Mailman 3 September 2006 - NumPy-Discussion

ISP changeover beginning in 30 minutes (7:00 PM Central)
by Jeff Strunk 13 Sep '06

13 Sep '06

Good evening, We will begin switching our internet service over in about 30 minutes. Please allow for up to two hours of downtime. I will send an email announcing the completion of this maintenance. This will effect all Enthought servers as well as the SciPy server which hosts many Open Source projects. We apologize for the inconvenience. Jeff Strunk Enthought, Inc.

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numpy.distutils compatibility with subversion-1.4
by Darren Dale 12 Sep '06

12 Sep '06

This morning I updated to subversion-1.4. There have been several significant enhancements in this release (see http://subversion.tigris.org/svn_1.4_releasenotes.html), and it appears that numpy.distutils is not compatible with working copies created with the new svn. I submitted a ticket (#276), but I figured it was worth a post here, just a "heads up" for anyone not watching the trac website. $ python setup.py build Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' No module named __svn_version__ Traceback (most recent call last): File "setup.py", line 89, in ? setup_package() File "setup.py", line 82, in setup_package configuration=configuration ) File "/home/darren/src/numpy/numpy/distutils/core.py", line 144, in setup config = configuration() File "setup.py", line 48, in configuration config.add_subpackage('numpy') File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 753, in add_subpackage caller_level = 2) File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 736, in get_subpackage caller_level = caller_level + 1) File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 683, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./numpy/setup.py", line 8, in configuration config.add_subpackage('f2py') File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 753, in add_subpackage caller_level = 2) File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 736, in get_subpackage caller_level = caller_level + 1) File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 683, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "numpy/f2py/setup.py", line 39, in configuration config.make_svn_version_py() File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 1298, in make_svn_version_py self.add_data_files(('', generate_svn_version_py())) File "/home/darren/src/numpy/numpy/distutils/misc_util.py", line 1281, in generate_svn_version_py assert revision is not None,'hmm, why I am not inside SVN tree???' AssertionError: hmm, why I am not inside SVN tree??? Darren

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REMINDER: ISP changeover today 9/12 7:00 PM Central
by Jeff Strunk 12 Sep '06

12 Sep '06

Good morning, This is a reminder for this evening's network maintenance. Unfortunately, our recent change in internet service providers is not working out. We will be switching to a more reliable provider tonight at 7:00 PM Central. Please allow for up to two hours of downtime. I will send an email announcing the start and completion of this maintenance. This will effect all Enthought servers as well as the SciPy server which hosts many Open Source projects. Please pass this message along to people that I have missed. If you have any questions, please direct them to me. We apologize for the inconvenience. Jeff Strunk Enthought, Inc.

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creating a masked array with a sequence containing a masked scalar array
by Michael Sorich 12 Sep '06

12 Sep '06

It seems that ma.array does not accept a sequence which contains a masked scalar array (not sure if this is the correct term). Is this deliberate? #numpy 1.0b5, python 2.3.x, winXP import numpy as N print N.ma.array([1,2,3, N.ma.array(1, mask=True)]) Traceback (most recent call last): File "C:\eclipse\plugins\org.python.pydev.debug_1.2.2\pysrc\pydevd_comm.py", line 529, in doIt result = pydevd_vars.evaluateExpression( self.thread_id, self.frame_id, self.expression, self.doExec ) File "C:\eclipse\plugins\org.python.pydev.debug_1.2.2\pysrc\pydevd_vars.py", line 258, in evaluateExpression exec expression in frame.f_globals, frame.f_locals File "<string>", line 1, in ? File "C:\Python23\Lib\site-packages\numpy\core\ma.py", line 562, in __init__ c = numeric.array(data, dtype=tc, copy=True, order=order) TypeError: an integer is required #works fine if scalar masked array is not masked print N.ma.array([1,2,3, N.ma.array(1)]) [1 2 3 1]

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代开发票
by 张先生 12 Sep '06

12 Sep '06

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ndarray.count() ?
by Martin Spacek 12 Sep '06

12 Sep '06

What's the most straightforward way to count, say, the number of 1s or Trues in the array? Or the number of any integer? I was surprised to discover recently that there isn't a count() method as there is for Python lists. Sorry if this has been discussed already, but I'm wondering if there's a reason for its absence. I came across a thread in March: http://aspn.activestate.com/ASPN/Mail/Message/numpy-discussion/3066460 that talked a bit about this in terms of speed, but what about just the convenience of having a count() method? Looks like masked arrays have a count method, don't know much about them though. Also, I understand the inaccuracies when converting between binary and decimal floating point representations, and therefore making counting of a specific float value in an array somewhat undefined, yet it seems to work in Python lists: >>> 1.1 1.1000000000000001 >>> a=[1.1, 1.1, 1.2] >>> a [1.1000000000000001, 1.1000000000000001, 1.2] >>> a.count(1.1) 2 >>> a.count(1.1000000000000001) 2 >>> a.count(1.2) 1 Comments? Martin

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DOE田口式品质工程
by "9月21-22日/上海" 12 Sep '06

12 Sep '06

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sum returns grand total?
by listservs＠mac.com 11 Sep '06

11 Sep '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I must have missed something -- since when does summing a multidimensional array return the grand total? I thought that it should sum over axis zero by default (at least, thats what the docs say). Here's what I am getting: (Pdb) pre Out[6]: array([[[ 13, 3, 1, 33, 52], [ 1, 0, 0, 0, 2], [ 4, 0, 0, 2, 6], [ 15, 1, 0, 20, 54]], [[380, 101, 9, 267, 321], [ 20, 4, 0, 7, 16], [ 31, 3, 1, 31, 22], [314, 27, 4, 276, 391]]], dtype=int64) (Pdb) sum(pre) Out[6]: 2432L Is this correct behaviour? - -- Christopher Fonnesbeck + Atlanta, GA + fonnesbeck at mac.com + Contact me on AOL IM using email address -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFBYSJGKaDpEGshJ0RAiPhAJ0d/MCGMciLgB2ZOwXf1FVj26NpTgCdG7h8 M83+mZsYGP2svVBGn8RtbNw= =mby0 -----END PGP SIGNATURE-----

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rfft different in numpy vs scipy
by Andrew Jaffe 11 Sep '06

11 Sep '06

Hi all, It seems that scipy and numpy define rfft differently. numpy returns n/2+1 complex numbers (so the first and last numbers are actually real) with the frequencies equivalent to the positive part of the fftfreq, whereas scipy returns n real numbers with the frequencies as in rfftfreq (i.e., two real numbers at the same frequency, except for the highest and lowest) [All of the above for even n; but the difference between numpy and scipy remains for odd n.] I think the numpy behavior makes more sense, as it doesn't require any unpacking after the fact, at the expense of a tiny amount of wasted space. But would this in fact require scipy doing extra work from whatever the 'native' real_fft (fftw, I assume) produces? Anyone else have an opinion? Andrew

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DOE田口式品质工程
by "9月21-22日/上海" 10 Sep '06

10 Sep '06

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Your PR man AETR
by whieofvv llolkgcls 10 Sep '06

10 Sep '06

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1.0b5 build failure
by Neal Becker 09 Sep '06

09 Sep '06

Fedora FC5 linux, with BLAS, LAPACK, ATLAS, FFTW compile options: '-Ibuild/src.linux-x86_64-2.4/numpy/core/src -Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c' gcc: numpy/core/src/multiarraymodule.c numpy/core/src/multiarraymodule.c: In function ‘initmultiarray’: numpy/core/src/multiarraymodule.c:6860: error: ‘NPY_ALLOW_THREADS’ undeclared (first use in this function) numpy/core/src/multiarraymodule.c:6860: error: (Each undeclared identifier is reported only once numpy/core/src/multiarraymodule.c:6860: error: for each function it appears in.) numpy/core/src/multiarraymodule.c: In function ‘initmultiarray’: numpy/core/src/multiarraymodule.c:6860: error: ‘NPY_ALLOW_THREADS’ undeclared (first use in this function) numpy/core/src/multiarraymodule.c:6860: error: (Each undeclared identifier is reported only once numpy/core/src/multiarraymodule.c:6860: error: for each function it appears in.) error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC -Ibuild/src.linux-x86_64-2.4/numpy/core/src -Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c numpy/core/src/multiarraymodule.c -o build/temp.linux-x86_64-2.4/numpy/core/src/multiarraymodule.o" failed with exit status 1

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cobblestone
by Roger Mclaughlin 09 Sep '06

09 Sep '06

We are taught that in the Bible, youremember. Possibly he meant to melt away in the darkness, leaving us in thewilderness to our fate. He did not seem in the least surprised, indeed he said he knew thatthis was so. Why must he be our companion, Macumazahn? In the end I did so, very unwillingly,to please my relations. Well, hereplied, with a twinkle in his eye, if I were you I should go andlook for the lady there. I realizedthis when I made up my mind to continue the journey to Lake Monealone. Also she was rude enoughto believe and to tell me she believed that I was mad. Odd to have met you in this fashion,but so is everything in this place. Do you mean to say that you tried to do that, Mr. Oh, only that I seemed different in every way. No, always when I was awake and looking at the stars, andgenerally when I was in the open air. I willfollow with the wanderer as soon as he can walk. Then he lay down in the tentand fell at once into a profound sleep. My father was cracked on astrology andcast mine when I was born. I suppose I inherited it frommy father, at any rate there it is. Then he lay down in the tentand fell at once into a profound sleep. This pistol is much lighter triggered than I thought or perhaps theheat has affected the spring. From that moment, for example, I hated thedissipations which had attracted me. Go with them to the borders of the lake, where perchanceone will meet you. From that moment, for example, I hated thedissipations which had attracted me. Indeed, you would be wise to turnback, for I think that death is very fond of Lake Mone. There you will find those who will guideyou. He did not seem in the least surprised, indeed he said he knew thatthis was so. Lastly it was necessary to provide him withone of the spare Winchester rifles and some cartridges. Quatermain, I am adreamer and what is called a mystic.

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gdal numpy/numeric/matplotlib problem
by Didrik Pinte 09 Sep '06

09 Sep '06

Hi, I am running a Debian/Sid system and face a problem when using the gdal python bindinds. The gdal python bindings are linked with Numeric. In one of my application i'm using some numpy methods. This is working fine BUT when I add the use of the matploblib library to my application all the calls to gdal specific methods are broken. I have attached a basic example. The first test fails if I import the pylab module. The second one that can be run with any shapefile shows that when pylab is loaded, some GDAL methods raises GEOS exceptions. Commenting the "import pylab" line shows that without pylab there is no exceptions, nor problems. They are two workarounds : [1] a real one : using matplotlib with the Numeric lib [2] a fake one : renaming /usr/lib/python2.4/site-packages/numpy/core/multiarray.so to another name, the tests does not fail. Does anybody have a suggestion to correct this problem ? I can provide more details if needed. Best regards, -- Didrik

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regurgitation
by Sadie Craft 09 Sep '06

09 Sep '06

Is it really true that no influence is ever brought to bear onanybody about anything? If Diana did want anything youd be on the spot. Andchanging her tone, she said coldly: After all, Captain Cherrellis a D. A good many, said Dinny, seem to drop first, and then do therunning. She did not talk, however,leaving him to begin if he wished. Personally, I dontbelieve Aunt May can put us up. Especially when theyve been to the same school. Not more than I am, dont worry about that. Its as good a place, I suppose, asyou could find. Arrived at Shropshire House Sir Lawrence said:Can we see the Marquess, Pommett? Her knowledge of London was small, and she hailed the first cab. She passed Dinny andAdrian as they were coming in. The man came in again and drewthe curtains. Itrepresented with a moderate degree of certainty a young womanwithout clothes. The man came in again and drewthe curtains. Is your extradition really likely,Hubert? The hat ropes did it, Dinny, and let me tell you that the grapeshave been sour ever since. Professor Hallorsen was expected in at five and should at once begiven the message. Lord Saxenden knows me, and raisedher eyes. I shall sleep with my emergency suit-case; one can always get a taxi here at a moments notice. Shake hands, Millie, and remember what I said. Then, swiftly, looking neither to left nor right, she returned toAdrian. Go off your chump, Cherrell,then youll know what it means to be lonely for the rest of yourdays. But privilege is only justified nowadays byrunning till you drop. Your Auntnever ceases to throw them in my teeth. Puzzlin, theyheard her say as they entered the library. Either Im over-sensitive, Dinny, or this particular afflictiondoes seem to me too dreadful. She bent her head, and still didnt speak.

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problems with numpy/f2py module on Intel Mac
by listservs＠mac.com 08 Sep '06

08 Sep '06

After building and installing numpy from svn on an Intel Mac, I can successfully build f2py modules, but I get the following linking error: ImportError: Failure linking new module: /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/PyMC/ flib.so: Symbol not found: ___dso_handle Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ lib/python2.4/site-packages/PyMC/flib.so Expected in: dynamic lookup I'm using gfortran. Has anyone seen these types of errors before? I do not get them on PPC. Thanks, -- Christopher Fonnesbeck + Atlanta, GA + fonnesbeck at mac.com + Contact me on AOL IM using email address

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missing import in numpy.oldnumeric.mlab
by Darren Dale 08 Sep '06

08 Sep '06

This was just reported on mpl-dev: In [1]: from numpy.oldnumeric import mlab In [2]: mlab.eye(3) --------------------------------------------------------------------------- exceptions.NameError Traceback (most recent call last) /home/darren/<ipython console> /usr/lib64/python2.4/site-packages/numpy/oldnumeric/mlab.py in eye(N, M, k, typecode, dtype) 22 dtype = convtypecode(typecode, dtype) 23 if M is None: M = N ---> 24 m = nn.equal(nn.subtract.outer(nn.arange(N), nn.arange(M)),-k) 25 if m.dtype != dtype: 26 return m.astype(dtype) NameError: global name 'nn' is not defined

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numpy test failure: "ctypes is not available"
by listservs＠mac.com 08 Sep '06

08 Sep '06

I have built and installed numpy from svn on an Intel mac, and am having test failures that do not occur on PPC: In [8]: numpy.test() Found 13 tests for numpy.core.umath Found 8 tests for numpy.lib.arraysetops Found 3 tests for numpy.fft.helper Found 1 tests for numpy.lib.ufunclike Found 4 tests for numpy.ctypeslib Found 1 tests for numpy.lib.polynomial Found 8 tests for numpy.core.records Found 26 tests for numpy.core.numeric Found 3 tests for numpy.lib.getlimits Found 31 tests for numpy.core.numerictypes Found 4 tests for numpy.core.scalarmath Found 10 tests for numpy.lib.twodim_base Found 46 tests for numpy.lib.shape_base Found 4 tests for numpy.lib.index_tricks Found 32 tests for numpy.linalg.linalg Found 5 tests for numpy.distutils.misc_util Found 42 tests for numpy.lib.type_check Found 163 tests for numpy.core.multiarray Found 36 tests for numpy.core.ma Found 10 tests for numpy.core.defmatrix Found 39 tests for numpy.lib.function_base Found 0 tests for __main__ .........................EEEE........................................... ........................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ ......................................................... ====================================================================== ERROR: check_dtype (numpy.tests.test_ctypeslib.test_ndpointer) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/tests/test_ctypeslib.py", line 10, in check_dtype p = ndpointer(dtype=dt) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/ctypeslib.py", line 15, in _dummy raise ImportError, "ctypes is not available." ImportError: ctypes is not available. ====================================================================== ERROR: check_flags (numpy.tests.test_ctypeslib.test_ndpointer) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/tests/test_ctypeslib.py", line 54, in check_flags p = ndpointer(flags='FORTRAN') File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/ctypeslib.py", line 15, in _dummy raise ImportError, "ctypes is not available." ImportError: ctypes is not available. ====================================================================== ERROR: check_ndim (numpy.tests.test_ctypeslib.test_ndpointer) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/tests/test_ctypeslib.py", line 36, in check_ndim p = ndpointer(ndim=0) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/ctypeslib.py", line 15, in _dummy raise ImportError, "ctypes is not available." ImportError: ctypes is not available. ====================================================================== ERROR: check_shape (numpy.tests.test_ctypeslib.test_ndpointer) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/tests/test_ctypeslib.py", line 46, in check_shape p = ndpointer(shape=(1,2)) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/numpy/ctypeslib.py", line 15, in _dummy raise ImportError, "ctypes is not available." ImportError: ctypes is not available. ---------------------------------------------------------------------- Ran 489 tests in 0.528s FAILED (errors=4) Out[8]: <unittest.TextTestRunner object at 0x322fe90> Any clues? -- Christopher Fonnesbeck + Atlanta, GA + fonnesbeck at mac.com + Contact me on AOL IM using email address

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Re: [Numpy-discussion] PHAruRMACY
by Mabelle Reach 08 Sep '06

08 Sep '06

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f2py with xmingw
by Flavio Coelho 08 Sep '06

08 Sep '06

Hi, I have a module that uses a Fortran extension which I would like to compile for windows with f2py. I wonder If I could do this from Linux using xmingw. Has anyone tried this? thanks, -- Flávio Codeço Coelho registered Linux user # 386432 --------------------------- "Laws are like sausages. It's better not to see them being made." Otto von Bismark

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ISP changeover Tuesday 9/12 7:00 PM Central
by Jeff Strunk 08 Sep '06

08 Sep '06

Good afternoon, Unfortunately, our recent change in internet service providers is not working out. We will be switching to a more reliable provider on Tuesday 9/12 at 7:00 PM Central. Please allow for up to two hours of downtime. I will send an email announcing the start and completion of this maintenance. This will effect all Enthought servers as well as the SciPy server which hosts many Open Source projects. The problem was that our in-building internet service provider neglected to mention that our internet connection was over a wireless link to a different building. This link had very high latency. They have fixed this problem, but we feel that wireless is not stable enough for our needs. In order to provide higher quality service, we will be using 3 bonded T1s from AT&T after this switchover. Please pass this message along to people that I have missed. If you have any questions, please direct them to me. We apologize for the inconvenience. Jeff Strunk Enthought, Inc.

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2 GB limit for memmap'ed files
by Glen W. Mabey 08 Sep '06

08 Sep '06

A long time ago, Travis wrote: > On a related, but orthogonal note: > > My understanding is that using memory-mapped files for *very* large > files will require modification to the mmap module in Python --- > something I think we should push. One part of that process would be > to add the C-struct array interface to the mmap module and the buffer > object -- perhaps this is how we get the array interface into Python > quickly. Then, if we could make a base-type mmap that did not use > the buffer interface or the sequence interface (similar to the > bigndarray in scipy_core) and therefore by-passed the problems with > Python in those areas, then the current mmap object could inherit from > the base class and provide current functionality while still exposing > the array interface for access to >2GB files on 64-bit systems. > > Who would like to take up the ball for modifying mmap in Python in > this fashion? > > -Travis Did anyone ever "pick up the ball" on this issue? Glen

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reshape: missing arg check?
by Sven Schreiber 07 Sep '06

07 Sep '06

Hi, never mind that the following syntax is wrong, but is it supposed to yield that SystemError instead of something more informative? (This is with b5 on win32 and python 2.4.3) >>> b.reshape(3,3,axis = 1) Traceback (most recent call last): File "<interactive input>", line 1, in ? SystemError: NULL result without error in PyObject_Call -sven

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Fix to Int64/string numexpr support
by Ivan Vilata i Balaguer 07 Sep '06

07 Sep '06

Hi all, I've detected some small errors in the patches I sent some time ago for adding Int64 and string support to numexpr (see http://www.mail-archive.com/numpy-discussion%40lists.sourceforge.net/msg015…). Basically: * ``numpy.string`` was accessed instead of ``numpy.string_`` (looks like one of those not-so-just-aesthetical last-time changes). * The ``copy_args`` argument to ``evaluate()`` and others was no longer needed since discontiguous/unaligned arrays are no longer a special case. I have attached the necessary patch. Bye! :: Ivan Vilata i Balaguer >qo< http://www.carabos.com/ Cárabos Coop. V. V V Enjoy Data ""

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Numpy that is compatible with Scipy windows installer version
by Ryan Krauss 07 Sep '06

07 Sep '06

I am a Linux user trying to install Numpy/Scipy on a Windows machine in my office. I went to the website and grabbed the two latest versions: scipy = scipy-0.5.0.win32-py2.4.exe numpy = numpy-1.0b5.win32-py2.4.exe Trying to import scipy I get: Python 2.4.3 (#69, Mar 29 2006, 17:35:34) [MSC v.1310 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Overwriting info=<function info at 0x00C974F0> from scipy.misc.helpmod (was <fun ction info at 0x00BF7030> from numpy.lib.utils) Overwriting who=<function who at 0x00C24830> from scipy.misc.common (was <functi on who at 0x00BEFF30> from numpy.lib.utils) Overwriting source=<function source at 0x00C9B670> from scipy.misc.helpmod (was <function source at 0x00BF7070> from numpy.lib.utils) RuntimeError: module compiled against version 1000000 of C-API but this version of numpy is 1000002 Fatal Python error: numpy.core.multiarray failed to import... exiting. I read about this problem on the list and there was mention of needing a different Numpy version. With a slightly older Numpy I got (numpy-0.9.8.win32-py2.4.exe): Python 2.4.3 (#69, Mar 29 2006, 17:35:34) [MSC v.1310 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "C:\Python24\Lib\site-packages\scipy\__init__.py", line 32, in ? from numpy import oldnumeric ImportError: cannot import name oldnumeric Are there windows installers available for compatible versions of Scipy and Numpy? Thanks, Ryan

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