Mailman 3 July 2007 - NumPy-Discussion

Sum, multiply are slow ?
by David Cournapeau 12 Jul '07

12 Jul '07

Hi, While profiling some code, I noticed that sum in numpy is kind of slow once you use axis argument: import numpy as N a = N.random.randn(1e5, 30) %timeit N.sum(a) #-> 26.8ms %timeit N.sum(a, 1) #-> 65.5ms %timeit N.sum(a, 0) #-> 141ms Now, if I use some tricks, I get: %timeit N.sum(a) #-> 26.8 ms %timeit N.dot(a, N.ones(a.shape[1], a.dtype)) #-> 11.3ms %timeit N.dot(N.ones((1, a.shape[0]), a.dtype), a) #-> 15.5ms I realize that dot uses optimized libraries (atlas in my case) and all, but is there any way to improve this situation ? Cheers, David

4 5

How do I tell f2py to generate Numeric modules?
by Ben ZX 12 Jul '07

12 Jul '07

I ran f2py. It seems to always generate NumPy modules. How do I tell f2py to generate Numeric modules? Ben

2 1

alter_code1.py changes .stddev() to .std() ...
by Xavier Saint-Mleux 11 Jul '07

11 Jul '07

Hello, I'm having a lot of fun converting python code from numarray to numpy and I just found out that the alter_code1.py conversion script changes numarray's '.stddev()' to numpy's '.std()', even though the semantics are different ("sample" std.dev. or not; divide by N-1 vs. by N). Should I open yet another ticket about '.std()'? http://projects.scipy.org/scipy/numpy/ticket/502 http://projects.scipy.org/scipy/numpy/ticket/461 http://projects.scipy.org/scipy/numpy/ticket/388 This will be easy to solve once .std() has a parameter to choose the divisor, but what is everybody using in the mean time? Thanks, Xavier Saint-Mleux

1 0

Conversion float64->int bugged?
by Xavier Saint-Mleux 11 Jul '07

11 Jul '07

Hi all, The conversion from a numpy scalar to a python int is not consistent with python's native conversion (or numarray's): if the scalar is out of bounds for an int, python and numarray automatically create a long while numpy still creates an int... with the wrong value. N.B. I am new to numpy, so please forgive me if this issue has already been discussed. I've quickly searched the archives and Travis's "Guide to NumPy", with no success. e.g. (using numpy 1.0.3): Python 2.4.3 (#2, Apr 27 2006, 14:43:58) [GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from numpy import * >>> l= [1e3, 1e9, 1e15, -1e3, -1e9, -1e15] >>> a= array(l) >>> map(int, l) [1000, 1000000000, 1000000000000000L, -1000, -1000000000, -1000000000000000L] >>> map(int, a) [1000, 1000000000, -2147483648, -1000, -1000000000, -2147483648] >>> map(long, a) [1000L, 1000000000L, 1000000000000000L, -1000L, -1000000000L, -1000000000000000L] >>> IMHO, numpy's conversions to int should behave like Python's 'float_int' or 'long_int' functions (see $PYTHON_SRC_DIR/Objects/floatobject.c, $PYTHON_SRC_DIR/Objects/longobject.c): if it doesn't fit in an int, return a long. For now (svn), it seems that numpy is always using PyInt_FromLong after an implicit C cast to long (which silently fails; see $NUMPY_SRC_DIR/numpy/core/src/scalarmathmodule.c.src) Is there any reason not to change this? Thanks, Xavier Saint-Mleux

3 2

scipy.test() warnings, errors and failures
by mpjohnson＠gmail.com 09 Jul '07

09 Jul '07

Hi, I just installed numpy (1.0.3) and scipy (0.5.2) on a Windows machine running Python 2.5.1. They both complete installation, and numpy.test() reports no errors. scipy.test() produces a huge stream (see below) of warnings, errors (19), and failures (2), however. Also, there's a deprecation warning when I import scipy. Is this behavior normal? These appear to be the latest versions of everything. Thanks, Matt Python 2.5.1 (r251:54863, Apr 18 2007, 08:51:08) [MSC v.1310 32 bit (Intel)] on win32 Type "copyright", "credits" or "license()" for more information. **************************************************************** Personal firewall software may warn about the connection IDLE makes to its subprocess using this computer's internal loopback interface. This connection is not visible on any external interface and no data is sent to or received from the Internet. **************************************************************** IDLE 1.2.1 >>> import numpy >>> import scipy Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\misc\__init__.py", line 25 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code >>> scipy.test() Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\ndimage\__init__.py", line 40 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\sparse\__init__.py", line 9 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\__init__.py", line 20 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\__init__.py", line 5 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linsolve\umfpack \__init__.py", line 7 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linsolve\__init__.py", line 13 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\optimize\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\__init__.py", line 32 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\special\__init__.py", line 22 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\stats\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\fftpack\__init__.py", line 21 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\integrate\__init__.py", line 16 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\lapack\__init__.py", line 93 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\signal\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\blas\__init__.py", line 61 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\maxentropy\__init__.py", line 12 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\__init__.py", line 77 return ScipyTest(scipy).test(level, verbosity) DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 1 tests for scipy.cluster.vq Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\fftpack\__init__.py", line 21 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\numpy\testing\numpytest.py", line 408 suite = obj(mthname) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 18 tests for scipy.fftpack.basic Found 4 tests for scipy.fftpack.helper Found 20 tests for scipy.fftpack.pseudo_diffs Found 1 tests for scipy.integrate Found 10 tests for scipy.integrate.quadpack Found 3 tests for scipy.integrate.quadrature Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 6 tests for scipy.interpolate Found 6 tests for scipy.interpolate.fitpack Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\__init__.py", line 20 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 4 tests for scipy.io.array_import Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\tests\test_mio.py", line 28 super(test_mio_array, self).__init__(*args, **kwargs) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 28 tests for scipy.io.mio Found 12 tests for scipy.io.mmio Found 4 tests for scipy.io.recaster Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\blas\__init__.py", line 61 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 16 tests for scipy.lib.blas Found 128 tests for scipy.lib.blas.fblas Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\lapack\__init__.py", line 93 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 42 tests for scipy.lib.lapack Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\__init__.py", line 32 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 41 tests for scipy.linalg.basic Found 14 tests for scipy.linalg.blas Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\tests \test_decomp.py", line 117 ScipyTestCase.__init__(self, *args) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 53 tests for scipy.linalg.decomp Found 128 tests for scipy.linalg.fblas Found 4 tests for scipy.linalg.lapack Found 7 tests for scipy.linalg.matfuncs Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '...\\linsolve\\umfpack\\__init__.pyc'> C:\Python25\Lib\site-packages\scipy\linsolve\umfpack\tests \test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in <module>) Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y\\linsolve\\umfpack\ \umfpack.pyc'> C:\Python25\Lib\site-packages\scipy\linsolve\umfpack\tests \test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in <module>) Found 2 tests for scipy.maxentropy Found 397 tests for scipy.ndimage Found 6 tests for scipy.optimize Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\optimize\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 1 tests for scipy.optimize.cobyla Found 4 tests for scipy.optimize.zeros Found 4 tests for scipy.signal.signaltools Found 96 tests for scipy.sparse Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\special\__init__.py", line 22 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 358 tests for scipy.special.basic Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\stats\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 98 tests for scipy.stats Found 70 tests for scipy.stats.distributions Found 10 tests for scipy.stats.morestats Found 0 tests for __main__ ...........................................Residual: 1.05006987327e-007 ...........Took 13 points. ......... Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\fitpack2.py", line 457 warnings.warn(message) UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. ...... Don't worry about a warning regarding the number of bytes read. ....EEEE.E.EE.E.E.EE.E.E.E.EEEEE....................................................F......................................................................................................................................................................................................................................................................................................................................................................................................Result may be inaccurate, approximate err = 1.82697723188e-008 ...Result may be inaccurate, approximate err = 1.50259560743e-010 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ................................................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ......................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F.Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ...... ====================================================================== ERROR: check loadmat case 3dmatrix ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case cell ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case cellnest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case complex ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case double ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case emptycell ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case minus ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case multi ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case object ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case onechar ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case sparse ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case sparsecomplex ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case string ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case stringarray ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case struct ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case structarr ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case structnest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case unicode ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== FAIL: check_y_stride (scipy.lib.blas.tests.test_fblas.test_cgemv) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\lib\blas\tests \test_fblas.py", line 367, in check_y_stride assert_array_almost_equal(desired_y,y) File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 16.6666666667%) x: array([-5.39065742 +5.39065742j, 1. +1.j , 3.86268878 +0.13731122j, 3. +3.j , -9.09618664+17.09618759j, 5. +5.j ], dtype=complex64) y: array([-5.39065742 +5.39065742j, 1. +1.j , 3.86268878 +0.13731124j, 3. +3.j , -9.09618664+17.09618568j, 5. +5.j ], dtype=complex64) ====================================================================== FAIL: check_expon (scipy.stats.tests.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\stats\tests \test_morestats.py", line 57, in check_expon assert_array_less(A, crit[-2:]) File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 235, in assert_array_less header='Arrays are not less-ordered') File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not less-ordered (mismatch 100.0%) x: array(1.9482886531944246) y: array([ 1.587, 1.934]) ---------------------------------------------------------------------- Ran 1596 tests in 20.720s FAILED (failures=2, errors=19) <unittest.TextTestRunner object at 0x022F6B90>

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Array protocol and wxPython
by Timothy Hochberg 09 Jul '07

09 Jul '07

This is mainly addressed to Chris Barker since he seems to follow wxPython pretty closely. Does anyone know if anyone ever tried to get wxPython to use the array protocol to speed up the internal conversion of arrays? I was toying with the idea of giving it a try if no one's got around to it. -- . __ . |-\ . . tim.hochberg(a)ieee.org

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Buildbot for numpy
by Stefan van der Walt 09 Jul '07

09 Jul '07

Hi all, Short version ============= We now have a numpy buildbot running at http://buildbot.scipy.org Long version ============ Albert Strasheim and I set up a buildbot for numpy this week. For those of you unfamiliar with The Buildbot, it is """ ...a system to automate the compile/test cycle required by most software projects to validate code changes. By automatically rebuilding and testing the tree each time something has changed, build problems are pinpointed quickly, before other developers are inconvenienced by the failure. The guilty developer can be identified and harassed without human intervention. By running the builds on a variety of platforms, developers who do not have the facilities to test their changes everywhere before checkin will at least know shortly afterwards whether they have broken the build or not. Warning counts, lint checks, image size, compile time, and other build parameters can be tracked over time, are more visible, and are therefore easier to improve. The overall goal is to reduce tree breakage and provide a platform to run tests or code-quality checks that are too annoying or pedantic for any human to waste their time with. Developers get immediate (and potentially public) feedback about their changes, encouraging them to be more careful about testing before checkin. """ While we are still working on automatic e-mail notifications, the system already provides valuable feedback -- take a look at the waterfall display: http://buildbot.scipy.org If your platform is not currently on the list, please consider volunteering a machine as a build slave. This machine will be required to run the buildbot client, and to build a new version of numpy whenever changes are made to the repository. (The machine does not have to be dedicated to this task, and can be your own workstation.) We'd like to thank Robert Kern, Jeff Strunk and Gert-Jan van Rooyen who helped us to get the ball rolling, as well as Neilen Marais for offering his workstation as a build slave. Regards Stéfan

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Another change in default type of ones and zeros.
by Charles R Harris 08 Jul '07

08 Jul '07

Hi All, Originally, ones and zeros defaulted to integer, later the default changed to float, now it looks like it is integer again. In [80]: ones(2).dtype Out[80]: dtype('int32') In [81]: zeros(2).dtype Out[81]: dtype('int32') In [82]: __version__ Out[82]: '1.0.4.dev3880' This could break some code. Did I miss a decision somewhere along the line? Chuck

1 2

fancy indexing/broadcasting question
by Mark.Miller 07 Jul '07

07 Jul '07

A quick question for the group. I'm working with some code to generate some arrays of random numbers. The random numbers, however, need to meet certain criteria. So for the moment, I have things that look like this (code is just an abstraction): import numpy normal=numpy.random.normal RNDarray = normal(25,15,(50,50)) tmp1 = (RNDarray < 0) | (RNDarray > 25) while tmp1.any(): print tmp1.size, tmp1.shape, tmp1[tmp1].size RNDarray[tmp1] = normal(5,3, size = RNDarray[tmp1].size) tmp1 = (RNDarray < 0) | (RNDarray > 25) This code works well. However, it might be considered inefficient because, for each iteration of the while loop, all values get reevaluated even if they have previously met the criteria encapsulated in tmp1. It would be better if, for each cycle of the while loop, only those elements that have previously not met criteria get reevaluated. I tried a few things that haven't worked. An example is provided below (changed code marked with *): RNDarray = normal(25,15,(50,50)) tmp1 = (RNDarray < 0) | (RNDarray > 25) while tmp1.any(): print tmp1.size, tmp1.shape, tmp1[tmp1].size RNDarray[tmp1] = normal(5,3, size = RNDarray[tmp1].size) * tmp1 = (RNDarray[tmp1] < 0) | (RNDarray[tmp1] > 25) I see why this doesn't work properly. When tmp1 is reevaluated in the while loop, it returns an array with a different shape. Does anyone have any suggestions for improvement here? Please let me know if any of this requires clarification. Thanks, -Mark

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problem compiling v.1.0.3 on a Mac
by John Cartwright 07 Jul '07

07 Jul '07

Hello All, I'm having trouble compile on a Mac 10.4.10. It seems as if it's not finding /usr/include: ... from /Library/Frameworks/Python.framework/Versions/ 2.4/include/python2.4/Python.h:81, from _configtest.c:2: /usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory ... I tried setting the "CFLAG=-I/usr/include", but w/o success. Can anyone help me? Thanks! --john

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