Mailman 3 July 2015 - SciPy-User

How to display a RGB image (MFISH)?
by jp April 3, 2023

April 3, 2023

Hi, I have written a script to try to combine five images into a three channels RGB images<http://dip4fish.blogspot.com/2011/05/trying-to-combine-mfish-images-into-rg…> . The resulting RGB image looks like a grey scale image instead of a color one. I have three np.array Rnorm, Gnorm, Bnorm which are copied into a rgb array: *rgb = np.zeros((shape[0],shape[1],3),dtype=float) mxr=np.max(R) mxg=np.max(G) mxb=np.max(B) Rnorm=np.uint8((255*(R/mxr)))Gnorm=np.uint8((255*(R/mxg)))Bnorm=np.uint8((255*(R/mxb)))#copy each RGB component in an RGB array rgb[:,:,0]=Rnorm rgb[:,:,1]=Gnorm rgb[:,:,2]=Bnorm* *pylab.subplot(224, aspect='equal',frameon=False, xticks=[], yticks=[]) pylab.imshow(rgb) pylab.show()* Any advice? Thank you Jean-Patrick

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Invitation to connect on LinkedIn
by Jelle Feringa via LinkedIn July 28, 2022

July 28, 2022

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2 1

Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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Playing numpy array over speakers
by Todd Oct. 17, 2015

Oct. 17, 2015

Is anyone aware of a well-maintained, simple, cross-platform python package that can play a numpy array as sound over speakers? I am aware of https://wiki.python.org/moin/Audio/. However, in all the cases there, as far as I can find they either do not support numpy arrays, are not cross-platform, cannot playback sound at all, or are unmaintained. There is also PySoundCard, which would do what I need but also appears to be unmaintained (no release in over a year, and no commits in 5 months, no release with serious bugfixes mentioned in commits).

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Re: [SciPy-User] How to fix Aborted SciPy version 0.16.0b2 test ?
by Sergio Rojas July 31, 2015

July 31, 2015

This is a followup of the question posed in the email subject. The issue is about fixing the aborted test: >---- > test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64 '> ,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double fre e or corruption (!prev): 0x0000000002d0d520 *** > Aborted >---- After some extra work, the error seems to be associated with ATLAS 3.11.34 as it does not happen after changing to ATLAS 3.10.2 In summary, Self tests of SciPy version 0.16.0 using ATLAS 3.10.2 and NumPy version 1.9.2 under Python 3.4.3 running on ubuntu 14.04 LTS, end outputing: ---------------------------------------------------------------------- Ran 19454 tests in 474.654s OK (KNOWNFAIL=129, SKIP=1319) <nose.result.TextTestResult run=19454 errors=0 failures=0> A failure, however, is found if using SciPy version 0.16.0 under Python 3.5.0b3: FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit) ---------------------------------------------------------------------- Ran 19454 tests in 457.759s FAILED (KNOWNFAIL=129, SKIP=1319, failures=1) Three failures are obtained if using SciPy version 0.16.0b2: under python 3.4.3 FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_sqr FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_tall test_decomp_update.TestQRinsert_f.test_fat_p_row_sqr ---------------------------------------------------------------------- Ran 19371 tests in 459.815s FAILED (KNOWNFAIL=129, SKIP=1319, failures=3) Regards, Sergio $ python3 Python 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.show_config() lapack_mkl_info: NOT AVAILABLE blas_mkl_info: NOT AVAILABLE atlas_3_10_blas_threads_info: include_dirs = ['/home/myProg/NumLibsAtlas102/include'] language = c library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] libraries = ['tatlas'] openblas_lapack_info: NOT AVAILABLE openblas_info: NOT AVAILABLE atlas_3_10_threads_info: include_dirs = ['/home/myProg/NumLibsAtlas102/include'] language = f77 library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] libraries = ['tatlas', 'tatlas', 'tatlas'] blas_opt_info: include_dirs = ['/home/myProg/NumLibsAtlas102/include'] language = c library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] libraries = ['tatlas'] lapack_opt_info: include_dirs = ['/home/myProg/NumLibsAtlas102/include'] language = f77 library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] libraries = ['tatlas', 'tatlas', 'tatlas'] mkl_info: NOT AVAILABLE >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/numpy SciPy version 0.16.0 SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/scipy Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] nose version 1.3.7 ... ... ... ---------------------------------------------------------------------- Ran 19454 tests in 474.654s OK (KNOWNFAIL=129, SKIP=1319) <nose.result.TextTestResult run=19454 errors=0 failures=0> >>> $ Script started on Thu 30 Jul 2015 04:57:34 PM EDT $ python3 Python 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.show_config() blas_mkl_info: NOT AVAILABLE openblas_info: NOT AVAILABLE blas_opt_info: libraries = ['tatlas'] language = c library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] lapack_mkl_info: NOT AVAILABLE lapack_opt_info: libraries = ['tatlas', 'tatlas', 'tatlas'] language = f77 library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] openblas_lapack_info: NOT AVAILABLE atlas_3_10_blas_threads_info: libraries = ['tatlas'] language = c library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] atlas_3_10_threads_info: libraries = ['tatlas', 'tatlas', 'tatlas'] language = f77 library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] mkl_info: NOT AVAILABLE >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/numpy SciPy version 0.16.0b2 SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/scipy Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] nose version 1.3.7 ... ... ... Test values of lambda outside the domains of the functions. ... ok ====================================================================== FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_sqr ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case .py", line 198, in runTest self.test(*self.arg) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 755, in test_fat_p_row_sqr self.base_fat_p_row_xxx(5) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx check_qr(q1, r1, a1, self.rtol, self.atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 32, in check_qr assert_unitary(q, rtol, atol, assert_sqr) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 21, in assert_unitary assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 1297, in assert_allclose verbose=verbose, header=header) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 665, in assert_array_compare raise AssertionError(msg) AssertionError: Not equal to tolerance rtol=0.0001, atol=1.19209e-06 (mismatch 100.0%) x: array([[ 0.998973 +5.587935e-09j, 0.009882 +7.026103e-02j, -0.129242 -4.287320e-02j, -0.030052 -6.515425e-02j, 0.005686 -9.261262e-02j, 0.031090 +1.492383e-02j,... y: array([[ 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],... ====================================================================== FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_tall ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case .py", line 198, in runTest self.test(*self.arg) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 759, in test_fat_p_row_tall self.base_fat_p_row_xxx(7) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx check_qr(q1, r1, a1, self.rtol, self.atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 32, in check_qr assert_unitary(q, rtol, atol, assert_sqr) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 21, in assert_unitary assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 1297, in assert_allclose verbose=verbose, header=header) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 665, in assert_array_compare raise AssertionError(msg) AssertionError: Not equal to tolerance rtol=0.0001, atol=1.19209e-06 (mismatch 100.0%) x: array([[ 1.006917 -6.984919e-09j, 0.009022 -8.255728e-02j, 0.178461 -3.312873e-02j, -0.047311 +1.095396e-01j, 0.059368 +8.496426e-02j, 0.031223 +1.194810e-02j,... y: array([[ 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,... ====================================================================== FAIL: test_decomp_update.TestQRinsert_f.test_fat_p_row_sqr ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case .py", line 198, in runTest self.test(*self.arg) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 755, in test_fat_p_row_sqr self.base_fat_p_row_xxx(5) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx check_qr(q1, r1, a1, self.rtol, self.atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 32, in check_qr assert_unitary(q, rtol, atol, assert_sqr) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin alg/tests/test_decomp_update.py", line 21, in assert_unitary assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 1297, in assert_allclose verbose=verbose, header=header) File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes ting/utils.py", line 665, in assert_array_compare raise AssertionError(msg) AssertionError: Not equal to tolerance rtol=0.0001, atol=1.19209e-06 (mismatch 100.0%) x: array([[ 8.658818e-01, 1.325921e-01, 2.875357e-01, 4.060289e-02, 1.853821e-01, 2.545137e-02, -2.103027e-01, 2.341471e-02, 1.182279e-01, -1.466596e-01, -4.916818e-02, -1.404783e-01],... y: array([[ 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0.],... ---------------------------------------------------------------------- Ran 19371 tests in 459.815s FAILED (KNOWNFAIL=129, SKIP=1319, failures=3) <nose.result.TextTestResult run=19371 errors=0 failures=3> >>> $ $ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.show_config() openblas_lapack_info: NOT AVAILABLE atlas_3_10_threads_info: language = f77 libraries = ['tatlas', 'tatlas', 'tatlas'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] blas_opt_info: language = c libraries = ['tatlas'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] mkl_info: NOT AVAILABLE lapack_opt_info: language = f77 libraries = ['tatlas', 'tatlas', 'tatlas'] define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')] library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] lapack_mkl_info: NOT AVAILABLE openblas_info: NOT AVAILABLE blas_mkl_info: NOT AVAILABLE atlas_3_10_blas_threads_info: language = c libraries = ['tatlas'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')] library_dirs = ['/home/myProg/NumLibsAtlas102/lib'] include_dirs = ['/home/myProg/NumLibsAtlas102/include'] >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack ages/numpy SciPy version 0.16.0 SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack ages/scipy Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] nose version 1.3.7 ... ... ... ====================================================================== FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/opt imize/tests/test_minpack.py", line 397, in test_indeterminate_covariance _assert_warns(OptimizeWarning, curve_fit, lambda x, a, b: a*x, xdata, ydata) File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy/tes ting/utils.py", line 1603, in assert_warns "%s( is %s)" % (func.__name__, warning_class, l[0])) AssertionError: First warning for curve_fit is not a <class 'scipy.optimize.opti mize.OptimizeWarning'>( is {message : DeprecationWarning('inspect.getargspec() i s deprecated, use inspect.signature() instead',), category : 'DeprecationWarning ', filename : '/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/sc ipy/optimize/minpack.py', lineno : 546, line : None}) ---------------------------------------------------------------------- Ran 19454 tests in 457.759s FAILED (KNOWNFAIL=129, SKIP=1319, failures=1) <nose.result.TextTestResult run=19454 errors=0 failures=1> >>> This reported issue, Ralf, apparently has to do with the atlas library. As shown in the following output, if instead using the mkl library (from Intel) this time a scipy failure is obtained: $ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.show_config() blas_opt_info: library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64' ] libraries = ['mkl_rt', 'pthread'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include'] lapack_opt_info: library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64' ] libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include'] lapack_mkl_info: library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64' ] libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include'] blas_mkl_info: library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64' ] libraries = ['mkl_rt', 'pthread'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include'] openblas_lapack_info: NOT AVAILABLE mkl_info: library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64' ] libraries = ['mkl_rt', 'pthread'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include'] >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack ages/numpy SciPy version 0.16.0b2 SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack ages/scipy Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] nose version 1.3.7 /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decora tor.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect. signature() instead ... ... ... test_y_stride (test_fblas.TestZswap) ... ok test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64' >,) ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.complex1 28'>,) ... ok test_interpolative.TestInterpolativeDecomposition.test_rand ... ok test_sing_val_update (test_lapack.TestDlasd4) ... ok ... ... ... Compare results with some values that were computed using mpmath. ... ok Test values of lambda outside the domains of the functions. ... ok ====================================================================== FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/opt imize/tests/test_minpack.py", line 397, in test_indeterminate_covariance _assert_warns(OptimizeWarning, curve_fit, lambda x, a, b: a*x, xdata, ydata) File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy/tes ting/utils.py", line 1603, in assert_warns "%s( is %s)" % (func.__name__, warning_class, l[0])) AssertionError: First warning for curve_fit is not a <class 'scipy.optimize.opti mize.OptimizeWarning'>( is {message : DeprecationWarning('inspect.getargspec() i s deprecated, use inspect.signature() instead',), category : 'DeprecationWarning ', filename : '/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/sc ipy/optimize/minpack.py', lineno : 546, line : None}) ---------------------------------------------------------------------- Ran 19371 tests in 441.458s FAILED (KNOWNFAIL=129, SKIP=1319, failures=1) <nose.result.TextTestResult run=19371 errors=0 failures=1> >>> For some reason I am not getting messages via the mailing list. I am reading them at the web [ http://mail.scipy.org/pipermail/scipy-user/2015-July/036660.html ] > >Hi Sergio, thanks for the report. A few questions: >- did 0.15.1 work for you with the same install method >- does the problem still occur with the final 0.16.0 release? >- is the issue specific to Python 3.5 or not? > >Opening an issue on Github and attaching a gdb traceback (see >http://scipy.org/bug-report.html[http://scipy.org/bug-report.html]) would be helpful. >Cheers, >Ralf At this stage, Ralf, I have confirmed that the issue is NO specific to Python 3.5 or to SciPy version 0.16.0b2 : $ python Python 2.7.10 (default, Jul 29 2015, 20:51:44) [GCC 4.8.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac kages/numpy SciPy version 0.16.0b2 SciPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac kages/scipy Python version 2.7.10 (default, Jul 29 2015, 20:51:44) [GCC 4.8.4] nose version 1.3.7 /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-packages/numpy/lib/utils. py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead! warnings.warn(depdoc, DeprecationWarning) test_hierarchy.TestCopheneticDistance.test_linkage_cophenet_tdist_Z ... ok ... ... ... test_y_bad_size (test_fblas.TestZswap) ... ok test_y_stride (test_fblas.TestZswap) ... ok test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64'> ,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double fre e or corruption (!prev): 0x0000000002d0d520 *** Aborted $ $ python3 Python 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/numpy SciPy version 0.13.3 SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack ages/scipy Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4] nose version 1.3.7 /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/lib/utils.p y:95: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas ` instead! warnings.warn(depdoc, DeprecationWarning) ... ... ... test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64' >,) ... /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/cor e/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.li nalg.matrix_rank`. VisibleDeprecationWarning) *** Error in `python3': double free or corruption (!prev): 0x0000000001b1edb0 ** * Aborted $ Sent: Tuesday, July 21, 2015 at 3:39 PM From: "Sergio Rojas" <sergio_r(a)mail.com> To: scipy-user(a)scipy.org Subject: How to fix Aborted SciPy version 0.16.0b2 test ? Hello all, Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the SciPy (version 0.16.0b2) test is aborting at #------------ test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 *** Aborted #------------ would it be possible to fix it? Thanks in advance for your help, Sergio PD. Some extra info is as follows: $ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.show_config() blas_mkl_info: NOT AVAILABLE atlas_3_10_threads_info: libraries = ['tatlas', 'tatlas', 'tatlas'] define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')] include_dirs = ['/home/myProg/NumLibs64b/include'] library_dirs = ['/home/myProg/NumLibs64b/lib'] language = f77 openblas_lapack_info: NOT AVAILABLE lapack_mkl_info: NOT AVAILABLE openblas_info: NOT AVAILABLE mkl_info: NOT AVAILABLE lapack_opt_info: libraries = ['tatlas', 'tatlas', 'tatlas'] define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')] include_dirs = ['/home/myProg/NumLibs64b/include'] library_dirs = ['/home/myProg/NumLibs64b/lib'] language = f77 atlas_3_10_blas_threads_info: libraries = ['tatlas'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')] include_dirs = ['/home/myProg/NumLibs64b/include'] library_dirs = ['/home/myProg/NumLibs64b/lib'] language = c blas_opt_info: libraries = ['tatlas'] define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')] include_dirs = ['/home/myProg/NumLibs64b/include'] library_dirs = ['/home/myProg/NumLibs64b/lib'] language = c >>> scipy.test('full', verbose=2) Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy SciPy version 0.16.0b2 SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4] nose version 1.3.7 /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead ... ... test_y_bad_size (test_fblas.TestZswap) ... ok test_y_stride (test_fblas.TestZswap) ... ok test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 *** Aborted

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ANN: PyWavelets 0.3.0 release
by Ralf Gommers July 31, 2015

July 31, 2015

Dear all, On behalf of the PyWavelets development team I'm excited to announce the availability of PyWavelets 0.3.0. This is the first release of the package in 3 years. It is the result of a significant effort of a growing development team to modernize the package, to provide Python 3.x support and to make a start with providing new features as well as improved performance. A 0.4.0 release will follow shortly, and will contain more significant new features as well as changes/deprecations to streamline the API. This release requires Python 2.6, 2.7 or 3.3-3.5 and Numpy 1.6.2 or greater. Sources and release notes can be found on https://pypi.python.org/pypi/PyWavelets and https://github.com/PyWavelets/pywt/releases. Activity on the project is picking up quickly. If you're interested in wavelets in Python, you are welcome and invited to join us at https://github.com/PyWavelets/pywt Enjoy, Ralf ============================== PyWavelets 0.3.0 Release Notes ============================== PyWavelets 0.3.0 is the first release of the package in 3 years. It is the result of a significant effort of a growing development team to modernize the package, to provide Python 3.x support and to make a start with providing new features as well as improved performance. A 0.4.0 release will follow shortly, and will contain more significant new features as well as changes/deprecations to streamline the API. This release requires Python 2.6, 2.7 or 3.3-3.5 and NumPy 1.6.2 or greater. Highlights of this release include: - Support for Python 3.x (>=3.3) - Added a test suite (based on nose, coverage up to 61% so far) - Maintenance work: C style complying to the Numpy style guide, improved templating system, more complete docstrings, pep8/pyflakes compliance, and more. New features ============ Test suite ---------- The test suite can be run with ``nosetests pywt`` or with:: >>> import pywt >>> pywt.test() n-D Inverse Discrete Wavelet Transform -------------------------------------- The function ``pywt.idwtn``, which provides n-dimensional inverse DWT, has been added. It complements ``idwt``, ``idwt2`` and ``dwtn``. Thresholding ------------ The function `pywt.threshold` has been added. It unifies the four thresholding functions that are still provided in the ``pywt.thresholding`` namespace. Backwards incompatible changes ============================== None in this release. Other changes ============= Development has moved to `a new repo <https://github.com/PyWavelets/pywt>`_. Everyone with an interest in wavelets is welcome to contribute! Building wheels, building with ``python setup.py develop`` and many other standard ways to build and install PyWavelets are supported now. Authors ======= * Ankit Agrawal + * François Boulogne + * Ralf Gommers + * David Menéndez Hurtado + * Gregory R. Lee + * David McInnis + * Helder Oliveira + * Filip Wasilewski * Kai Wohlfahrt + A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

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Re: [SciPy-User] How to fix Aborted SciPy version 0.16.0b2 test ?
by Sergio Rojas July 30, 2015

July 30, 2015

1 0

How to fix Aborted SciPy version 0.16.0b2 test ?
by Sergio Rojas July 30, 2015

July 30, 2015

2 2

Decimal dtype
by Todd July 28, 2015

July 28, 2015

Traditional base-2 floating-point numbers have a lot of well-known issues. The python standard library has a Decimal module that provides base-10 floating-point numbers, which avoid some (although not all) of these issues. Is there any possibility of numpy having one or more dtypes for base-10 floating-point numbers? I understand fully if a lack of support from underlying libraries makes this infeasible at the present time. I haven't been able to find much good information on the issue, which leads me to suspect the situation is probably not good.

4 5

scipy-0.16.0 self-test result
by Neal Becker July 28, 2015

July 28, 2015

fedora 22 x86_64 built with: CFLAGS="-O3 -march=native" ATLAS=/usr/lib64/openblas FFTW=/usr/lib64 BLAS=/usr/lib64 LAPACK=/usr/lib64 python3 setup.py install --user [nbecker@nbecker2 ~]$ python -c 'import scipy; scipy.test("full");' Running unit tests for scipy NumPy version 1.9.2 NumPy is installed in /home/nbecker/.local/lib/python2.7/site-packages/numpy SciPy version 0.16.0 SciPy is installed in /home/nbecker/.local/lib/python2.7/site-packages/scipy Python version 2.7.10 (default, Jul 5 2015, 14:15:43) [GCC 5.1.1 20150618 (Red Hat 5.1.1-4)] nose version 1.3.7 ====================================================================== FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/nbecker/.local/lib/python2.7/site- packages/scipy/spatial/tests/test_qhull.py", line 294, in test_degenerate_barycentric_transforms assert_(bad_count < 20, bad_count) File "/home/nbecker/.local/lib/python2.7/site- packages/numpy/testing/utils.py", line 53, in assert_ raise AssertionError(smsg) AssertionError: 20 ====================================================================== FAIL: test_qhull.TestUtilities.test_more_barycentric_transforms ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/nbecker/.local/lib/python2.7/site- packages/scipy/spatial/tests/test_qhull.py", line 353, in test_more_barycentric_transforms unit_cube_tol=1e7*eps) File "/home/nbecker/.local/lib/python2.7/site- packages/scipy/spatial/tests/test_qhull.py", line 280, in _check_barycentric_transforms assert_(ok.all(), "%s %s" % (err_msg, np.where(~ok))) File "/home/nbecker/.local/lib/python2.7/site- packages/numpy/testing/utils.py", line 53, in assert_ raise AssertionError(smsg) AssertionError: ndim=4 (array([ 8071, 10512, 10513]),) ---------------------------------------------------------------------- Ran 19618 tests in 588.242s FAILED (KNOWNFAIL=149, SKIP=1195, failures=2)

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