Mailman 3 November 2008 - SciPy-User

Wrapping TWPBVPLC BVP solver
by John Salvatier 16 Nov '08

16 Nov '08

I want to wrap the Fortran Boundary Value Problem Solver TWPBVPLC (http:// www.ma.ic.ac.uk/~jcash/BVP_software/readme.php<http://www.ma.ic.ac.uk/%7Ejcash/BVP_software/readme.php>) which I believe I have arranged to have released under a BSD license. Has someone else done this before? I don't want to repeat work unnecessarily.

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interpolate
by AndrewF 15 Nov '08

15 Nov '08

Why does tck1=interpolate.splrep(scipy.array([1.0,2.0]),scipy.array([1.0,4.0]),k=1) work okay, but tck2=interpolate.splrep(scipy.array([8.2,2.0]),scipy.array([1.0,4.0]),k=1) does not? I ultimately want to interpolate a more complicated, non-linear data set, but here I am trying to reduce the problem to the simplest possible level. Thanks. -- View this message in context: http://www.nabble.com/interpolate-tp20509445p20509445.html Sent from the Scipy-User mailing list archive at Nabble.com.

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calculating numerical jacobian
by Tony S Yu 15 Nov '08

15 Nov '08

Does scipy provide any functions to calculate the Jacobian of a function? I noticed that minpack (used by scipy.optimize) approximates a Jacobian numerically, but scipy doesn't seem to provide a wrapper for these minpack functions. Any ideas? Thanks, -Tony

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weave/blitz problem
by Kristian Hans Sandberg 14 Nov '08

14 Nov '08

I'm having exactly the same problem as reported in Ticket # 739: http://www.scipy.org/scipy/scipy/ticket/739 That is, I get the error /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: 'labs' is not a member of 'std' for many of my weave codes when using g++ 4.3. (It works fine with g++ 4.2.) Is there any fix to this problem? Thanks! Kristian Kristian Sandberg, Ph.D. Dept. of Applied Mathematics and The Boulder Laboratory for 3-D Electron Microscopy of Cells University of Colorado at Boulder Campus Box 526 Boulder, CO 80309-0526, USA Phone: (303) 492 0593 (work) (303) 499 4404 (home) (303) 547 6290 (cell) Home page: http://amath.colorado.edu/faculty/sandberg

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Uninstalling python
by Mannucci, Anthony J 14 Nov '08

14 Nov '08

I have tried to install Scipy with python 2.6. I am beginning to think this was a mistake. I see there are pre-built binaries for python 2.5 but not 2.6. Is there any way to revert back to python 2.5 (in effect, "uninstall" version 2.6 which is now my current version)? Thanks for any help you can provide! -Tony -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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Scipy fails to build in Mac OS X 10.5
by Mannucci, Anthony J 13 Nov '08

13 Nov '08

I am trying to build numpy and scipy on Mac OS X 10.5.5. I recently installed Apple's Developer Tools (3.1.1) and am using gfortran 4.2.3. Gcc is at version 4.0.1. I installed the latest python (2.6) from the offcial python site using a binary. I then installed fftw 3.1.2. This appeared to install (no explicit tests were run). I created three softlinks as suggested on the site: http://www.scipy.org/Installing_SciPy/Mac_OS_X Then I tried numpy. I incorrectly tried to install a binary for numpy with python 2.5. Not surprisngly, that did not work (numpy not found). I then grabbed the source for numpy from SourceForge and compiled that, which seemed to finish. For numpy, I installed like this: sudo python setup.py build >& build.log sudo python setup.py install I then turned to SciPy. I obtained the tarball for version 0.6.0. I unpacked it and ran the following python setup.py build_src build_clib --fcompiler=gnu95 build_ext --fcompiler=gnu95 build >& config.log This produced lots of error messages, such as: > mkl_info: > libraries mkl,vml,guide not found in > /Library/Frameworks/Python.framework/Versions/2.6/lib > libraries mkl,vml,guide not found in /usr/local/lib > libraries mkl,vml,guide not found in /usr/lib > NOT AVAILABLE > > fftw3_info: > libraries fftw3 not found in > /Library/Frameworks/Python.framework/Versions/2.6/lib > FOUND: > libraries = ['fftw3'] > library_dirs = ['/usr/local/lib'] > define_macros = [('SCIPY_FFTW3_H', None)] > include_dirs = ['/usr/local/include'] > > djbfft_info: > NOT AVAILABLE > > blas_opt_info: > FOUND: > extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] > define_macros = [('NO_ATLAS_INFO', 3)] > extra_compile_args = ['-msse3', > '-I/System/Library/Frameworks/vecLib.framework/Headers'] > > lapack_opt_info: > FOUND: > extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] > define_macros = [('NO_ATLAS_INFO', 3)] > extra_compile_args = ['-msse3'] > > non-existing path in 'scipy/linsolve': 'tests' > umfpack_info: > libraries umfpack not found in > /Library/Frameworks/Python.framework/Versions/2.6/lib > libraries umfpack not found in /usr/local/lib > libraries umfpack not found in /usr/lib Etc. Some of the build seemed to go OK, and then I found these errors near the end: > building 'scipy.linsolve._zsuperlu' extension > compiling C sources > C compiler: gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -fno-strict-aliasing -fno-common -dy > namic -DNDEBUG -g -O3 > > compile options: '-DNO_ATLAS_INFO=3 -DUSE_VENDOR_BLAS=1 > -I/Library/Frameworks/Python.framework/Versions/2.6/lib/pyt > hon2.6/site-packages/numpy/core/include > -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c' > extra options: '-msse3' > gcc: scipy/linsolve/_superluobject.c > In file included from scipy/linsolve/_superluobject.h:8, > from scipy/linsolve/_superluobject.c:5: > scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for > '_Py_c_abs' > /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/complexobj > ect.h:30: error: previous declaration > of '_Py_c_abs' was here > In file included from scipy/linsolve/_superluobject.h:8, > from scipy/linsolve/_superluobject.c:5: > scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for > '_Py_c_abs' > /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/complexobj > ect.h:30: error: previous declaration > of '_Py_c_abs' was here > lipo: can't figure out the architecture type of: /var/tmp//ccWenONq.out > In file included from scipy/linsolve/_superluobject.h:8, > from scipy/linsolve/_superluobject.c:5: > scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for > '_Py_c_abs' > /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/complexobj > ect.h:30: error: previous declaration > of '_Py_c_abs' was here > In file included from scipy/linsolve/_superluobject.h:8, > from scipy/linsolve/_superluobject.c:5: > scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for > '_Py_c_abs' > /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/complexobj > ect.h:30: error: previous declaration > of '_Py_c_abs' was here > lipo: can't figure out the architecture type of: /var/tmp//ccWenONq.out > error: Command "gcc -arch ppc -arch i386 -isysroot > /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common > -dynamic -DNDEBUG -g -O3 -DNO_ATLAS_INFO=3 -DUSE_VENDOR_BLAS=1 > -I/Library/Frameworks/Python.framework/Versions/2.6 > /lib/python2.6/site-packages/numpy/core/include > -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2 > .6 -c scipy/linsolve/_superluobject.c -o > build/temp.macosx-10.3-i386-2.6/scipy/linsolve/_superluobject.o -msse3" fa > iled with exit status 1 Running numpy tests fails as follows: > Tonys-Mac-2:286:scipy-0.6.0 $ python > Python 2.6 (trunk:66714:66715M, Oct 1 2008, 18:36:04) > [GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import numpy >>>> numpy.test('1') > Running unit tests for numpy > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 240, in test > self._show_system_info() > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 151, in _show_system_info > nose = import_nose() > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 51, in import_nose > raise ImportError(msg) > ImportError: Need nose >= 0.10.0 for tests - see > http://somethingaboutorange.com/mrl/projects/nose I found the nose package and installed it, using easy_install (no direct download), like this: $ sudo easy_install nose Numpy tests continue to fail, as follows: > Tonys-Mac-2:286:scipy-0.6.0 $ python > Python 2.6 (trunk:66714:66715M, Oct 1 2008, 18:36:04) > [GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import numpy >>>> numpy.test('1') > Running unit tests for numpy > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 240, in test > self._show_system_info() > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 151, in _show_system_info > nose = import_nose() > File > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages > /numpy/testing/nosetester.py", line 51, in import_nose > raise ImportError(msg) > ImportError: Need nose >= 0.10.0 for tests - see > http://somethingaboutorange.com/mrl/projects/nose I believe when I did easy_install, version 0.10.4 of nose was used. Any help is appreciated. Thank you! -Tony -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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scipy.odr crashes when raising odr_stop
by Daniel 13 Nov '08

13 Nov '08

I'm using scipy.odr and trying to constrain my parameter values to a certain range, by raising stop_odr from my fitting function -- however raising stop_odr causes a crash. This happens both on a mac (Leopard, Python 2.5.2, Numpy 1.2.1, Scipy 0.7.0.dev4576) and on Windows (Vista32, Python 2.5.2, Numpy 1.2, Scipy 0.6.0). A simplified version along with its output is below. Any suggestions on how to fix, or workarounds? Thanks! --Daniel ---test.py----------------------------------------------- import sys from numpy import arange, abs from scipy.odr import odr_stop, Model, RealData, ODR def f(B, x): print >>sys.stderr, "f called, B=", B if B[1] < 0: raise odr_stop return B[0]*x + B[1] x = arange(10.) y = .1*x**2+1 m = Model(f) d = RealData(x, y) o = ODR(d, m, [.5, 1]) out = o.run() out.pprint() --------------------------------------------------------- $ python test.py f called, B= [ 0.5 1. ] ...a few more times... f called, B= [ 0.9 -0.20000001] /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/warnings.py:80: RuntimeWarning: tp_compare didn't return -1 or -2 for exception if registry.get(key): Bus error

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Forcing quad to use endpoints?
by Michael McNeil Forbes 13 Nov '08

13 Nov '08

Does anyone familiar with the details of QUADPACK have a suggestion of a way to force it to used specified endpoints? I am running into a problem like the following: def f(p): return (400.0/(p*p + 400.0))**2 points = [20.0] scipy.integrate.quad(f, 0, 1e16, points=points) (12.853981633974485, 1.4270786368147365e-13) The answer is actually 15.707963267949529 ~ 20*pi/4. The problem is that the quadrature points do not include the endpoints, so quad does not sample the function sufficiently closely to 20.0 to realize that it is still significant there. Basically, I would like to have a way of specifying both potential singularities (which is what `points` is for) as well as specifying important points that should be included in the quadrature (such as the 20 above which specifies the typical length-scale for the problem). I suspect that this is orthogonal to the QUADPACK quadratures, but if you have a suggestion, please let me know. Thanks, Michael.

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ANN: PyDSTool 0.87 released
by Rob Clewley 13 Nov '08

13 Nov '08

Dear Scipy and Numpy user lists, The latest update to the open-source python dynamical systems modeling toolbox, PyDSTool 0.87, has been released on Sourceforge. http://www.sourceforge.net/projects/pydstool/ Major highlights are: * Implemented a more natural hybrid model specification format * Supports quadratic interpolation of data points in Trajectory objects (courtesy of Anne Archibald's poly_int class) * Supports more sophisticated data-driven model inference * Improved efficiency of ODE solvers * Various bug fixes and other API improvements * New demonstration scripts and more commenting for existing scripts in PyDSTool/tests/ * New wiki tutorial (courtesy of Daniel Martí) This is a modest update in preparation for a substantial upgrade at version 0.90, which will move symbolic expression support over to SymPy, and greatly improve the implementation of C-based ODE integrators. We are also trying to incorporate basic boundary-value problem solving, and we aim to further improve the parameter estimation / model inference tools to work effectively with OpenOpt. For installation and setting up, see the GettingStarted page at our wiki, http://pydstool.sourceforge.net The download contains full API documentation, BSD license information, and further details of recent code changes. Further documentation is on the wiki. As ever, all feedback is welcome as we try to find time to improve our code base. If you would like to contribute effort in improving the tutorial and wiki documentation, or to the code itself, please contact me. -Rob Clewley

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About arrays and objects
by Enrique Comesaña Figueroa 13 Nov '08

13 Nov '08

Hello, Is it possible to list a property from an object array without using a 'for' loop? I've created the array using: In [1]: from numpy import * In [2]: class nodo: ...: def __init__(self, pos=0): ...: self.pos = pos ...: In [3]: nodo_array = array ([nodo(1),nodo(2),nodo(3),nodo(4),nodo(5)]) I want to print the "node_array" using something like this: In [4]: print nodo_array[:].pos without using a for loop. Is that possible? Thanks, Enrique

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