Mailman 3 January 2010 - NumPy-Discussion

how to do a proper 2 column sort on a 2 dimensional array ??
by robert somerville 19 Jan '10

19 Jan '10

Hi; i am having trouble trying to sort the rows of a 2 dimensional array by the values in the first column .. does anybody know how or have an example of how to do this ??? while leaving the remain columns remain relative to the leading column from numpy import * a=array( [ [4, 4, 3], [4, 5, 2], [3, 1, 1] ] ) i would like to generate the output (or get the output ...) b = [ [3,1,1], [4,4,3], [4,5,2] ] to be specific the primary sort is on the the first column, and within the primary key, i would like to do a seconday sort of the matrix based on 2nd column .. does Numpy have this finctionality, or do part have to be programmed in Python ?? thanks; bob

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Numpy.dot segmentation fault
by Mark Lescroart 18 Jan '10

18 Jan '10

Hello, I've encountered a segfault in numpy when trying to compute a dot product for two arrays - see code below. The problem only seems to occur when the arrays reach a certain size. I'm using Numpy version 1.3.0, installed via macports, on a 2.33 GHz Intel Core2 Duo Macbook Pro running Leopard (OSX 10.5.8). I've posted this as a bug on the numpy page, where I was told it might have to do with my ATLAS installation (version 3.8.3_1, also installed via macports). Has anyone run into anything like this before? Cheers, Mark Example code: import numpy as N print 'Demonstration of Numpy Bug:' print 'loading X (random numbers)' SzList = [10,20,30,40,50,60,70,80,90,100] for Sz in SzList: print 'X size = %d,%d'%(300,Sz) X = N.random.rand(300,Sz) Y = N.random.rand(300,3) print 'Attempting dot product of X and Y' N.dot(X.T,Y) print 'Finished without bug.' Result (run through gdb): (There were a number of warnings like this - so many that they went off the top of the screen and I couldn't copy them all. This was typical of the warnings.) Reading symbols for shared libraries warning: Could not find object file "/opt/local/var/macports/ build_opt_local_var_macports_sources_rsync .macports.org_release_ports_lang_python26/work/Python-2.6.4/build/ temp.macosx-10.5-i386-2.6/opt/local/var/macports/ build_opt_local_var_macports_sources_rsync.macports.org_release _ports_lang_python26/work/Python-2.6.4/Modules/_collectionsmodule.o" - no debug information available for "/opt/local/var/macports/build/ _opt_local_var_macports_sources_rsync .macports.org_release_ports_lang_python26/work/Python-2.6.4/Modules/ _collectionsmodule.c". . done Demonstration of Numpy Bug: loading X (random numbers) X size = 300,10 Attempting dot product of X and Y Finished without bug. X size = 300,20 Attempting dot product of X and Y Finished without bug. X size = 300,30 Attempting dot product of X and Y Finished without bug. X size = 300,40 Attempting dot product of X and Y Finished without bug. X size = 300,50 Attempting dot product of X and Y Finished without bug. X size = 300,60 Attempting dot product of X and Y Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: 13 at address: 0x00000000 [Switching to process 56005 thread 0x117] 0x01038884 in ATL_dupMBmm0_2_0_b0 ()

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logic problem
by Ernest Adrogué 18 Jan '10

18 Jan '10

Hi, This is hard to explain. In this code: reduce(np.logical_or, [m1 & m2, m1 & m3, m2 & m3]) where m1, m2 and m3 are boolean arrays, I'm trying to figure out an expression that works with an arbitrary number of arrays, not just 3. Any idea?? Bye.

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Re: [Numpy-discussion] performance matrix multiplication vs. matlab
by Bruce Southey 18 Jan '10

18 Jan '10

On 01/18/2010 12:47 PM, Vicente Sole wrote: > Quoting Bruce Southey <bsouthey(a)gmail.com>: > >> >> If you obtain the code from any package then you are bound by the terms >> of that code. So while a user might not be 'inconvenienced' by the LGPL, >> they are required to meet the terms as required. For some licenses (like >> the LGPL) these terms do not really apply until you distribute the code >> but that does not mean that the user is exempt from the licensing terms >> of that code because they have not distributed their code (yet). >> >> Furthermore there are a number of numpy users that download the numpy >> project for further distribution such as Enthought, packagers for Linux >> distributions and developers of projects like Python(x,y). Some of these >> users would be inconvenienced because binary-only distributions would >> not be permitted in any form. >> > > I think people are confusing LGPL and GPL... Not at all. > > I can distribute my code in binary form without any restriction when > using an LGPL library UNLESS I have modified the library itself. I do not interpret the LGPL version 3 in this way: A "Combined Work" is a work produced by combining or linking an Application with the Library. So you must apply section 4, in particular, provide the "Minimal Corresponding Source": The "Minimal Corresponding Source" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. So a binary-only is usually not appropriate. Bruce

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Re: [Numpy-discussion] performance matrix multiplication vs. matlab
by Benoit Jacob 18 Jan '10

18 Jan '10

>> Hi, >> >> I while back, someone talked about aigen2(http://eigen.tuxfamily.org/). In >> their benchmark they give info that they are competitive again mkl and goto >> on matrix matrix product. They are not better, but that could make a good >> default implementation for numpy when their is no blas installed. I think >> the license would allow to include it in numpy directly. > >It is licensed under the LGPLv3, so it is not compatible with the numpy license. Hi, I'm one of Eigen's authors. Eigen is indeed LGPL3 licensed. Our intent and understanding is that this makes Eigen usable by virtually any software, whence my disappointment to learn that LGPL3 software can't be used by NumPy. Just for my information, could you tell my why NumPy can't use LGPL3-licensed libraries? I found this page: http://www.scipy.org/License_Compatibility It does say that LGPL-licensed code can't be added to NumPy, but there's a big difference between adding LGPL code directly into NumPy, and just letting NumPy _use_ LGPL code. Couldn't you simply: - either add LGPL-licensed code to a third_party subdirectory not subject to the NumPy license, and just use it? This is common practice, see e.g. how Qt puts a copy of WebKit in a third_party subdirectory. - or use LGPL-licensed code as an external dependency? FYI, several BSD-licensed projects are using Eigen ;) Thanks for your consideration Benoit

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EPD 6.0 and IPython Webinar Friday
by Amenity Applewhite 18 Jan '10

18 Jan '10

Email not displaying correctly? View it in your browser. Happy 2010! To start the year off, we've released a new version of EPD and lined up a solid set of training options. Scientific Computing with Python Webinar This Friday, Travis Oliphant will then provide an introduction to multiprocessing and iPython.kernal. Scientific Computing with Python Webinar Multiprocessing and iPython.kernal Friday, January 22: 1pm CST/7pm UTC Register Enthought Live Training Enthought's intensive training courses are offered in 3-5 day sessions. The Python skills you'll acquire will save you and your organization time and money in 2010. Enthought Open Course February 22-26, Austin, TX • Python for Scientists and Engineers • Interfacing with C / C++ and Fortran • Introduction to UIs and Visualization Enjoy! The Enthought Team EPD 6.0 Released Now available in our repository, EPD 6.0 includes Python 2.6, PiCloud's cloud library, and NumPy 1.4... Not to mention 64-bit support for Windows, OSX, and Linux. Details. Download now. New: Enthought channel on YouTube Short instructional videos straight from the desktops of our developers. Get started with a 4-part series on interpolation with SciPy. Our mailing address is: Enthought, Inc. 515 Congress Ave. Austin, TX 78701 Copyright (C) 2009 Enthought, Inc. All rights reserved. Forward this email to a friend

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Structured array sorting
by Thomas Robitaille 18 Jan '10

18 Jan '10

I am having trouble sorting a structured array - in the example below, sorting by the first column (col1) seems to work, but not sorting by the second column (col2). Is this a bug? I am using numpy svn r8071 on MacOS 10.6. Thanks for any help, Thomas Python 2.6.1 (r261:67515, Jul 7 2009, 23:51:51) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy as np >>> data = np.array([('a ', 2.), ('b', 4.), ('d', 3.), ('c', 1.)], ... dtype=[('col1', '|S5'), ('col2', '>f8')]) >>> >>> data array([('a ', 2.0), ('b', 4.0), ('d', 3.0), ('c', 1.0)], dtype=[('col1', '|S5'), ('col2', '>f8')]) >>> data.sort(order=['col1']) >>> data array([('a ', 2.0), ('b', 4.0), ('c', 1.0), ('d', 3.0)], dtype=[('col1', '|S5'), ('col2', '>f8')]) >>> data.sort(order=['col2']) >>> data array([('a ', 2.0), ('d', 3.0), ('b', 4.0), ('c', 1.0)], dtype=[('col1', '|S5'), ('col2', '>f8')])

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Pandas LongPanel/WidePanel for 3d timeseries?
by totalbull＠mac.com 17 Jan '10

17 Jan '10

Hello, I am successfully using the new Pandas library for series and matrix analysis using 2 dimensional arrays. I am using the "fromDict" method which works well, and I am creating 2-dimensional arrays where each axis is indexed by FX currency names. So for example pandas DataFrame called aa: >>> aa.columns Index([AUDUSD, EURCHF, EURCZK, EURHUF, EURPLN, EURSEK, EURUSD, GBPUSD, NZDUSD, USDBRL, USDCAD, USDCLP, USDILS, USDJPY, USDKRW, USDMXN, USDRUB, USDSGD, USDTRY, USDTWD, USDZAR], dtype=object) >>> aa.rows <bound method DataFrame.rows of <class 'pandas.core.frame.DataFrame'> Index: 21 entries, AUDUSD to USDZAR Data columns: AUDUSD 20 non-null values EURCHF 20 non-null values EURCZK 20 non-null values EURHUF 20 non-null values EURPLN 20 non-null values EURSEK 20 non-null values EURUSD 20 non-null values GBPUSD 20 non-null values NZDUSD 20 non-null values USDBRL 20 non-null values USDCAD 20 non-null values USDCLP 20 non-null values USDILS 20 non-null values USDJPY 20 non-null values USDKRW 20 non-null values USDMXN 20 non-null values USDRUB 20 non-null values USDSGD 20 non-null values USDTRY 20 non-null values USDTWD 20 non-null values USDZAR 20 non-null values > >>> aa['USDZAR']['USDTWD'] 1.2711725043942563 >>> (each cell contains the number of standard errors of today's prices in the linear regression of the two currency pairs). Now I want to create a 3 dimensional stack of these aa-style matrices, where the z axis is indexed by historical dates. IE one matrix for each date, from today, going back 2 years. What is the best pandas function for doing this? Is it pandas.WidePanel or pandas.LongPanel, and how do I use these functions to construct this 3d stack? (I would ideally like to append each 2d matrix to the 3d stack as I create each one). Thanks for the help...... unfortunately can't find this in the online docs. Tom

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Wanted: new release manager for 1.5 and above
by David Cournapeau 16 Jan '10

16 Jan '10

Hi, as I already hinted to some people in person, I won't make new releases of numpy (and scipy) as I used to. To ease the transition, I think it would be good to have new people with who we could make say the 1.4.1 release together. Making installers is relatively streamlined now, it can be done almost 100 % automatically - the testing is still manual. I still think it would be a good idea to have a different release manager for each release - it may be easier to find someone to do it if it is only for one release cycle. cheers, David

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Python coders for Haiti disaster relief
by Peter Clarke 16 Jan '10

16 Jan '10

Apologies for off topic posting but I think this in an important project. Python programmers are required immediately for assistance in coding a disaster management framework for the Earthquake in Haiti. >From http://wiki.python.org/moin/VolunteerOpportunities: ----------------- URGENT REQUEST, Sahana Disaster Management System, Haiti Earthquake *Job Description*:This is an urgent call for experienced Python programmers to help in the Sahana Disaster Management System immediately - knowledge of Web2Py <http://wiki.python.org/moin/Web2Py> platform would be best. The Sahana Disaster Management System is used to coordinate relief efforts. Please recruit any available programmers for the Haiti effort as quickly as possible and have them contact me immediately so that I can put them in touch with the correct people. Thank you kindly and I do hope that we can quickly identify some contributors for this monumental effort - they are needed ASAP. http://sahanapy.org/ is the developer site and the demo is http://demo.sahanapy.org/ - *Contact*: Connie White, PhD, Institute for Emergency Preparedness, Jacksonville State University - *E-mail contact*: connie.m.white(a)gmail.com - *Web*: http://sahanapy.org/ ----------------------------- Please help if you can. -Peter Clarke

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