Mailman 3 June 2004 - NumPy-Discussion

Re: [SciPy-user] IRIX problems
by Martin Wiechert 28 Jun '04

28 Jun '04

Hi Pearu, thanks for your help. The solution is to replace libcomplib.sgimath with the newer libscs, which has the missing symbol. Our sysadmin pointed me to that. Martin. On Monday 28 June 2004 17:39, Pearu Peterson wrote: > On Mon, 28 Jun 2004, Martin Wiechert wrote: > > Hi all, > > > > I'm trying to install scipy on our dunno-how-old IRIX server. > > I've used a lib called complib.sgimath instead of atlas/LAPACK ... > > Now I get the following error: > > > > import lapack_lite > > ImportError: 563534:python2.3: rld: Fatal Error: unresolvable symbol > > in /user/wiechert/lib/python2.3/site-packages/Numeric/lapack_lite.so: > > zgelsd_ > > (This is a Numeric installation problem, not scipy.) > > > lapack_lite is linked against following libs: > > ldd lapack_lite.so > > libcomplib.sgimath.so => /usr/lib32/libcomplib.sgimath.so > > libblas.so => /usr/lib32/libblas.so > > libftn.so => /usr/lib32/libftn.so > > libm.so => /usr/lib32/libm.so > > libc.so.1 => /usr/lib32/libc.so.1 > > > > What can I do? > > Try to find out which libraries in your system contain zgelsd_ and use it > when linking lapack_lite. When that's unsuccessful then I suggest building > LAPACK libraries yourself, see the relevant section in > > http://www.scipy.org/documentation/buildatlas4scipy.txt > > HTH, > Pearu > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user

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numarray equivalent to sign() function
by Mike Zingale 26 Jun '04

26 Jun '04

Hi, I am in the process of converting some code from Numeric to numarray, and it seems that numarray no longer has the sign() function -- is that so? ex: sign(-30.0) = -1 sign(0) = 0 sign(1000) = 1 Is there a replacement? Thanks, Mike

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numarray.sum should raise exception for wrong axis argument - and slicing ...
by Sebastian Haase 26 Jun '04

26 Jun '04

Hi, please take a look at this: >>> na.sum( na.zeros((2,6)) ) [0 0 0 0 0 0] >>> na.sum( na.zeros((2,6)) , 0) [0 0 0 0 0 0] >>> na.sum( na.zeros((2,6)) , 1) [0 0] >>> na.sum( na.zeros((2,6)) , 2) [0 0] >>> na.sum( na.zeros((2,6)) , 3) [0 0] >>> na.sum( na.zeros((2,6)) , 4) [0 0] >>> na.sum( na.zeros((2,6)) , -1) [0 0] >>> na.sum( na.zeros((2,6)) , -2) [0 0 0 0 0 0] >>> na.sum( na.zeros((2,6)) , -3) [0 0] >>> na.sum( na.zeros((2,6)) , -4) [0 0] >>> I think here should be a ValueError exception thrown rather than defaulting to the '-1'-axis. Comments ? Also this applies to (all?) other functions that have an 'axis' argument. And further I just found that putting "too many slicings" to an array also gets silently ignored: >>> b.shape (7, 128, 128, 128) >>> b[2,2,2,2,3] Traceback (most recent call last): File "<input>", line 1, in ? IndexError: too many indices. BUT: >>> b[2:3 , 2:3 , 2:3 , 2:3 , 2:3 , 2:3] [[[[ 0.]]]] I find this very confusing !! Is there any good reason not to have the "IndexError" exception in all cases ? Thanks, Sebastian Haase

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compress function
by Peter Verveer 25 Jun '04

25 Jun '04

The documentation of the compress function states that the condition must be equal to the given axis of the array that is compressed. e.g.: >>> a = array([[1,2],[3,4]]) >>> print compress([1,0], a, axis = 1) [[1] [3]] However, this also works fine: >>> print compress([[1,0],[0,1]], a) [1, 4] which is great (I need that) but not documented. Is that behaviour intended? If so it maybe should be documented. Cheers, Peter

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ObjectArray paramter order poll
by Todd Miller 25 Jun '04

25 Jun '04

A while back Colin Williams suggested that we change the parameter order of numarray.objects.ObjectArray from: def __init__(self, shape=None, objects=None, rank=None) to: def __init__(self, objects=None, shape=None, rank=None) The new order emphasizes building object arrays from existing sequences, while the old order emphasizes building empty (full of None) object arrays of a specific shape. Since array() and fromlist() already exist to build from sequences, I thought it was fine to keep the order as is, plus I hate breaking s/w interfaces unless it was my idea. :-) Opinions please? Regards, Todd

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comparing string array with None raises ValueError
by Sebastian Haase 24 Jun '04

24 Jun '04

Hi, I'm not sure if this is fixed already in CVS but here it goes: I'm working with record arrays, and trying to access a field with type '10a80' - that is, an array of 10 80 char 'strings' : >>> q.Mrc.hdr = q.Mrc.hdrArray[0].field >>> q.Mrc.hdr('title') != None Traceback (most recent call last): File "<input>", line 1, in ? File "/jws30/haase/PrLin/numarray/strings.py", line 431, in __ne__ return self.StrCmp(other).__ne__(0) File "/jws30/haase/PrLin/numarray/strings.py", line 385, in StrCmp b = asarray(b0, kind=self.__class__) File "/jws30/haase/PrLin/numarray/strings.py", line 1024, in asarray return array(buffer, itemsize, shape, byteoffset, bytestride, kind) File "/jws30/haase/PrLin/numarray/strings.py", line 994, in array byteoffset=byteoffset, bytestride=bytestride) File "/jws30/haase/PrLin/numarray/strings.py", line 84, in __init__ raise ValueError("Must define both shape & itemsize if buffer is None") ValueError: Must define both shape & itemsize if buffer is None >>> >>> print q.Mrc.hdr('title') ['tit1e seb says hi' '' '' '' '' '' '' '' '' ''] >>> Thanks for numarray ;-) Sebastian Haase

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Compiling on windows?
by Tim Hochberg 24 Jun '04

24 Jun '04

I've been using numarray 0.8 since 0.9 has some bugs that I can't easily work around. Since these have been fixed in CVS, I finally decided to try to download and compile a copy of numarray from CVS. Unfortunately, 'python setup.py build' bombs out almost imediately: creating build\temp.win32-2.3 creating build\temp.win32-2.3\Release creating build\temp.win32-2.3\Release\Src C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG -IInclude/numarray -IC:\python23\include -IC:\python23\PC /TcSrc\_convmodule.c /Fobuild\temp.win32-2.3\Release\Src\_convmodule.obj_convmodule.c Src\_convmodule.c(683) : warning C4244: '=' : conversion from 'int ' to 'float ', possible loss of data .... Src\_convmodule.c(2310) : error C2520: conversion from unsigned __int64 to double not implemented, use signed __int64 error: command '"C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe"' failed with exit status 2 This on Windows XP, Python 2.3.2, VC++ 6.0. Any hints as to what I could to make this work? I downloaded the source for version 0.9 and tried compiling it but got the same set of errors. Alternatively, is there going to be a 0.9.1 or 0.10 release soon? Thanks, -tim

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type of matrixmultiply result
by Curzio Basso 24 Jun '04

24 Jun '04

Hi. I noticed that when multiplying two matrices of type Float32, the result is Float64: ----------------------------------------- In [103]: a=NA.ones((2,2), NA.Float32) In [104]: b=NA.ones((2,2), NA.Float32) In [105]: c=NA.matrixmultiply(a,b) In [106]: c.type() Out[106]: Float64 ----------------------------------------- Since the matrix I'm going to multiply in practice are quite big, I'd like to do the operation in Float32. Otherwise this is what I get: Traceback (most recent call last): File "/home/basso/work/python/port/apps/pca-heads.py", line 141, in ? pc = NA.array(NA.matrixmultiply(cent, c), NA.Float32) File "/home/basso/usr//lib/python/numarray/numarraycore.py", line 1150, in dot return ufunc.innerproduct(array1, _gen.swapaxes(array2, -1, -2)) File "/home/basso/usr//lib/python/numarray/ufunc.py", line 2047, in innerproduct r = a.__class__(shape=adots+bdots, type=rtype) MemoryError Any suggestion (apart from doing the operation one column at a time)? thanks

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Re: median filtering question -- masked arrays
by Peter Verveer 24 Jun '04

24 Jun '04

> Does anyone have a hint for applying a median filter to a masked 2D > array in numarray? > > I"ve been using the kludge of extracting a normal array with the > masked data replaced by the overall median of the array and median > filtering that (with the appropriate nd_image method). But this is a > crude approximation and I"d like to do better -- preferably without > coding my own median filter in C. Masks are not supported by the filters in nd_image. It could be done, but that would be a considerable effort for a rather exotic feature, so that won't happen soon. In the near future I will however add support for generic filters where you can provide your own filter function to be executed at each point. That may make it easy enough to roll your own function. Cheers, Peter

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23 Jun '04

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