +nanj]) >>> N.isinf(1j/(N.array([1])-1)) array([False], dtype=bool) Thanks, Kilian -- Kilian Koepsell Redwood Center for Theoretical Neuroscience Helen Wills Neuroscience Institute, UC Berkeley 132 Barker Hall, #3190, Berkeley, CA 94720-3190

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Suppressing "nesting" (recursion, descent) in array construction.
by Michael McNeil Forbes June 21, 2007

June 21, 2007

Hi, I have a list of tuples that I am using as keys and I would like to sort this along with some other arrays using argsort. How can I do this? I would like to do something like: # These are constructed using lists because they accumulate using append() data = [1.0, 3,0] keys = [('a',1),('b',2)] # Convert to arrays for indexing data = array(data1) keys = array(keys) # <--Converts to a 2d array rather than 1d array of tuples . inds = argsort(data) data[:] = data[inds] keys[:] = keys[inds] It seems there should be some way of specifying to the array constructor not to 'descend' (perhaps by specifying the desired dimensions of the final array or something) but I cannot find a nice way around this. Any suggestions? Thanks, Michael.

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