Mailman 3 August 2003 - NumPy-Discussion

Blitz++, NumArray...
by Fernando Perez 26 Sep '03

26 Sep '03

Hi all, as some of you know, I'm a big fan of weave.inline() for the ease of development it offers. Essentially C++ becomes a scripting part of python, with only the occasional recompile overhead (but this is transparent to the users). inline() makes heavy use of the blitz++ library, to represent numpy arrays as blitz arrays and therefore index them as Arr(i,j,k...). This seems to me like a very sound decision, as the blitz library was specifically written to provide simultaneously fortran-like performance with high-level object orientation. With this in mind, I have a few questions: - Is there anything in Numarray's design which prevents this same trick from being used? The core of getting a Numpy array into a blitz one is simply a call to: // Convert a Numpy array to a blitz one, using the original's data (no copy) template<class T, int N> static blitz::Array<T,N> py_to_blitz(PyArrayObject *arr_obj) { blitz::TinyVector<int,N> shape(0); blitz::TinyVector<int,N> strides(0); for (int i=0;i<N;i++) { shape[i] = arr_obj->dimensions[i]; strides[i] = arr_obj->strides[i]/sizeof(T); } return blitz::Array<T,N>((T*) arr_obj->data,shape,strides, blitz::neverDeleteData); } I would not be surprised if something much like this would work for Numarrays, but I'd like to know for sure. - If the above is indeed possible for Numarray, do you guys feel that blitz should be considered an integral part of python's low-level arsenal, or not? I view its advantages especially in the field of an extremely clean, simple syntax (compared to the low-level Numpy API, I'm not familiar with Numarray yet). I've seen examples where a numpy algorithm can be recoded using blitz in a _far_ smaller amount of code, and with performance gains to boot (in some cases, not all). Please note that I am NOT second-guessing any of the design decisions made by the Numarray crowd. I just want to clarify if it's possible to have a C++ API which gives access to numarray with the simplest, highest-level syntax and behavior which is reasonable. This is important for teams where not everyone is an expert on C pointer manipulation details, but they may be perfectly ok with writing loops over things which can be indexed as A(i,j,k). - If any of this seems worthy of more detailed discussion, I told Eric Jones that I'd be happy to coordinate something along these lines at Scipy'03. If there's time in the schedule I'd be glad to do it officially, otherwise we can just try to keep it in mind for a lunch/dinner meeting. Documenting a 'Best Practices for low-level numerical work in python' would probably be a beneficial thing to do for the community. Right now there are so many options that I'm sure I'm not the only one to feel a bit confused. - If Blitz++ is indeed deemed a worthy piece of this puzzle, I wonder if we could contact some of its developers to bring them into this discussion. I worry a bit that activity on its mailing lists seems rather slow, but I noticed that an apparently central guy, Julian C. Cummings, is at CACR/Caltech. Perhaps he could stop by and let us know what the future for blitz looks like. I can fire off an email to him if there is interest in the blitz thing. Anyway, I'm just trying to 'pre-soak' a few ideas for discussion at scipy'03 on these topics. Best regards, Fernando.

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ANN: Job posting -- developer position available
by eric jones 23 Sep '03

23 Sep '03

Hey group, We have a developer position open here at Enthought, and I thought I'd see if anyone is interested. The posting is below. There is also a tech writer and HCI opening listed on the website: http://www.enthought.com/careers.html thanks! eric Position: Python Developer Type: Full-Time Enthought, Inc. is a technology startup in the Austin, TX area that is looking for a motivated Python Developer to join our development team. Responsibilities include developing and deploying scientific applications within the Fortune 500. Our size and prospects provide significant opportunity for growth and advancement for Enthought employees. Candidates should have the following qualifications: - BS or MS in Computer Science or Engineering or other scientific field - 3+ years experience in the software industry - Experience developing solutions in the following languages: - Python - C/C++ - User interface design experience - Developing and deploying custom solutions for clients - Excellent verbal and written communication skills Ideal candidates will also demonstrate the following skills: - Use of the wxPython user interface library - Experience with Geophysics applications - Experience in the fields of statistics, linear algebra and calculus Please send resumes to jobs(a)enthought.com.

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bug?
by Peter Verveer 02 Sep '03

02 Sep '03

Consider conversion of a slice using the astype() method: >>> a = array([[1,2],[3,4]]) >>> b = a[1, ...] >>> print b [3 4] Conversion using the astype() method goes wrong: >>> print b.astype(Float32) [ 1. 2.] This fixes it: >>> print b.copy().astype(Float32) [ 3. 4.] A bug? Cheers, Peter -- Dr. Peter J. Verveer Cell Biology and Cell Biophysics Programme EMBL Meyerhofstrasse 1 D-69117 Heidelberg Germany Tel. : +49 6221 387245 Fax : +49 6221 387242 Email: Peter.Verveer(a)embl-heidelberg.de

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Re: [Numpy-discussion] Numarray web site and google
by Sebastian Haase 30 Aug '03

30 Aug '03

Hi all, It already worked - see for yourself. http://www.google.com/search?q=numarray See you all at SciPy'03 ;-) Sebastian Haase >----- Original Message ----- >From: "Perry Greenfield" <perry(a)stsci.edu> >To: "Sebastian Haase" <haase(a)msg.ucsf.edu>; ><numpy-discussion(a)lists.sourceforge.net> >Sent: Thursday, August 21, 2003 5:47 AM >Subject: RE: [Numpy-discussion] Numarray web site and google > > > > Thanks for pointing this out and particularly for doing research > > into how to fix the problem! We will give this a try (though it may > > take a few days). > > > > > -----Original Message----- > > > From: numpy-discussion-admin(a)lists.sourceforge.net > > > [mailto:numpy-discussion-admin@lists.sourceforge.net]On Behalf Of > > > Sebastian Haase > > > Sent: Wednesday, August 20, 2003 6:42 PM > > > To: numpy-discussion(a)lists.sourceforge.net > > > Subject: [Numpy-discussion] Numarray web site and google > > > > > > > > > Hi, > > > I'm not sure how much time you guys wants to spend on the > > > numarray web site, > > > but I find that a google search for 'numarray' still points to > > > http://stsdas.stsci.edu/numarray/ > > > saying numarray has moved! > > > (OK it does bring me to the right page after some seconds) > > > Anyway - doing some search on Usenet I found this > > > http://groups.google.com/groups?threadm=vc3bh351prjbd8%40corp.supe > > > rnews.com&rnum=8&prev=/groups%3Fq%3D%2522search%2Bengines%2522%2B%2522%252Bh > > as%> 2Bmoved%2522%2B%2Bhtml%2Bhead%26hl%3Den%26lr%3D%26ie%3DISO-8859-1% > > > 26safe%3Doff > > > From: Guy Macon (guymacon+"_http://www.guymacon.com/_"03(a)spamcop.net) > > > Subject: Re: If I can't redirect to new url, how bad is forwarding it? > > > Newsgroups: alt.internet.search-engines > > > Date: 2003-05-13 19:48:05 PST > > > > > > he essentially says adding this to the html-page might fix it soon: > > > <head> > > > <meta name="robots" content="noindex, follow" /> > > > <title>http://www.example.com</title> > > > <meta http-equiv="refresh" content="http://www.example.com" /> > > > </head> > > > > > > > > > Just a thought ... > > > > > > Thanks for numarray - have a great day. > > > > > > Sebastian Haase > > > > > > > > > > > > ------------------------------------------------------- > > > This SF.net email is sponsored by Dice.com. > > > Did you know that Dice has over 25,000 tech jobs available today? From > > > careers in IT to Engineering to Tech Sales, Dice has tech jobs from the > > > best hiring companies. http://www.dice.com/index.epl?rel_code=104 > > > _______________________________________________ > > > Numpy-discussion mailing list > > > Numpy-discussion(a)lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/numpy-discussion > > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: VM Ware > > With VMware you can run multiple operating systems on a single machine. > > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines > > at the same time. Free trial click > here:http://www.vmware.com/wl/offer/358/0 > > _______________________________________________ > > Numpy-discussion mailing list > > Numpy-discussion(a)lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/numpy-discussion > > >

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numarray.linear_algrebra > cholesky_decomposition problem
by Justin Worrall 30 Aug '03

30 Aug '03

Hi, I'm having problems using the cholesky decomposition function - perhaps someone could point out where I am going wrong. Many thanks, Justin dingy /ms/user/w/worrall 22$ python Python 2.3 (#1, Aug 19 2003, 16:53:06) [GCC 2.95.2 19991024 (release)] on sunos5 Type "help", "copyright", "credits" or "license" for more information. >>> from numarray import * >>> from numarray.linear_algebra import * >>> x=array([[1.0,0.0],[0.5,1.0]]) >>> x array([[ 1. , 0. ], [ 0.5, 1. ]]) >>> cholesky_decomposition(x) Traceback (most recent call last): File "<stdin>", line 1, in ? File "/u/worrall/Python-2.3/numarray/linear_algebra/LinearAlgebra2.py", line 159, in cholesky_decomposition return copy.copy(num.transpose(mlab.triu(a,k=0))) File "/u/worrall/Python-2.3/numarray/linear_algebra/mlab.py", line 134, in triu svsp = m.spacesaver() AttributeError: 'NumArray' object has no attribute 'spacesaver' >>> -- This is not an offer (or solicitation of an offer) to buy/sell the securities/instruments mentioned or an official confirmation. Morgan Stanley may deal as principal in or own or act as market maker for securities/instruments mentioned or may advise the issuers. This may refer to a research analyst/research report. Unless indicated, these views are the author?s and may differ from those of Morgan Stanley research or others in the Firm. We do not represent this is accurate or complete and we may not update this. Past performance is not indicative of future returns. For additional information, research reports and important disclosures, contact me or see https://secure.ms.com/servlet/cls. You should not use email to request, authorize or effect the purchase or sale of any security or instrument, to send transfer instructions, or to effect any other transactions. We cannot guarantee that any such requests received via email will be processed in a timely manner. This communication is solely for the addres

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ANN: numarray-0.7
by Todd Miller 29 Aug '03

29 Aug '03

Release Notes for numarray-0.7 Numarray is an array processing package designed to efficiently manipulate large multi-dimensional arrays. Numarray is modelled after Numeric and features c-code generated from python template scripts, the capacity to operate directly on arrays in files, and improved type promotions. I. ENHANCEMENTS 1. Object Arrays numarray now has an object array facility. numarray.objects provides array indexing and ufuncs for fixed length collections of arbitrary Python objects. 2. Merger of NumArray/ComplexArray classes Numarray's NumArray and ComplexArray classes have been unified into a single class. Thus, a single base class can be used to derive array classes which operate on integer, real or complex numbers. Thanks to Colin Williams for this suggestion. 3. Indexing improvements The implementation of numarray's indexing has been simplified and improved. Ad-hoc logic for getting single array elements fast has been replaced by a full conversion to C of the top level of numarray's Python indexing code. The resulting code is simpler, prototyped in Python, and adds an additional kind of indexing which occurs entirely in C for speed: sub-arrays. Slicing and array indexing, however, still involve significant amounts of Python code. 4. IEEE Special Value Constants Standard constants for nan, plus_inf, minus_inf, and inf have been added to numarray.ieeespecial making it easier to assign IEEE special values to arrays in addition to finding or replacing special values. 5. Better Numeric interoperability (wxPyPlot port) numarray-0.7 addresses a couple compatibility and speed issues which hindered numarray's use with wxPyPlot. numarray now works fine with the wxPyPlot demos by changing "import Numeric" to "import numarray as Numeric". II. BUGS FIXED See http://sourceforge.net/tracker/?atid=450446&group_id=1369&func=browse for more details. 793421 PyArray_INCREF / PyArray_XDECREF deprecated 791354 Integer overflow bugs? 785458 Crash subclassing the NumArray class 784866 astype() fails sometimes 779755 Mac OS 10 installation problem 740035 Possible problem with dot III. CAUTIONS 1. numarray extension writers should note that the documented use of PyArray_INCREF and PyArray_XDECREF (in numarray) has been found to be incompatible with Numeric and has therefore been deprecated. numarray wrapper functions using PyArray_INCREF and PyArray_XDECREF should switch to ordinary Py_INCREF and Py_XDECREF. 2. Writers of numarray subclasses should note that the "protected" _getitem/_setitem interface for NDArray has changed. WHERE ----------- Numarray-0.7 windows executable installers, source code, and manual is here: http://sourceforge.net/project/showfiles.php?group_id=1369 Numarray is hosted by Source Forge in the same project which hosts Numeric: http://sourceforge.net/projects/numpy/ The web page for Numarray information is at: http://stsdas.stsci.edu/numarray/index.html Trackers for Numarray Bugs, Feature Requests, Support, and Patches are at the Source Forge project for NumPy at: http://sourceforge.net/tracker/?group_id=1369 REQUIREMENTS ------------------------------ numarray-0.7 requires Python 2.2.2 or greater. AUTHORS, LICENSE ------------------------------ Numarray was written by Perry Greenfield, Rick White, Todd Miller, JC Hsu, Paul Barrett, Phil Hodge at the Space Telescope Science Institute. Thanks go to Jochen Kupper of the University of North Carolina for his work on Numarray and for porting the Numarray manual to TeX format. Thanks also to Edward C. Jones, Francesc Alted, Paul Dubois, Eric Jones, Travis Oliphant, Pearu Peterson, Colin Williams, and everyone who has contributed with comments and feedback. Numarray is made available under a BSD-style License. See LICENSE.txt in the source distribution for details. -- Todd Miller jmiller(a)stsci.edu

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by 238924＠bigfoot.com 24 Aug '03

24 Aug '03

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Resume
by Electrician 22 Aug '03

22 Aug '03

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Numarray web site and google
by Sebastian Haase 21 Aug '03

21 Aug '03

Hi, I'm not sure how much time you guys wants to spend on the numarray web site, but I find that a google search for 'numarray' still points to http://stsdas.stsci.edu/numarray/ saying numarray has moved! (OK it does bring me to the right page after some seconds) Anyway - doing some search on Usenet I found this http://groups.google.com/groups?threadm=vc3bh351prjbd8%40corp.supernews.com… From: Guy Macon (guymacon+"_http://www.guymacon.com/_"03(a)spamcop.net) Subject: Re: If I can't redirect to new url, how bad is forwarding it? Newsgroups: alt.internet.search-engines Date: 2003-05-13 19:48:05 PST he essentially says adding this to the html-page might fix it soon: <head> <meta name="robots" content="noindex, follow" /> <title>http://www.example.com</title> <meta http-equiv="refresh" content="http://www.example.com" /> </head> Just a thought ... Thanks for numarray - have a great day. Sebastian Haase

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How are Booleans to be handled?
by Colin J. Williams 18 Aug '03

18 Aug '03

This statement: z= _n.array([True, False, True, True], type= _nt.BooleanType) gives an exception: Traceback (most recent call last): File "<interactive input>", line 1, in ? File "C:\PROGRA~1\Python23\lib\site-packages\numarray\numarraycore.py", line 284, in array type = getTypeObject(sequence, type, typecode) File "C:\PROGRA~1\Python23\lib\site-packages\numarray\numarraycore.py", line 217, in getTypeObject return getType(type) File "C:\PROGRA~1\Python23\lib\site-packages\numarray\numarraycore.py", line 324, in getType raise TypeError("Not a numeric type") TypeError: Not a numeric type If we leave out the type parameter, the array is created with 32 bit words. Colin W.

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