Mailman 3 September 2010 - SciPy-User

scipy odr testing failed
by Jing Sept. 24, 2010

Sept. 24, 2010

I have Lucid 10.04 ubuntu x86_64 and python 2.6.5. After install numpy1.3.0 and scipy 0.7.0 from repository, I run a test on numpy and scipy. The numpy test was OK, but the scipy test was failed on ODR testing. The screen print-out was shown below: >>> scipy.test() Running unit tests for scipy NumPy version 1.3.0 NumPy is installed in /usr/lib/python2.6/dist-packages/numpy SciPy version 0.7.0 SciPy is installed in /usr/lib/python2.6/dist-packages/scipy Python version 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3] nose version 0.11.4 ... .........warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ...warning: specified build_dir '..' does not exist or is not writable. Trying default locations ..warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ...warning: specified build_dir '..' does not exist or is not writable. Trying default locations .................................................. .................................................. ........................ ================================================== ==================== ERROR: test_implicit (test_odr.TestODR) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/dist-packages/scipy/odr/tests/test_odr.py", line 88, in test_implicit out = implicit_odr.run() File "/usr/lib/python2.6/dist-packages/scipy/odr/odrpack.py", line 1055, in run self.output = Output(apply(odr, args, kwds)) TypeError: y must be a sequence or integer (if model is implicit) ---------------------------------------------------------------------- Ran 2587 tests in 27.774s FAILED (KNOWNFAIL=3, SKIP=13, errors=1) <nose.result.TextTestResult run=2587 errors=1 failures=0> >>> Is scipy broken in this build or do I miss something? Thanks for the help.

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Cannot build SciPy : File contains no section headers.
by Sena Johns Sept. 24, 2010

Sept. 24, 2010

Hi, I'm trying to install Numpy and SciPy using this following method : http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894… But I get this error : python setup.py config --compiler=intel --fcompiler=intel build_clib --compiler=intel --fcompiler=intel build_ext --compiler=intel --fcompiler=intel install Warning: No configuration returned, assuming unavailable.Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 152, in setup_package configuration=configuration ) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 118, in configuration config.add_subpackage('scipy') File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 878, 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/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 878, 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/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 310, in get_info return cl().get_info(notfound_action) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 409, in __init__ self.parse_config_files() File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 416, in parse_config_files self.cp.read(self.files) File "/opt/cluster/software/python-2.5.4//lib/python2.5/ConfigParser.py", line 267, in read self._read(fp, filename) File "/opt/cluster/software/python-2.5.4//lib/python2.5/ConfigParser.py", line 462, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /var/tmp/NUMPY/scipy-0.8.0/site.cfg, line: 57 'library_dirs = /usr/lib/:/usr/lib64/\n' terrawulf:/var/tmp/NUMPY/scipy-0.8.0 # vi site.cfg terrawulf:/var/tmp/NUMPY/scipy-0.8.0 # python setup.py config --compiler=intel --fcompiler=intel build_clib --compiler=intel --fcompiler=intel build_ext --compiler=intel --fcompiler=intel install Warning: No configuration returned, assuming unavailable.Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 152, in setup_package configuration=configuration ) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 118, in configuration config.add_subpackage('scipy') File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 878, 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/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/misc_util.py", line 878, 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/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 310, in get_info return cl().get_info(notfound_action) File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 409, in __init__ self.parse_config_files() File "/opt/cluster/software/python-2.5.4/lib/python2.5/site-packages/numpy/distutils/system_info.py", line 416, in parse_config_files self.cp.read(self.files) File "/opt/cluster/software/python-2.5.4//lib/python2.5/ConfigParser.py", line 267, in read self._read(fp, filename) File "/opt/cluster/software/python-2.5.4//lib/python2.5/ConfigParser.py", line 462, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /var/tmp/NUMPY/scipy-0.8.0/site.cfg, line: 60 ' library_dirs = /opt/intel/mkl/10.0.1.014/lib/64/\n' Do you have any suggestions ? I'm on Suse 10.1. Thanks & regards, Sena

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format for chunked file save and read ?
by josef.pktd＠gmail.com Sept. 22, 2010

Sept. 22, 2010

What is the best file format for storing temporary data, for chunked saving and loading, that only uses numpy and scipy? I would like a file format that could be shared cross-platform and across python/numpy versions if needed. usecase: Stata is (optionally) saving all Bootstrap samples to a file so that the same samples will be available if a follow-up analysis is desired/required. We could also just save the seed and redo the same samples which might however not be fast for some models Josef

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Integer dtype comparisons
by Flipper Sept. 22, 2010

Sept. 22, 2010

Hello, is there a nice way to check whether an object is an Integer? Including all python and numpy Integers? I tried out subclass, but uint is not a subclass of Int: >>> a = numpy.zeros(1,numpy.uint32) >>> aType = type(a[0]) >>> issubclass(aType,types.IntType) False I tried out enumerating, but numpy seems to slightly change datatypes during some calculations, which complicates comparisons: >>> a = numpy.zeros(1,numpy.uint8) >>> aValue = a[0] >>> b = numpy.zeros(1,numpy.int32) >>> bValue = b[0] >>> result = aValue + bValue >>> type(result) <type 'numpy.int32'> >>> numpy.int32 <type 'numpy.int32'> >>> type(result) == numpy.int32 False thanks, Michael

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numpy.nansum bug?
by Jeremy Sanders Sept. 22, 2010

Sept. 22, 2010

I've hit this problem with numpy (1.3.0 on x86-64). In [12]: a = numpy.array([numpy.nan]) In [13]: numpy.nansum(a) Out[13]: nan I assume that this is a bug? It's pretty nasty if you assume that nansum always returns a non nan. This is also pretty weird: In [14]: numpy.nansum([]) Out[14]: nan Jeremy

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Sigmoid Curve Fitting
by Chris Spencer Sept. 22, 2010

Sept. 22, 2010

Hi, Does Scipy contain the ability to fit a sigmoid curve to a set of data points? I found some Numpy code (http://pingswept.org/2009/01/24/least-squares-polynomial-fitting-in-python/) for fitting curves using the least squares method, but it only seems to fit parabolas to my sigmoid data. Regards, Chris

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[ANN] SciPy India 2009 Call for Presentations
by Jarrod Millman Sept. 21, 2010

Sept. 21, 2010

========================== SciPy 2010 Call for Papers ========================== The second `SciPy India Conference <http://scipy.in>`_ will be held from December 13th to 18th, 2010 at `IIIT-Hyderabad <http://www.iiit.ac.in/>`_. At this conference, novel applications and breakthroughs made in the pursuit of science using Python are presented. Attended by leading figures from both academia and industry, it is an excellent opportunity to experience the cutting edge of scientific software development. The conference is followed by two days of tutorials and a code sprint, during which community experts provide training on several scientific Python packages. We invite you to take part by submitting a talk abstract on the conference website at: http://scipy.in Talk/Paper Submission ========================== We solicit talks and accompanying papers (either formal academic or magazine-style articles) that discuss topics regarding scientific computing using Python, including applications, teaching, development and research. Papers are included in the peer-reviewed conference proceedings, published online. Please note that submissions primarily aimed at the promotion of a commercial product or service will not be considered. Important Dates ========================== Monday, Oct. 11: Abstracts Due Saturday, Oct. 30: Schedule announced Tuesday, Nov. 30: Proceedings paper submission due Monday-Tuesday, Dec. 13-14: Conference Wednesday-Friday, Dec. 15-17: Tutorials/Sprints Saturday, Dec. 18: Sprints Organizers ========================== * Jarrod Millman, Neuroscience Institute, UC Berkeley, USA (Conference Co-Chair) * Prabhu Ramachandran, Department of Aerospace Engineering, IIT Bombay, India (Conference Co-Chair) * FOSSEE Team

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weighted griddata
by Adam Ryan Sept. 20, 2010

Sept. 20, 2010

Hi. First, kudos to the scipy community; great package. I was wondering if there is a way to use scipy.interpolate.griddata with weights. Specifically, I have a list of lines. Each line represents the position of a wave on a beach at a timestamp, and is comprised of a list of mostly connected points. I can use griddata and all the points of all the lines to create an interpolation of the position of the wave vs time. The problem is that the lines are the result of image processing and the points vary in confidence level. Currently I'm just tossing out points that don't pass muster, but I'd like a more robust solution, something like a weighted griddata, or some other method. Any advice would be great. Thanks, Adam

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Re: [SciPy-User] [Matplotlib-users] Sigmoid Curve Fitting
by Gökhan Sever Sept. 20, 2010

Sept. 20, 2010

On Mon, Sep 20, 2010 at 3:36 PM, Chris Spencer <chrisspen(a)gmail.com> wrote: > Hi, > > Does Matplotlib/Numpy/Scipy contain the ability to fit a sigmoid curve > to a set of data points? > You could also experiment at zunzun.com. Choose 2D sigmoidal from the 2D function scroll list. -- Gökhan

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Re: [SciPy-User] [Matplotlib-users] Sigmoid Curve Fitting
by Gökhan Sever Sept. 20, 2010

Sept. 20, 2010

On Mon, Sep 20, 2010 at 3:36 PM, Chris Spencer <chrisspen(a)gmail.com> wrote: > Hi, > > Does Matplotlib/Numpy/Scipy contain the ability to fit a sigmoid curve > to a set of data points? > > Regards, > Chris > I am very curious to know how this is done. I have seen in many Cloud Condensation Nuclei (CCN) counter calibration experiments [e.g. Rose et. al. (2008) - p1156, fig2 http://www.atmos-chem-phys.net/8/1153/2008/acp-8-1153-2008.html] people use sigmoidal fits. Never seen a code is shared so far or how it is obtained. from scipy.optimize import leastsq could be a good point to start. To me this fit is very likely a least square minimization problem. You have your tanh(x) or 1/(1+e^-x) as a sigmoidal function, and you should find the points that will make the error minimal for a given discrete points/measurements. from scipy.optimize import curve_fit might be another way to approach. -- Gökhan

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