Re: [Numpy-discussion] So...

2011-03-25 Thread Pauli Virtanen
Fri, 25 Mar 2011 13:23:11 +0100, Sturla Molden wrote: FFTs should keep the GIL locked, because sharing the interpreter is not funny. Array indices should be sizeof(void*), because following C standard and Python C API is lame. Median should be calculated in O(n log n) instead of O(n) time,

Re: [Numpy-discussion] So...

2011-03-25 Thread Pauli Virtanen
Fri, 25 Mar 2011 13:40:54 +0100, Sturla Molden wrote: Den 25.03.2011 13:33, skrev Pauli Virtanen: That npy_intp will not be redefined as ssize_t does not mean that the type of array indices could not be changed. By the way, what is the resonable array index for AMD64, where 32-bit

Re: [Numpy-discussion] 1.6.0b1 half float buffer bug?

2011-03-25 Thread Pauli Virtanen
, you'd need to detect when you are working with Numpy arrays, and get the half-float type information from the Numpy dtype rather than from the exported buffer. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http

Re: [Numpy-discussion] Compiling numpy using icc gets missing library error

2011-03-25 Thread Pauli Virtanen
. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] loadtxt/savetxt tickets

2011-03-26 Thread Pauli Virtanen
Hi, Thanks! On Sat, 26 Mar 2011 13:11:46 +0100, Paul Anton Letnes wrote: [clip] I hope you find this useful! Is there some way of submitting the patches for review in a more convenient fashion than e-mail? You can attach them on the trac to each ticket. That way they'll be easy to find later

Re: [Numpy-discussion] Array views

2011-03-26 Thread Pauli Virtanen
is the approach to use if you want to share the data. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Array views

2011-03-26 Thread Pauli Virtanen
temporaries, and probably easier to write than doing things via the out= arguments. For sparse matrices, things then depend on how they are laid out in memory. You can probably alter the `.data` attribute of the arrays directly, if you know how the underlying representation works. -- Pauli

Re: [Numpy-discussion] Array views

2011-03-26 Thread Pauli Virtanen
On Sat, 26 Mar 2011 19:13:43 +, Pauli Virtanen wrote: [clip] If you want to have control over temporaries, you can make use of the out= argument of ufuncs (`numpy.dot` will gain it in 1.6.1 --- you can call LAPACK routines from scipy.lib in the meantime, if your data is in Fortran order

Re: [Numpy-discussion] npz load on numpy 3

2011-03-29 Thread Pauli Virtanen
Tue, 29 Mar 2011 04:16:00 -0400, josef.pktd wrote: Traceback (most recent call last): File stdin, line 1, in module File C:\Programs\Python32\lib\site-packages\numpy\lib\npyio.py, line 222, in __getitem__ return format.read_array(value) File

Re: [Numpy-discussion] npz load on numpy 3

2011-03-29 Thread Pauli Virtanen
Tue, 29 Mar 2011 08:27:52 +, Pauli Virtanen wrote: Tue, 29 Mar 2011 04:16:00 -0400, josef.pktd wrote: Traceback (most recent call last): File stdin, line 1, in module File C:\Programs\Python32\lib\site-packages\numpy\lib\npyio.py, line 222, in __getitem__ return format.read_array

Re: [Numpy-discussion] bug in genfromtxt for python 3.2

2011-03-30 Thread Pauli Virtanen
. Personally, I don't think going unicode makes much sense here. First, it would be a Py3-only feature. Second, there is a real need for it only when dealing with multibyte encodings, which are seldom used these days with utf-8 rightfully dominating. -- Pauli Virtanen

Re: [Numpy-discussion] 1.6.0b1 half float buffer bug?

2011-04-01 Thread Pauli Virtanen
Thu, 31 Mar 2011 11:15:08 -0700, Mark Wiebe wrote: [clip] My reading of Pauli's thoughts was that putting it in unilaterally is undesirable, something I definitely agree with. I think with Eli doing the legwork of getting input and acceptance from the relevant parties, we should help him out

Re: [Numpy-discussion] How to use a function into import function in python

2011-04-08 Thread Pauli Virtanen
Fri, 08 Apr 2011 16:24:58 +0530, dileep kunjaai wrote: I defined a function hit_rate( ) i want to use this into import function(name of function). Please read the Python tutorial first: http://docs.python.org/tutorial/ http://docs.python.org/tutorial/modules.html

Re: [Numpy-discussion] Zero row in SVD's unitary matrix on some Mac's

2011-04-25 Thread Pauli Virtanen
are somewhat difficult to track. You could try switching to another BLAS library (or, if you use ATLAS, compile it differently) and checking if the problem disappears. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http

Re: [Numpy-discussion] Zero row in SVD's unitary matrix on some Mac's

2011-04-26 Thread Pauli Virtanen
Tue, 26 Apr 2011 11:36:19 -0500, Jason Grout wrote: [clip] Okay, just one more data point. Our people that are seeing the problem with numpy returning a non-unitary V also see a non-unitary V being returned by the test C call to zgesdd. In other words, it really appears that zgesdd follows

Re: [Numpy-discussion] Zero row in SVD's unitary matrix on some Mac's

2011-04-26 Thread Pauli Virtanen
On Tue, 26 Apr 2011 10:33:07 -0500, Jason Grout wrote: [clip] I was just looking up the documentation for ZGESDD and noticed that the value we have for rwork in the numpy call [1] does not match the Lapack docs. This was changed in Lapack 3.2.2 [2]. I've submitted a pull request:

Re: [Numpy-discussion] Zero row in SVD's unitary matrix on some Mac's

2011-04-26 Thread Pauli Virtanen
On Tue, 26 Apr 2011 14:52:52 -0500, Jason Grout wrote: [clip] The updated rwork calculation makes no difference with a 3x4 matrix (both the old calculation and the new calculation give 66 in the 3x4 case), so I don't think that is affecting anything. Actually, there *is* a difference for the

Re: [Numpy-discussion] FYI -- numpy.linalg.lstsq as distributed by Ubuntu is crashing on some inputs

2011-05-06 Thread Pauli Virtanen
/+source/atlas/+bug/778217 So I thought people might like a heads up in case they run into it as well. It's terminating with SIGILL, which means that Ubuntu no longer ships a precompiled version of Atlas usable on machines without SSE3. -- Pauli Virtanen

Re: [Numpy-discussion] FYI -- numpy.linalg.lstsq as distributed by Ubuntu is crashing on some inputs

2011-05-06 Thread Pauli Virtanen
On Fri, 06 May 2011 10:06:20 -0700, Nathaniel Smith wrote: On Fri, May 6, 2011 at 3:04 AM, Pauli Virtanen p...@iki.fi wrote: It's terminating with SIGILL, which means that Ubuntu no longer ships a precompiled version of Atlas usable on machines without SSE3. Yes, that's right. BTW

Re: [Numpy-discussion] Mapping of dtype to C types

2011-05-09 Thread Pauli Virtanen
Sun, 08 May 2011 14:45:45 -0700, Keith Goodman wrote: I'm writing a function that accepts four possible dtypes: int32, int64, float32, float64. The function will call a C extension (wrapped in Cython). What are the equivalent C types? int, long, float, double, respectively? Will that work on

Re: [Numpy-discussion] Trying to turn warning to errors

2011-05-13 Thread Pauli Virtanen
Fri, 13 May 2011 17:39:26 +0200, Ondrej Marsalek wrote: [clip] while this does not (i.e. still produces just a warning): $ python -W error -c 'import numpy; x=numpy.ones(2); x+=1j' numpy.core.numeric.ComplexWarning: Casting complex values to real discards the imaginary part This is with

Re: [Numpy-discussion] Documentation errors

2011-05-14 Thread Pauli Virtanen
On Sat, 14 May 2011 09:45:12 -0600, Charles R Harris wrote: [clip] These are generated by the .. autosummary:: command, so the error probably lies there. The problem is that the signature of these routines is written as remainder(x1, x2[, out]) and not as remainder(x1, x2,

Re: [Numpy-discussion] Documentation errors

2011-05-15 Thread Pauli Virtanen
On Sun, 15 May 2011 10:32:17 +0200, Ralf Gommers wrote: OK, the format for that part of the signature is in line 4910 in ufunc_object.c. The question is, which should we fix, the format or the autosummary? The format please. That [, out] never made sense to me. The problem here is that there

Re: [Numpy-discussion] cPickle.load says 'invalid signature'

2011-05-18 Thread Pauli Virtanen
Wed, 18 May 2011 07:39:18 -0400, Neal Becker wrote: The file is pickle saved on i386 and loaded on x86_64. It contains a numpy array (amoungst other things). On load it says: RuntimeError: invalid signature There's no such message in Numpy source code, so the error does not come directly

Re: [Numpy-discussion] Memory leak/fragmentation when using np.memmap

2011-05-18 Thread Pauli Virtanen
On Wed, 18 May 2011 15:09:31 -0700, G Jones wrote: [clip] import numpy as np x = np.memmap('mybigfile.bin',mode='r',dtype='uint8') print x.shape # prints (42940071360,) in my case ndat = x.shape[0] for k in range(1000): y = x[k*ndat/1000:(k+1)*ndat/1000].astype('float32') #The astype

Re: [Numpy-discussion] Memory leak/fragmentation when using np.memmap

2011-05-18 Thread Pauli Virtanen
. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Conversion from structured dtype to object changed in Numpy 1.6.0.

2011-05-19 Thread Pauli Virtanen
to it in the changelog or release notes. Looks like a bug -- the change was not intentional. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] filtering rows from a numpy.ndarray

2011-05-24 Thread Pauli Virtanen
Tue, 24 May 2011 11:41:28 +0200, Jan Wuyts wrote: bmidata=np.asarray([x for x in data if x['paramname']=='bmi'], dtype=data.dtype) Use indexing: bmidata = data[data['paramname'] == 'bmi'] ___ NumPy-Discussion mailing list

Re: [Numpy-discussion] Numpy question

2011-05-26 Thread Pauli Virtanen
%20Numeric/24.2/ No pre-made binaries for Python 2.7, for obvious reasons, however. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Numpy question

2011-05-26 Thread Pauli Virtanen
at the same time as their product. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Contribution

2011-05-27 Thread Pauli Virtanen
the new page. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Abinit question

2011-05-30 Thread Pauli Virtanen
Fri, 27 May 2011 21:06:45 +0300, Talla wrote: [clip: AbinitBandStructuremaker.py] FYI: try getting a newer version of the abinit software from abinit.org They seem to have an updated version of this particular script in their source package. Any further discussion should probably go to their

Re: [Numpy-discussion] Changing milestones on tickets

2011-05-31 Thread Pauli Virtanen
Tue, 31 May 2011 11:44:15 -0500, Mark Wiebe wrote: [clip] I find very commendable to strive for consistency, mind you. I'm just not not very comfortable with the idea of modifying old records a posteriori to adjust to new policies... I was under the impression this already was the policy,

Re: [Numpy-discussion] numpy type mismatch

2011-06-10 Thread Pauli Virtanen
. Maybe they can be memcpy'd to make aliases, although that sounds dirty... -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] numpy type mismatch

2011-06-10 Thread Pauli Virtanen
On Fri, 10 Jun 2011 18:51:14 -0700, Keith Goodman wrote: [clip] Maybe this is the same question, but are you maybe yes, maybe no on this too: type(np.sum([1, 2, 3], dtype=np.int32)) == np.int32 False Note that this is a comparison between two Python types... Ben, what happens if

Re: [Numpy-discussion] ANN: Numpy 1.6.1 release candidate 1

2011-06-13 Thread Pauli Virtanen
On Mon, 13 Jun 2011 11:08:18 -0500, Bruce Southey wrote: [clip] OSError: /usr/local/lib/python3.2/site-packages/numpy/core/multiarray.pyd: cannot open shared object file: No such file or directory I think that's a result of Python 3.2 changing the extension module file naming scheme (IIRC to a

Re: [Numpy-discussion] ANN: Numpy 1.6.1 release candidate 1

2011-06-14 Thread Pauli Virtanen
On Tue, 14 Jun 2011 15:37:36 -0500, Mark Wiebe wrote: [clip] It would be nice to get a fix to this newly reported regression in: http://projects.scipy.org/numpy/ticket/1867 I see that regression only in master, not in 1.6.x, so I don't think it will delay 1.6.1. Pauli

Re: [Numpy-discussion] crash in multiarray

2011-06-17 Thread Pauli Virtanen
On Fri, 17 Jun 2011 15:39:21 -0500, Robert Kern wrote: [clip] File /home/bvr/Programs/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py, line 378 in test_ticket_1459_arpack_crash Well, if it's testing that it crashes, test passed! Here is the referenced ticket and the relevant

Re: [Numpy-discussion] replacing the mechanism for dispatching ufuncs

2011-06-22 Thread Pauli Virtanen
Tue, 21 Jun 2011 16:43:13 -0500, Mark Wiebe wrote: [clip: __array_wrap__] Those could stay as they are, and just the ufunc usage of __array_wrap__ can be deprecated. For classes which currently use __array_wrap__, they would just need to also implement _numpy_ufunc_ to eliminate any

Re: [Numpy-discussion] Using numpy array in C code ?

2011-07-01 Thread Pauli Virtanen
Hi, Fri, 01 Jul 2011 16:45:47 +0200, Marc Labadens wrote: I am trying to interface some python code using numpy array with some C code. You can read: http://docs.scipy.org/doc/numpy/user/c-info.how-to-extend.html#writing-an-extension-module However, using Cython often saves you from writing

Re: [Numpy-discussion] PyBUF_SIMPLE requests

2011-07-18 Thread Pauli Virtanen
Sat, 16 Jul 2011 12:42:36 +0200, Stefan Krah wrote: x = ndarray(buffer=bytearray([1,2,3,4,5,6,7,8,9,10]), shape=[10], strides=[-1], dtype=B, offset=9) [clip] I do not understand the PyBUF_SIMPLE result. According to the C-API docs a consumer would be allowed to access buf[9], which

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-19 Thread Pauli Virtanen
Tue, 19 Jul 2011 11:05:18 +0200, Carlos Becker wrote: Hi, I started with numpy a few days ago. I was timing some array operations and found that numpy takes 3 or 4 times longer than Matlab on a simple array-minus-scalar operation. This looks as if there is a lack of vectorization, even though

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-19 Thread Pauli Virtanen
On Tue, 19 Jul 2011 17:49:14 +0200, Carlos Becker wrote: I made more tests with the same operation, restricting Matlab to use a single processing unit. I got: - Matlab: 0.0063 sec avg - Numpy: 0.026 sec avg - Numpy with weave.blitz: 0.0041 To check if it's an issue with building without

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-19 Thread Pauli Virtanen
operation runs exactly at the same speed as C, so this issue must have a platform-dependent explanation. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] X11 system info

2011-07-20 Thread Pauli Virtanen
Tue, 19 Jul 2011 21:55:28 +0200, Ralf Gommers wrote: On Sun, Jul 17, 2011 at 11:48 PM, Darren Dale dsdal...@gmail.com wrote: In numpy.distutils.system info: default_x11_lib_dirs = libpaths(['/usr/X11R6/lib','/usr/X11/lib', '/usr/lib'], platform_bits)

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-20 Thread Pauli Virtanen
the same speed as an equivalent C implementation, which *does* pre-allocation, using exactly the same benchmark codes as you have posted? -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-20 Thread Pauli Virtanen
Wed, 20 Jul 2011 09:04:09 +, Pauli Virtanen wrote: Wed, 20 Jul 2011 08:49:21 +0200, Carlos Becker wrote: Those are very interesting examples. I think that pre-allocation is very important, and something similar happens in Matlab if no pre-allocation is done: it takes 3-4x longer than

Re: [Numpy-discussion] Array vectorization in numpy

2011-07-20 Thread Pauli Virtanen
Wed, 20 Jul 2011 11:31:41 +, Pauli Virtanen wrote: [clip] There is a sharp order-of-magnitude change of speed in malloc+memset of an array, which is not present in memset itself. (This is then also reflected in the Numpy performance -- floating point operations probably don't cost much

Re: [Numpy-discussion] Optimizing recursive loop - updated example

2011-07-25 Thread Pauli Virtanen
doesn't vectorize the slice operations such as b[:,j-g] but falls back to Numpy on them. You'll need to convert the slice notation to a loop to get speed gains. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org

Re: [Numpy-discussion] c-api return two arrays

2011-07-29 Thread Pauli Virtanen
Fri, 29 Jul 2011 10:52:12 +0200, Yoshi Rokuko wrote: [clip] A, B = mod.meth(C, prob=.95) is ith possible to return two arrays? The way to do this in Python is to build a tuple with Py_BuildValue(OO, A, B) and return that. ___ NumPy-Discussion

Re: [Numpy-discussion] PEP 3118 array size check

2011-08-10 Thread Pauli Virtanen
) -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] [SciPy-User] disabling SVN (was: Trouble installing scipy after upgrading to Mac OS X 10.7 aka Lion)

2011-08-13 Thread Pauli Virtanen
Sat, 13 Aug 2011 18:14:11 +0200, Ralf Gommers wrote: [clip] We should check if there's still any code in SVN branches that is useful. If so the people who are interested in it should move it somewhere else. Anyone? All the SVN branches are available in Git, though some are hidden. Do

Re: [Numpy-discussion] [SciPy-User] disabling SVN (was: Trouble installing scipy after upgrading to Mac OS X 10.7 aka Lion)

2011-08-16 Thread Pauli Virtanen
Sat, 13 Aug 2011 22:00:33 -0400, josef.pktd wrote: [clip] Does Trac require svn access to dig out old information? for example links to old changesets, annotate/blame, ... ? It does not require HTTP access to SVN, as it looks directly at the SVN repo on the local disk. It also probably doesn't

Re: [Numpy-discussion] [SciPy-User] disabling SVN (was: Trouble installing scipy after upgrading to Mac OS X 10.7 aka Lion)

2011-08-19 Thread Pauli Virtanen
Fri, 19 Aug 2011 12:48:29 +0200, Ralf Gommers wrote: [clip] Hi Ognen, Could you please disable http access to numpy and scipy svn? Turns out also I had enough permissions to disable this. Now: $ svn co http://svn.scipy.org/svn/numpy/trunk numpy svn: Repository moved permanently to

Re: [Numpy-discussion] How to start at line # x when using numpy.memmap

2011-08-19 Thread Pauli Virtanen
of lines instead of a number of bytes? First use standard Python I/O functions to determine the number of bytes to skip at the beginning and the number of data items. Then pass in `offset` and `shape` parameters to numpy.memmap. -- Pauli Virtanen ___ NumPy

Re: [Numpy-discussion] saving groups of numpy arrays to disk

2011-08-21 Thread Pauli Virtanen
in several Python-for-science distributions), and how difficult would it be for you to ship them with your stuff, or to require the users to install them. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org

Re: [Numpy-discussion] Removing numscons, adding bento scripts to main branch ?

2011-08-27 Thread Pauli Virtanen
Hey, Sat, 27 Aug 2011 12:28:14 +0200, David Cournapeau wrote: I am finally at a stage where bento can do most of what numscons could do. I would rather avoid having 3 different set of build scripts (distutils+bento+numscons) to maintain in the long term, so I would favor removing numscons

Re: [Numpy-discussion] Question on LinAlg Inverse Algorithm

2011-08-31 Thread Pauli Virtanen
in exact arithmetic, for a computer it may still be invertible (by a given algorithm). This type of things are not unusual in floating-point computations. The matrix condition number (`np.linalg.cond`) is a better measure of whether a matrix is invertible or not. -- Pauli Virtanen

Re: [Numpy-discussion] load from text files Pull Request Review

2011-09-08 Thread Pauli Virtanen
Wed, 07 Sep 2011 12:52:44 -0700, Chris.Barker wrote: [clip] In [9]: temp['x'] = 3 In [10]: temp['y'] = 4 In [11]: temp['z'] = 5 [clip] maybe it wouldn't be any faster, but with re-using temp, and one less list-tuple conversion, and fewer python type to numpy type conversions, maybe it

Re: [Numpy-discussion] How to apply Numpy ufunc to Scipy sparse matrices?

2011-09-11 Thread Pauli Virtanen
Sun, 11 Sep 2011 03:03:26 -0500, Pengkui Luo wrote: [clip] However, converting a large sparse matrix to dense would easily eat up the memory. Is there a way for np.sign (as well as other ufunc) to take a sparse matrix as parameter, and return a sparse matrix? For CSR, CSC, and DIA you can do

Re: [Numpy-discussion] Fancy indexing with masks

2011-09-22 Thread Pauli Virtanen
Thu, 22 Sep 2011 08:12:12 +0200, Han Genuit wrote: [clip] I also noticed that it does strange things when using a list: c[[True, False, True]] array([[3, 4, 5], [0, 1, 2], [3, 4, 5]]) It casts the list with booleans to an integer array. Probably shouldn't work like that...

Re: [Numpy-discussion] ImportError: libptf77blas.so.3: cannot open shared object file: No such file or directory

2011-09-22 Thread Pauli Virtanen
Hi, Thu, 22 Sep 2011 13:09:51 +0200, Marijn Verkerk wrote: [clip] ImportError: libptf77blas.so.3: cannot open shared object file: No such file or directory In the __config.py file the folder where libptf77 should be is present. Any suggestions? You need to make the dynamic linker able to

Re: [Numpy-discussion] Ticket review process

2011-09-23 Thread Pauli Virtanen
On Fri, 23 Sep 2011 11:57:15 -0600, Charles R Harris wrote: [clip] We're falling behind. The real world is impacting hard at the moment. Matthew's suggestion is a good one. Should we stop recommending using Trac for contributions, and just say use git? (I think we recommend it somewhere.) I'd

Re: [Numpy-discussion] array.tofile() refuses to write into a StringIO

2011-09-25 Thread Pauli Virtanen
** Yes, this is a known shortcoming of .tofile(). -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] factorization updates in numpy

2011-09-27 Thread Pauli Virtanen
: your qrupdate code is licensed under the GPL. To include it in Scipy, we need to have it distributable under a BSD-compatible license. Would you be willing to relicense it? -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org

Re: [Numpy-discussion] oblique text

2011-10-04 Thread Pauli Virtanen
(words): i = np.arange(len(word)) canvas[i+j, 2*i] = list(word) canvas[:,-1] = '\n' return canvas.tostring().rstrip() -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman

Re: [Numpy-discussion] np.where and broadcasting

2011-10-10 Thread Pauli Virtanen
10.10.2011 23:02, Jesper Larsen kirjoitti: Hi numpy-users I have a 2d array of shape (ny, nx). I want to broadcast (copy) this array to a target array of shape (nt, nz, ny, nz) or (nt, ny, nx) so that the 2d array is repeated for each t and z index (corresponding to nt and nz). I am not sure

Re: [Numpy-discussion] speeding up operations on small vectors

2011-10-11 Thread Pauli Virtanen
that it can be vectorized. Without knowing more about the actual algorithm you are trying to implement, it's not easy to give more detailed help. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman

Re: [Numpy-discussion] speeding up operations on small vectors

2011-10-11 Thread Pauli Virtanen
as all the lattice points inside the bounding box are checked. The only way to vectorize this I see is to do write the floodfill algorithm on rectangular supercells, so that the constant costs are amortized. Sounds a bit messy to do, though. -- Pauli Virtanen

Re: [Numpy-discussion] NumPy example list is corrupted

2011-10-16 Thread Pauli Virtanen
' in it on the upper right corner of the page. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] dtyping with .astype()

2011-10-17 Thread Pauli Virtanen
13.10.2011 12:59, Alex van der Spek kirjoitti: gives me a confusing result. I only asked to name the columns and change their types to half precision floats. Structured arrays shouldn't be thought as an array with named columns, as they are somewhat different. What am I missing? How to do

Re: [Numpy-discussion] dtyping with .astype()

2011-10-17 Thread Pauli Virtanen
17.10.2011 15:48, josef.p...@gmail.com kirjoitti: On Mon, Oct 17, 2011 at 6:17 AM, Pauli Virtanen p...@iki.fi wrote: [clip] What am I missing? How to do this? np.rec.fromarrays(arr.T, dtype=dt) y.astype(float16).view(dt) I think this will give surprises if the original array is not in C

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-23 Thread Pauli Virtanen
understand. No, master is supposed to be the integration branch with only finished stuff in it. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Pauli Virtanen
(or explicitly creates masked arrays), but as far as I understand that's about the same situation as with np.ma. .. [1] http://docs.scipy.org/doc/numpy/reference/arrays.maskna.html -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org

Re: [Numpy-discussion] float128 / longdouble on PPC - is it broken?

2011-10-25 Thread Pauli Virtanen
25.10.2011 06:59, Matthew Brett kirjoitti: res = np.longdouble(2)**64 res-1 36893488147419103231.0 Can you check if long double works properly (not a given) in C on that platform: long double x; x = powl(2, 64); x -= 1; printf(%g %Lg\n, (double)x, x); or, in

Re: [Numpy-discussion] float128 / longdouble on PPC - is it broken?

2011-10-25 Thread Pauli Virtanen
gives something wrong. Can you try to check this by doing something like: - do some set of calculations using np.longdouble in Numpy (that requires the extra accuracy) - at the end, cast the result back to double -- Pauli Virtanen ___ NumPy

Re: [Numpy-discussion] float128 / longdouble on PPC - is it broken?

2011-10-25 Thread Pauli Virtanen
before formatting one. In the latter case, one would have to maintain a list of broken C libraries (ugh). -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] np.in1d() capacity limit?

2011-10-26 Thread Pauli Virtanen
why the error occurs in only some of the cases. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] float128 / longdouble on PPC - is it broken?

2011-10-26 Thread Pauli Virtanen
26.10.2011 10:07, Nathaniel Smith kirjoitti: On Tue, Oct 25, 2011 at 4:49 PM, Matthew Brett matthew.br...@gmail.com wrote: I guess from your answer that such a warning would be complicated to implement, and if that's the case, I can imagine it would be low priority. I assume the problem

Re: [Numpy-discussion] NumPy nogil API

2011-10-30 Thread Pauli Virtanen
C library. It's been in a merge-limbo for some time now, however. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] NumPy nogil API

2011-10-31 Thread Pauli Virtanen
31.10.2011 09:44, mark florisson kirjoitti: [clip] Ah, that's too bad. Is it anywhere near ready, or was it abandoned for ironclad? Could you point me to the code? It's quite ready and working, and as far as I understand, Enthought is shipping it. I haven't used it, though. The code is here:

Re: [Numpy-discussion] in the NA discussion, what can we agree on?

2011-11-04 Thread Pauli Virtanen
04.11.2011 17:31, Gary Strangman kirjoitti: [clip] The question does still remain what to do when performing operations like those above in IGNORE cases. Perform the operation underneath? Or not? I have a feeling that if you don't start by mathematically defining the scalar operations first,

Re: [Numpy-discussion] Array of Arrays

2007-03-26 Thread Pauli Virtanen
a[0,0] = 2.0 print a[0,0] [ 2. 2. 2. 2.] a[1,0] = 3.0 a[0,1] = a[0,0] * a[1,0] print a[0,1] [ 6. 6. 6. 6.] -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy

Re: [Numpy-discussion] matlab vs. python question

2007-04-26 Thread Pauli Virtanen
autoreload.run() to some startup file. Created: Thomas Heller, 2000-04-17 Modified: Pauli Virtanen, 2006 # $Id: autoreload.py 3117 2006-09-27 20:28:46Z pauli $ # # $Log: autoreload.py,v $ # Revision 1.9 2001/11/15 18:41:18 thomas # Cleaned up and made working again before posting to c.l.p

Re: [Numpy-discussion] can't import repmat from numpy

2007-04-30 Thread Pauli Virtanen
wrapper library) Maybe this should be fixed? -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Iterate over all 1-dim views

2007-10-07 Thread Pauli Virtanen
Neal Becker [EMAIL PROTECTED] kirjoitti: Suppose I have a function F(), which is defined for 1-dim arguments. If the user passes an n1 dim array, I want to apply F to each 1-dim view. For example, for a 2-d array, apply F to each row and return a 2-d result. For a 3-d array, select each

Re: [Numpy-discussion] a simple question about f2py

2007-10-24 Thread Pauli Virtanen
pointers, type(Typename), pointer, from the Python side to the Fortran side, as opaque handles. -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] segfault

2007-11-04 Thread Pauli Virtanen
su, 2007-11-04 kello 11:13 -1000, Eric Firing kirjoitti: A quick scan of the tickets did not show me anything like the following, but I might have missed it. The attached script generates a segfault on my ubuntu feisty system with svn numpy. Running inside of ipython, the segfault occurs

Re: [Numpy-discussion] segfault with atlas3-sse2, works with atlas3-sse

2007-12-20 Thread Pauli Virtanen
tm pbe nx constant_tsc pni monitor est tm2 xtpr so imho I do have SSE2. If it's not wrong instructions for the processor type, this reminds me of http://scipy.org/scipy/numpy/ticket/551 which also seemed to be SSE2-specific on Debian/Ubuntu in my tests. -- Pauli Virtanen signature.asc

Re: [Numpy-discussion] segfault problem with numpy and pickle

2008-01-26 Thread Pauli Virtanen
: LD_LIBRARY_PATH=/usr/lib/atlas python crasher.py -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] major bug in fromstring, ascii mode

2008-01-27 Thread Pauli Virtanen
function is interpreting numbers beginning with zero as octal, and recognizing also hexadecimals. This is a bit surprising, and whether this is the desired behavior is questionable. -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion

Re: [Numpy-discussion] Read-only mercurial mirror of numpy trunk available

2008-01-27 Thread Pauli Virtanen
la, 2008-01-19 kello 14:15 +0900, David Cournapeau kirjoitti: Pauli Virtanen wrote: pe, 2008-01-18 kello 18:06 +0900, David Cournapeau kirjoitti: Hi there, I got a mercurial mirror of numpy available. I put some basic info on the wiki http://scipy.org/scipy/numpy/wiki/HgMirror

Re: [Numpy-discussion] major bug in fromstring, ascii mode

2008-01-27 Thread Pauli Virtanen
([809119794, 825375289]) I guess some more testcases should be written... -- Pauli Virtanen ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] partial_sum/adj_difference?

2008-02-19 Thread Pauli Virtanen
ti, 2008-02-19 kello 13:38 -0500, Neal Becker kirjoitti: Does numpy/scipy have a partial_sum and adj_difference function? partial_sum[i] = \sum_{j=0}^{i} x[j] adj_diff[i] = x[i] - x[i-1] : i 1, x[i] otherwise cumsum and diff do something like this: import numpy a = [1,2,3,4,5,3,1]

Re: [Numpy-discussion] numpy and roundoff(?)

2008-03-01 Thread Pauli Virtanen
%) in the complete nonlinear solution loop than the one using the F90 code wrapped with f2py. A silly question: did you check directly that the pure-numpy code and the F90 code give the same results for the Jacobian-vector product J(z0) z for some randomly chosen vectors z0, z? -- Pauli Virtanen

Re: [Numpy-discussion] 1.4.0: Setting a firm release date for 1st december.

2009-11-02 Thread Pauli Virtanen
functions to npy_math for 1.4.0: could be useful for the next Scipy? This is pretty quick to do, I can just write up some more tests one evening and commit. -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http

Re: [Numpy-discussion] persistent ImportError: No module named multiarray when moving cPickle files between machines

2009-11-05 Thread Pauli Virtanen
, and noticed that they were different (sha1sum). -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Deprecate np.max/np.min ?

2009-11-07 Thread Pauli Virtanen
to axis=None. These seemed to be required by at least the masked arrays unit tests... -- Pauli Virtanen ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] initializing an array of lists

2009-11-09 Thread Pauli Virtanen
((3, 4), dtype=np.object) filler(a, a); array([[[], [], [], []], [[], [], [], []], [[], [], [], []]], dtype=object) a[0,3].append(9) a array([[[], [], [], [9]], [[], [], [], []], [[], [], [], []]], dtype=object) -- Pauli Virtanen

Re: [Numpy-discussion] Release notes for arraysetops changes

2009-11-09 Thread Pauli Virtanen
ma, 2009-11-09 kello 23:13 +, Neil Crighton kirjoitti: I've written some release notes (below) describing the changes to arraysetops.py. If someone with commit access could check that these sound ok and add them to the release notes file, that would be great. Thanks, added! Pauli

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