Mailman 3 February 2013 - NumPy-Discussion

[ANN] SciPy2013 Sponsorships: Apply Now!
by Jonathan Rocher 28 Feb '13

28 Feb '13

[Apologies for cross-posts] Dear all, The SciPy2013 conference <http://conference.scipy.org/scipy2013/> will continue the tradition of offering sponsorships to attend the conference. These sponsorships provide funding for airfare, lodging, and conference registration. This year, these sponsorships will be *open to community members rather than just students*. Applications will be judged both on merit as well as need. If you would like to apply for yourself or a worthy candidate <http://conference.scipy.org/scipy2013/reg_fin_aid.php>, please note our application due date of *Monday, March 25th*. Winners will be announced on April 22nd. Looking forward to a very exciting conference! The SciPy 2013 Financial Aid Chairs Jeff Daily, Pacific Northwest National Lab. John Wiggins, Enthought Inc. -- Jonathan Rocher, PhD Scientific software developer Co-chair of SciPy2013 Conference Enthought, Inc. jrocher(a)enthought.com 1-512-536-1057 http://www.enthought.com

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[ANN] SciPy2013 Tutorials: Call for Submissions
by Jonathan Rocher 28 Feb '13

28 Feb '13

[Apologies for cross-posts] Dear all, We are excited to kick off the SciPy2013 conference<http://conference.scipy.org/scipy2013/>with two days of tutorials. This year we are proud to expand the session to include *THREE parallel tracks*: introductory, intermediate and advanced. Teachers will receive a stipend for their service. We are accepting tutorial proposals from individuals or teams until *April 1st*. Click here for more details and to submit applications<http://conference.scipy.org/scipy2013/tutorial_overview.php> . Looking forward to a very exciting conference! The SciPy 2013 Tutorial Chairs Francesc Alted, Continuum Analytics Inc. Dharhas Pothina, Texas Water Development Board -- Jonathan Rocher, PhD Scientific software developer Co-chair of SciPy2013 Conference Enthought, Inc. jrocher(a)enthought.com 1-512-536-1057 http://www.enthought.com

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scipy build errors
by raghu330 28 Feb '13

28 Feb '13

Dear All, I am trying to install iris, which needs scipy0.10 or above. My machine is RHEL6 with gfortran and g95 installed. I was able to install numpy without any trouble, but have issues with scipy. I have installed ATLAS, BLAS and LAPACK, but I still get this error. Kindly let me know how to go ahead.. Thanks in advance & Regards Raghu ----------------- /opt/python2.7.3/bin/python setup.py build --fcompiler=gfortran Running from scipy source directory. blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /opt/python2.7.3/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /opt/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /opt/python2.7.3/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /opt/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /opt/python2.7.3/lib libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /opt/lib libraries f77blas,cblas,atlas not found in /usr/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE /opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/system_info.py:1425 : UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /opt/python2.7.3/lib libraries blas not found in /usr/local/lib64 libraries blas not found in /usr/local/lib libraries blas not found in /opt/lib libraries blas not found in /usr/lib64 libraries blas not found in /usr/lib NOT AVAILABLE /opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/system_info.py:1434 : UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/system_info.py:1437 : UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 208, in <module> setup_package() File "setup.py", line 199, in setup_package configuration=configuration ) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/core.py", l ine 152, in setup config = configuration() File "setup.py", line 136, in configuration config.add_subpackage('scipy') File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 1002, in add_subpackage caller_level = 2) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 971, in get_subpackage caller_level = caller_level + 1) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 8, in configuration config.add_subpackage('integrate') File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 1002, in add_subpackage caller_level = 2) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 971, in get_subpackage caller_level = caller_level + 1) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/misc_util.p y", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/system_info .py", line 321, in get_info return cl().get_info(notfound_action) File "/opt/python2.7.3/lib/python2.7/site-packages/numpy/distutils/system_info .py", line 472, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. ------------------------------------ EOM -------------------------------------- -- View this message in context: http://numpy-discussion.10968.n7.nabble.com/scipy-build-errors-tp33032.html Sent from the Numpy-discussion mailing list archive at Nabble.com.

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interactive distutils
by Charles R Harris 28 Feb '13

28 Feb '13

It's there, it uses raw_input, does anyone use it? Chuck

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embeding numpy in c++
by Sunghwan Choi 28 Feb '13

28 Feb '13

Hi, I am now trying to embedding numpy in my c++ code (more correctly ase module, which is dependent to numpy). My test code is simple test.cpp #include "Python.h" #include <stdio.h> #include <iostream> extern "C" void Py_Initialize(); extern "C" void PyErr_Print(); using namespace std; int main(int argc, char* argv[]) { double answer = 0; PyObject *modname, *mod, *mdict, *func, *stringarg, *args, *rslt; Py_Initialize(); modname = PyString_FromString("numpy"); mod = PyImport_Import(modname); PyErr_Print(); cout << mod << endl; return 0; } shchoi@aims0:~/tmp/test2$ vi test.cpp shchoi@aims0:~/tmp/test2$ icpc -c test.cpp -I ~/program/epd/include/python2.7/ shchoi@aims0:~/tmp/test2$ icpc -o exe test.o -L ~/program/epd/lib/ -lpython2.7 shchoi@aims0:~/tmp/test2$ ./exe Traceback (most recent call last): File "/home/shchoi/program/epd/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module> import add_newdocs File "/home/shchoi/program/epd/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/home/shchoi/program/epd/lib/python2.7/site-packages/numpy/lib/__init__.py" , line 4, in <module> from type_check import * File "/home/shchoi/program/epd/lib/python2.7/site-packages/numpy/lib/type_check.p y", line 8, in <module> import numpy.core.numeric as _nx File "/home/shchoi/program/epd/lib/python2.7/site-packages/numpy/core/__init__.py ", line 5, in <module> import multiarray ImportError: /home/shchoi/program/epd/lib/python2.7/site-packages/numpy/core/multiarray.s o: undefined symbol: PyUnicodeUCS2_AsASCIIString How to solve this problem? Can anyone help me? If anyone know the solution, please let me know as soon as possible Sincerely Sunghwan Choi

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polyfit in NumPy v1.7
by David Pine 28 Feb '13

28 Feb '13

As of NumPy v1.7, numpy.polyfit includes an option for providing weighting to data to be fit. It's a welcome addition, but the implementation seems a bit non-standard, perhaps even wrong, and I wonder if someone can enlighten me. 1. The documentation does not specify what the weighting array "w" is supposed to be. After some fooling around I figured out that it is 1/sigma, where sigma is the standard deviation uncertainty "sigma" in the y data. A better implementation, which would be consistent with how weighting is done in scipy.optimize.curve_fit, would be to specify "sigma" directly, rather than "w". This is typically what the user has at hand, this syntax is more transparent, and it would make polyfit consistent with the nonlinear fitting routine scipy.optimize.curve_fit. 2. The definition of the covariance matrix in polyfit is peculiar (or maybe wrong, I'm not sure). Towards the end of the code for polyfit, the standard covariance matrix is calculated and given the variable name "Vbase". However, instead of returning Vbase as the covariance matrix, polyfit returns the quantity Vbase * fac, where fac = resids / (len(x) - order - 2.0). fac scales as N, the number of data points, so the covariance matrix is about N times larger than it should be for large values of N; the increase is smaller for small N (of order 10). Perhaps the authors of polyfit want to use a more conservative error estimate, but the references given in the poyfit code make no mention of it. I think it would be much better to return the standard definition of the covariance matrix (see, for example, the book Numerical Recipes). David Pine

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Apply transform to many small matrices
by Jorge Scandaliaris 27 Feb '13

27 Feb '13

Hi, First of all excuse me if this is a trivial question. I have the feeling it is, but searching and looking through the docs has proven unsuccesful so far. I have an ndarray A of shape (M,2,2) representing M 2 x 2 matrices. Now I want to apply a transform T of shape (2,2) to each of matrix. The way I do this now is by iterating over all rows of A multiplying the matrices using numpy.dot(): for row in np.arange(A.shape[0]): A[row] = np.dot(A[row],T) but this seems to be slow when M is large and I have the feeling there must be a way of doing it better. Thanks, jorges

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swig interface file (numpy.i) warning
by Tom Krauss 27 Feb '13

27 Feb '13

Hi, I've been happy to use numpy.i for generating SWIG interfaces to C++. For a while, I've noticed this warning while compiling: /Users/tkrauss/projects/dev_env/lib/python2.7/site-packages/numpy-1.8.0.dev_f2f0ac0_20120725-py2.7-macosx-10.8-x86_64.egg/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" and today tried to get rid of the warning. So, in numpy.i, I followed the warning's advice. I added the # def here: %{ #ifndef SWIG_FILE_WITH_INIT # define NO_IMPORT_ARRAY #endif #include "stdio.h" *#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION* #include <numpy/arrayobject.h> %} SWIG was happy, but when compiling the C++ wrapper, there were many warnings followed by many errors. The warnings were for redefinition of NPY_MIN_BYTE and similar. The errors were for all kinds of stuff, excerpt here: native_wrap.cpp:3632: error: ‘PyArray_NOTYPE’ was not declared in this scope native_wrap.cpp:3633: error: cannot convert ‘PyObject*’ to ‘const PyArrayObject*’ for argument ‘1’ to ‘int PyArray_TYPE(const PyArrayObject*)’ native_wrap.cpp: At global scope: native_wrap.cpp:3877: error: ‘intp’ has not been declared native_wrap.cpp: In function ‘int require_fortran(PyArrayObject*)’: native_wrap.cpp:3929: error: ‘struct tagPyArrayObject’ has no member named ‘nd’ native_wrap.cpp:3933: error: ‘struct tagPyArrayObject’ has no member named ‘flags’ native_wrap.cpp:3933: error: ‘FARRAY’ was not declared in this scope native_wrap.cpp:20411: error: ‘struct tagPyArrayObject’ has no member named ‘data’ It looks like there is a new C API for numpy, and the version of numpy.i that I have doesn't use it. Is there a new version of numpy.i available (or in development) that works with the new API? Short term it will just get rid of a warning but I am interested in a good long term solution in case I need to upgrade numpy. Thanks, Tom

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[ANN] SciPy2013: Call for abstracts
by Jonathan Rocher 27 Feb '13

27 Feb '13

[Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python)<http://conference.scipy.org/scipy2013/about.php> allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. *The deadline for abstract submissions is March 20th, 2013. * Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning & reproducible science), or the domain-specific mini-symposia<http://conference.scipy.org/scipy2013/about.php>held during the conference (Meteorology, climatology, and atmospheric and oceanic science, Astronomy and astrophysics, Medical imaging, Bio-informatics). Please submit your abstract at the SciPy 2013 website abstract submission form <http://conference.scipy.org/scipy2013/speaking_submission.php>. Abstracts will be accepted for posters or presentations. Optional papers to be published in the conference proceedings will be requested following abstract submission. This year the proceedings will be made available prior to the conference to help attendees navigate the conference. We look forward to an exciting and interesting set of talks, posters, and discussions and hope to see you at the conference. The SciPy 2013 Program Committee Chairs Matt McCormick, Kitware, Inc. Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory

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Plans for missing data
by Lluís 27 Feb '13

27 Feb '13

Hi there, I haven't been able to find an answer after a quick search, but are there any plans regarding the (re)inclusion of missing data support into some future version of numpy? Thanks a lot! Lluis -- "And it's much the same thing with knowledge, for whenever you learn something new, the whole world becomes that much richer." -- The Princess of Pure Reason, as told by Norton Juster in The Phantom Tollbooth

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