Mailman 3 April 2006 - SciPy-User

Any SPLUS to scipy ideas for lm and summary(lm)?
by Webb Sprague April 13, 2006

April 13, 2006

Hi Scipy-ers, I would like to duplicate the following piece of SPLUS/R code in Python-scipy, and would love somebody smarter than me to give me some ideas. (If you don't know SPLUS/R, you may not want to bother with this.) model.kt <- summary(lm(kt.diff ~ 1 )) kt.drift <- model.kt$coefficients[1,1] # Coefficient sec <- model.kt$coefficients[1,2] # Standard Error of the Coefficient (SEC) see <- model.kt$sigma # Standard error of the Equation (SEE) Getting a least-squares fit in scipy is not a problem, but getting all that other nice stuff IS kind of a problem. I don't mind either hacking scipy.stats, or writing my own function, but maybe someone has some ideas for this, maybe it can be contributed, or ???. I also realize that the SPLUS formula notation doesn't exist at all in scipy-Python, so no need to point that out to me. Perhaps there should be a scipy.stats working group? It seems like scipy.stats (not including the probability distributions and basic summary functions, which are fine) is kind of a forgotten stepchild in scipy, and probably needs a nurturing aunt or uncle or several.... Thx, sorry for such an open ended question. W

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ANN: SciPy 2006 Conference
by Travis N. Vaught April 12, 2006

April 12, 2006

Greetings, The *SciPy 2006 Conference* is scheduled for August 17-18, 2006 at CalTech. A tremendous amount of work has gone into SciPy and Numpy over the past few months, and the scientific python community around these and other tools has truly flourished[1]. The Scipy 2006 Conference is an excellent opportunity to exchange ideas, learn techniques, contribute code and affect the direction of scientific computing with Python. Conference details are at http://www.scipy.org/SciPy2006 Keynote ------- Python language author Guido van Rossum (!) has agreed to be the Keynote speaker at this year's Conference. http://www.python.org/~guido/ Registration: ------------- Registration is now open. You may register early online for $100.00 at http://www.enthought.com/scipy06. Registration includes breakfast and lunch Thursday & Friday and a very nice dinner Thursday night. After July 14, 2006, registration will cost $150.00. Call for Presenters ------------------- If you are interested in presenting at the conference, you may submit an abstract in Plain Text, PDF or MS Word formats to abstracts(a)scipy.org -- the deadline for abstract submission is July 7, 2006. Papers and/or presentation slides are acceptable and are due by August 4, 2006. Tutorial Sessions ----------------- Several people have expressed interest in attending a tutorial session. The Wednesday before the conference might be a good day for this. Please email the list if you have particular topics that you are interested in. Here's a preliminary list: - Migrating from Numeric or Numarray to Numpy - 2D Visualization with Python - 3D Visualization with Python - Introduction to Scientific Computing with Python - Building Scientific Simulation Applications - Traits/TraitsUI Please rate these and add others in a subsequent thread to the SciPy-user mailing list. Perhaps we can pick 4-6 top ideas and recruit speakers as demand dictates. The authoritative list will be tracked here: http://www.scipy.org/SciPy2006/TutorialSessions Coding Sprints -------------- If anyone would like to arrive earlier (Monday and Tuesday the 14th and 15th of August), we can borrow a room on the CalTech campus to sit and code against particular libraries or apps of interest. Please register your interest in these coding sprints on the SciPy-user mailing list as well. The authoritative list will be tracked here: http://www.scipy.org/SciPy2006/CodingSprints Mailing list address: scipy-user(a)scipy.org Mailing list archives: http://dir.gmane.org/gmane.comp.python.scientific.user Mailing list signup: http://www.scipy.net/mailman/listinfo/scipy-user [1] Some stats: NumPy has averaged over 16,000 downloads per month Sept. 05 to March 06. SciPy has averaged over 3,800 downloads per month in Feb. and March 06. (both scipy and numpy figures do not include the 2000 instances per month downloaded as part of the Python Enthought Edition Distribution for Windows.)

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ndimage | LOG/DOG operator
by Jelle Feringa / EZCT Architecture & Design Research April 11, 2006

April 11, 2006

A question on the (terrific!) ndimage module: Is the LOG operator (laplace of gauss) == scipy.ndimage.gaussian_laplace? Is the DOG operator (difference of Gaussians) already implemented in ndimage or have I just overlooked it? # A snippet on how to compute efficiently difference of Gaussians would # greatly appreciated... -jelle --- Sorry for posting this again, I mistakenly posted it in another thread ---

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SciPy with gcc4 and gfortran on OS X
by Zachary Pincus April 11, 2006

April 11, 2006

Hi folks, Emboldened by the some reported successes with compiling SciPy with gfortran and gcc4 on OSX/Intel machines, I thought I'd give it a try on my powerbook. Unfortunately, it did not work -- but hopefully it's close, because the problems I saw are all things that various people on this list have seen and solved. VITALS OS X 10.4.6, on a PPC G4 gcc: powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5250) gfortran: GNU Fortran 95 (GCC) 4.2.0 20060218 (experimental) (gfortran binary downloaded from hpc.sf.net today.) SVN checkout of numpy and scipy from today. BUILD PROBLEM I only had one problem during the build -- there were errors like: /usr/bin/ld: can't locate file for: -lcc_dynamic I fixed this by modifying numpy/distutils/fcompiler/gnu.py so that the Gnu95FCompiler class had a method like: def get_libraries(self): opt = GnuFCompiler.get_libraries(self) if sys.platform=='darwin': opt.remove('cc_dynamic') return opt so that the unnecessary cc_dynamic library was not included. RUNTIME PROBLEMS > In [1]: import scipy > import linsolve.umfpack -> failed: No module named _umfpack I think that people had seen this problem before, but using a more recent gfortran solved it for them on intel macs. I'm using the most recent gfortran from hpc.sf.net on my G4, so this problem still persists. > In [2]: scipy.test() > import linsolve.umfpack -> failed: No module named _umfpack > Overwriting fft=<function fft at 0x284f570> from > scipy.fftpack.basic (was <function fft at 0x1395930> from > numpy.dft.fftpack) > Overwriting ifft=<function ifft at 0x284f5f0> from > scipy.fftpack.basic (was <function inverse_fft at 0x1395970> from > numpy.dft.fftpack) ... > Adjust D1MACH by uncommenting data statements > appropriate for your machine. > STOP 779 Also a problem people had seen with gfortran, but one that I thought had been patched. For the time being, I'll just switch back to gcc3/g77. Hopefully this information will help, though. Zach

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Re: [SciPy-user] NameError
by Huang, Zhong April 10, 2006

April 10, 2006

Yes, thank you, Robert. Zhong -----Original Message----- From: scipy-user-bounces(a)scipy.net on behalf of Robert Kern Sent: Mon 4/10/2006 6:21 PM To: SciPy Users List Subject: Re: [SciPy-user] NameError Huang, Zhong wrote: > Hi, I am trying to use least-squares procedure > of scipy. I encountered NameError problem: > > from scipy.optimize import leastsq > plsq=leastsq(residuals,p0,args(y_meas,x)) You are missing an equals sign. plsq=leastsq(residuals,p0,args=(y_meas,x)) -- Robert Kern robert.kern(a)gmail.com "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

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Re: [SciPy-user] NameError
by Huang, Zhong April 10, 2006

April 10, 2006

Quite right. I tried plsq=leastsq(residuals,p0,(y_meas,x)) it works, too. Thank you, Travis. Zhong -----Original Message----- From: scipy-user-bounces(a)scipy.net on behalf of Travis Oliphant Sent: Mon 4/10/2006 6:15 PM To: SciPy Users List Subject: Re: [SciPy-user] NameError Huang, Zhong wrote: >Hi, I am trying to use least-squares procedure >of scipy. I encountered NameError problem: > >from scipy.optimize import leastsq >plsq=leastsq(residuals,p0,args(y_meas,x)) > >NameError: name 'args' is not defined > >Could anybody help me out? > > I think you mean: args = (y_meas, x) i.e. plsq=leastsq(residuals,p0,args=(y_meas,x)) -Travis _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

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NameError
by Huang, Zhong April 10, 2006

April 10, 2006

Hi, I am trying to use least-squares procedure of scipy. I encountered NameError problem: from scipy.optimize import leastsq plsq=leastsq(residuals,p0,args(y_meas,x)) NameError: name 'args' is not defined Could anybody help me out? Thanks!

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Error while installing Scipy
by Rahul Kanwar April 9, 2006

April 9, 2006

Hello, I am working on 64 bit Xeon machine running Suse 10. I am using Intel's MKL and ifort for compiling Numpy and Scipy. I succesfuly compiled Numpy using this combination and was able to load it in the python interpreter. But i get errors while compiling Scipy, here is what i am getting: --------------------------------------------------------------- ifort: Command line warning: ignoring unknown option '-fno-second-underscore' ifort: Command line warning: overriding '-O3' with '-O2' ifort:f77: Lib/integrate/odepack/cfode.f ifort: Command line warning: ignoring option '-W'; no argument required ifort: Command line warning: ignoring unknown option '-fno-second-underscore' ifort: Command line warning: overriding '-O3' with '-O2' ifort:f77: Lib/integrate/odepack/iprep.f ifort: Command line warning: ignoring option '-W'; no argument required ifort: Command line warning: ignoring unknown option '-fno-second-underscore' ifort: Command line warning: overriding '-O3' with '-O2' ifort:f77: Lib/integrate/odepack/prepj.f ifort: Command line warning: ignoring option '-W'; no argument required ifort: Command line warning: ignoring unknown option '-fno-second-underscore' ifort: Command line warning: overriding '-O3' with '-O2' ar: adding 50 object files to build/temp.linux-x86_64-2.4/libodepack.a ar: adding 9 object files to build/temp.linux-x86_64-2.4/libodepack.a running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize IntelFCompiler customize LaheyFCompiler customize PGroupFCompiler customize AbsoftFCompiler customize NAGFCompiler customize VastFCompiler customize GnuFCompiler customize CompaqFCompiler customize IntelItaniumFCompiler customize Gnu95FCompiler customize G95FCompiler customize GnuFCompiler customize Gnu95FCompiler warning: build_ext: fcompiler=gnu is not available. building 'scipy.cluster._vq' extension compiling C++ sources c++ options: '-pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC' creating build/temp.linux-x86_64-2.4/Lib/cluster creating build/temp.linux-x86_64-2.4/Lib/cluster/src compile options: '-I/usr/local/lib64/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c' c++: Lib/cluster/src/vq_wrap.cpp In file included from /usr/include/python2.4/Python.h:8, from Lib/cluster/src/vq_wrap.cpp:176: /usr/include/python2.4/pyconfig.h:838:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/string.h:26, from Lib/cluster/src/vq_wrap.cpp:27: /usr/include/features.h:154:1: warning: this is the location of the previous definition In file included from Lib/cluster/src/vq_wrap.cpp:499: Lib/cluster/src/vq.h:57:7: warning: no newline at end of file Lib/cluster/src/vq_wrap.cpp: In function 'int char_to_numtype(char)': Lib/cluster/src/vq_wrap.cpp:590: warning: control reaches end of non-void function Lib/cluster/src/vq_wrap.cpp: In function 'int char_to_size(char)': Lib/cluster/src/vq_wrap.cpp:582: warning: control reaches end of non-void function Lib/cluster/src/vq_wrap.cpp: At global scope: Lib/cluster/src/vq_wrap.cpp:147: warning: 'void* SWIG_TypeQuery(const char*)' defined but not used Lib/cluster/src/vq_wrap.cpp:301: warning: 'void SWIG_addvarlink(PyObject*, char*, PyObject* (*)(), int (*)(PyObject*))' defined but not used Lib/cluster/src/vq_wrap.cpp:315: warning: 'int SWIG_ConvertPtr(PyObject*, void**, swig_type_info*, int)' defined but not used Lib/cluster/src/vq_wrap.cpp:516: warning: 'PyObject* l_output_helper(PyObject*, PyObject*)' defined but not used [] c++ -pthread -shared build/temp.linux-x86_64-2.4/Lib/cluster/src/vq_wrap.o -Lbuild/temp.linux-x86_64-2.4 -o build/lib.linux-x86_64-2.4/scipy/cluster/_vq.so building 'scipy.integrate._quadpack' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC' compile options: '-I/usr/local/lib64/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c' gcc: Lib/integrate/_quadpackmodule.c In file included from Lib/integrate/_quadpackmodule.c:6: Lib/integrate/__quadpack.h: In function 'quad_function': Lib/integrate/__quadpack.h:60: warning: unused variable 'nb' Traceback (most recent call last): File "setup.py", line 48, in ? setup_package() File "setup.py", line 41, in setup_package setup( **config.todict() ) File "/usr/local/lib64/python2.4/site-packages/numpy/distutils/core.py", line 85, in setup return old_setup(**new_attr) File "/usr/lib64/python2.4/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib64/python2.4/distutils/dist.py", line 946, in run_commands self.run_command(cmd) File "/usr/lib64/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/usr/lib64/python2.4/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/usr/lib64/python2.4/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib64/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/usr/local/lib64/python2.4/site-packages/numpy/distutils/command/build_ext.py", line 109, in run self.build_extensions() File "/usr/lib64/python2.4/distutils/command/build_ext.py", line 405, in build_extensions self.build_extension(ext) File "/usr/local/lib64/python2.4/site-packages/numpy/distutils/command/build_ext.py", line 301, in build_extension link = self.fcompiler.link_shared_object AttributeError: 'NoneType' object has no attribute 'link_shared_object' -------------------------------------------------------------------------------- Can anyone please help me with it ? Thanks. regard, Rahul

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Doesn't work: setup.py config_fc --help-fcompiler
by Zachary Pincus April 8, 2006

April 8, 2006

Hi folks, I'm playing around with getting scipy to build with gfortran and gcc4 on my OS X box. Unfortunately, for some reason when I run 'python setup.py config_fc --help-fcompiler' I get absolutely no output. This is with the latest SVN scipy and numpy, with numpy installed. Any ideas? Zach

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Re: [SciPy-user] SciPy with gcc4 and gfortran on OS X
by Andres Gonzalez-Mancera April 8, 2006

April 8, 2006

I agree in that your problem does not have to do with gfortran at this point. I tried installing Scipy from yesterdays SVN and run into the same error regarding _umfpack. I was able to install the latest released versions of Numpy and Scipy on Mac Os X 10.4.6 in a G4 but using G77 and GCC 3.3. From my experience the SVN versions are a little difficult since one day can work while other may not. May I ask you why you want to use Gfortran and the newer version of GCC. I don't think this will bring any improvements in speed over g77 but I might be wrong though. Andres

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