Mailman 3 August 2012 - SciPy-User

Request for usage examples on scipy.stats.rv_continuous and scipy.ndimage.grey_dilate(structure)
by Christoph Deil Dec. 5, 2012

Dec. 5, 2012

Hi, I am having some trouble figuring out how to use the following two aspects of scipy: 1) How can I create a random distribution given by some python formula, e.g. pdf(x) = x**2 in the range x = 1 to 2. The example given in the rv_continuous docstring doesn't work for me: In [1]: import matplotlib.pyplot as plt In [2]: numargs = generic.numargs AttributeError: type object 'numpy.generic' has no attribute 'numargs' Is it also possible to use rv_continuous for multidimensional distributions, say pdf(x,y)=x*y in the range x = 1 to 2 and y = 0 to 3? Or for pdfs that are just given numerically on a grid (say as the result of a gaussian_kde() ), not by a python function? It would be nice if someone could add a few examples that show rv_continuous usage to the docstring or tutorial. 2) How to use the 'structure' argument of scipy.ndimage.grey_dilate() correctly? There are some explanations at http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html but I think they are inconsistent with the implementation: -------------------------------------------------------------- In [98]: a = zeros((7,7)); a[3,3]=1; a Out[98]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 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., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) In [100]: s = generate_binary_structure(2,2); s Out[100]: array([[ True, True, True], [ True, True, True], [ True, True, True]], dtype=bool) In [101]: grey_dilation(a,size=(3,3)) Out[101]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) In [102]: grey_dilation(a,size=(3,3),structure=s) Out[102]: array([[ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.]]) In [103]: grey_dilation(a,structure=s) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/deil/<ipython console> in <module>() /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/ndimage/morphology.pyc in grey_dilation(input, size, footprint, structure, output, mode, cval, origin) 354 sz = footprint.shape[ii] 355 else: --> 356 sz = size[ii] 357 if not sz & 1: 358 origin[ii] -= 1 TypeError: 'NoneType' object is unsubscriptable In [104]: grey_dilation(a,footprint=s) Out[104]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) -------------------------------------------------------------- Why doesn't grey_dilation(a,structure=s) work? Why doesn't grey_dilation(a,size=(3,3),structure=s) give the same result as grey_dilation(a,size=(3,3),footprint=s)? I am running on numpy version 1.4.0 and scipy version 0.7.1 Thanks! --Christoph

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Problem with Installation of Scipy on Macbook
by manisha pujari Nov. 22, 2012

Nov. 22, 2012

Hello everyone, This is the first time I am using scipy and I am having much trouble to just install it on my macbook. I am using Python 2.6 and numpy 1.6.0. I downloaded scipy0.9.0 tar.gz file from the web link http://sourceforge.net/projects/scipy/files/scipy/ and tried to install it from the source. But on giving the command scipy-0.9.0$ python setup.py build it is always giving the following problem : Warning: No configuration returned, assuming unavailable.blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers'] non-existing path in 'scipy/io': 'docs' lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/Python.framework/Versions/2.6/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib /Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/system_info.py:463: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 181, in <module> setup_package() File "setup.py", line 173, in setup_package configuration=configuration ) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 122, in configuration config.add_subpackage('scipy') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 20, in configuration config.add_subpackage('special') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/special/setup.py", line 54, in configuration extra_info=get_info("npymath") File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2184, in get_info pkg_info = get_pkg_info(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2136, in get_pkg_info return read_config(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 390, in read_config v = _read_config_imp(pkg_to_filename(pkgname), dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 326, in _read_config_imp meta, vars, sections, reqs = _read_config(filenames) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 309, in _read_config meta, vars, sections, reqs = parse_config(f, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 281, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/core/lib/npy-pkg-config/npymath.ini'] I am unable to understand where and what exactly the problem is. Can anyone please help me? I will be really thankful for a response. -- Regards, Manisha

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Bessel function of complex order
by Andreas Pritschet Oct. 5, 2012

Oct. 5, 2012

Hi, I have noticed in the docs and some "bug reports" that Bessel functions in SciPy support only real order. But for my work I require a modified Bessel function of second kind of complex(!) order for complex values. Is in SciPy a chance of calculating something like scipy.special.kv(1j*k,1j), whereby k is an array?? Thanks and best regards Andi -- Andreas Pritschet Phone: +49 151 11728439 Homepage: http://www.pritschet.me GPG Pub Key: http://goo.gl/4mOsM

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A unified face for the scipy ecosystem
by Thomas Kluyver Sept. 7, 2012

Sept. 7, 2012

Hi all, Almar Klein and I floated this idea at Euroscipy this year, to some positive feedback. I'm posting it here to get some more opinions. We think it's a problem for newcomers that there isn't a clear starting point with the scipy ecosystem. We all understand that tools like numpy and matplotlib are critical for our field, but a newcomer searching for 'Python' will have to install these things separately. The conferences are called 'scipy', and scipy.org has some ambition to be a general portal for scientific computing in Python, but the name is confounded by the scipy package, and the downloads page is for packages, not complete distributions. Pylab is even more confusing. EPD and Python(x,y) are more helpful, but code is often not specific to those distributions. This is in contrast to systems like R and Matlab, where searching for the most obvious name turns up a complete system that's ready for scientific work. So what we propose comes in three parts: - A standard: like Linux Standard Base, it would specify minimum versions of packages for any distribution that wanted to advertise its compliance. I envisage it would include Python itself, numpy, scipy and matplotlib, but the exact list is open to debate. - A name: something that we would all use to refer to the core packages, regardless of how we installed them. If we don't use the name, newcomers won't search for it. I'm terrible with names, but Almar has proposed: scipy-base, unipy, pyengine, pycraft. Personally, I'd lean towards an abstract name without 'py'. Your suggestions are welcome! - A website: The first thing newcomers will see when searching for the name. It will describe the set of packages, and how to get them installed (probably giving precedence to inclusive Python distributions, but with instructions for separate installation as well). It will also link in to relevant documentation and example code, and it could have curated lists of packages for specific topics. It's important that this doesn't obscure the identity of the individual packages; the aim is not to stop anyone getting the credit they deserve. But I know we do often work closely together - getting involved with IPython, I've seen that clearly - and I think we sell ourselves short by not presenting a single face. Another important question is whether the standard should include a coding interface - the Matlab built-in IDE is touted as an advantage of that platform, for instance. As an IPython developer, I'm keen to see IPython included, but then I know there are other intriguing solutions, such as Spyder and IEP. We'd love to hear what you think, whether you're an experienced developer, a beginner with scientific Python, someone trying to introduce others to Python, or indeed anyone else with an interest in this. Best wishes, Thomas

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Installing issue with python 2.7, numpy 1.5.0b1 in my Mac
by Markus Hubig Sept. 5, 2012

Sept. 5, 2012

Hi @all, maybe this is a known issue but I didn't find any useful information out there. When I try to install scipy-0.8.0 with pip I get this strange error about missing files ... File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/npy_pkg_config.py", line 276, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini'] The complete error can be found here: http://gist.github.com/527697 Is there a known solution for this? Any help would be nice ... - Markus -- Can't read my mail? Just don't hold it that way!

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[ANN] guiqwt v2.2.0
by Pierre.RAYBAUT＠CEA.FR Sept. 3, 2012

Sept. 3, 2012

Hi all, I am pleased to announce that `guiqwt` v2.2.0 has been released (http://guiqwt.googlecode.com). Based on PyQwt (plotting widgets for PyQt4 graphical user interfaces) and on the scientific modules NumPy and SciPy, guiqwt is a Python library providing efficient 2D data-plotting features (curve/image visualization and related tools) for interactive computing and signal/image processing application development. The Mercurial repository is now publicly available here: http://code.google.com/p/guiqwt/source/checkout Complete change log is available here: http://code.google.com/p/guiqwt/wiki/ChangeLog Documentation with examples, API reference, etc. is available here: http://packages.python.org/guiqwt/ This version of `guiqwt` includes a demo software, Sift (for Signal and Image Filtering Tool), based on `guidata` and `guiqwt`: http://packages.python.org/guiqwt/sift.html Windows users may even download the portable version of Sift 0.2.6 to test it without having to install anything: http://code.google.com/p/guiqwt/downloads/detail?name=sift-0.2.6-guiqwt-2.2… When compared to the excellent module `matplotlib`, the main advantages of `guiqwt` are: * Performance: see http://packages.python.org/guiqwt/overview.html#performances * Interactivity: see for example http://packages.python.org/guiqwt/_images/plot.png * Powerful signal processing tools: see for example http://packages.python.org/guiqwt/_images/fit.png * Powerful image processing tools: * Real-time contrast adjustment: http://packages.python.org/guiqwt/_images/contrast.png * Cross sections (line/column, averaged and oblique cross sections!): http://packages.python.org/guiqwt/_images/cross_section.png * Arbitrary affine transforms on images: http://packages.python.org/guiqwt/_images/transform.png * Interactive filters: http://packages.python.org/guiqwt/_images/imagefilter.png * Geometrical shapes/Measurement tools: http://packages.python.org/guiqwt/_images/image_plot_tools.png * Perfect integration of `guidata` features for image data editing: http://packages.python.org/guiqwt/_images/simple_window.png But `guiqwt` is more than a plotting library; it also provides: * Framework for signal/image processing application development: see http://packages.python.org/guiqwt/examples.html * And many other features like making executable Windows programs easily (py2exe helpers): see http://packages.python.org/guiqwt/disthelpers.html guiqwt has been successfully tested on GNU/Linux and Windows platforms. Python package index page: http://pypi.python.org/pypi/guiqwt/ Documentation, screenshots: http://packages.python.org/guiqwt/ Downloads (source + Python(x,y) plugin): http://guiqwt.googlecode.com -- Dr. Pierre Raybaut CEA - Commissariat à l'Energie Atomique et aux Energies Alternatives

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possible bug in scipy.optimize.newton_krylov
by Matt Chan Sept. 1, 2012

Sept. 1, 2012

Hi, I'm having trouble setting the tolerance for the inner method of the newton-krylov method. Although the documentation says it is possible, setting inner_tol returns an error complaining about duplicate arguments. http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.newton_k… I've pasted the stack trace below. Is there something I am doing incorrectly? Traceback (most recent call last): File "<zip>", line 758, in <module> x_star= op.newton_krylov(my_fn, x0, method='lgmres', inner_tol=1e-8) File "<string>", line 8, in newton_krylov File "/usr/lib64/python2.7/site-packages/scipy/optimize/nonlin.py", line 294, in nonlin_solve dx = -jacobian.solve(Fx, tol=tol) File "/usr/lib64/python2.7/site-packages/scipy/optimize/nonlin.py", line 1394, in solve sol, info = self.method(self.op, rhs, tol=tol, **self.method_kw) TypeError: lgmres() got multiple values for keyword argument 'tol' Thanks, Matt

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[ANN] guidata v1.5.0
by Pierre.RAYBAUT＠CEA.FR Aug. 31, 2012

Aug. 31, 2012

Hi all, I am pleased to announce that `guidata` v1.5.0 has been released (http://guidata.googlecode.com). Based on the Qt Python binding module PyQt4 (and mostly compatible with PySide), guidata is a Python library generating graphical user interfaces for easy dataset editing and display. It also provides helpers and application development tools for PyQt4. guidata also provides the following features: * guidata.qthelpers: PyQt4 helpers * guidata.disthelpers: cx_Freeze/py2exe helpers (or how to build a self-consistent executable in three lines of code!) * guidata.userconfig: .ini configuration management helpers (based on Python standard module ConfigParser) * guidata.configtools: library/application data management * guidata.gettext_helpers: translation helpers (based on the GNU tool gettext) * guidata.guitest: automatic GUI-based test launcher * guidata.utils: miscelleneous utilities guidata has been successfully tested on GNU/Linux and Windows platforms. This is mostly a maintenance release with a couple of bugfixes and minor new features (see changelog here: http://code.google.com/p/guidata/wiki/ChangeLog). The Mercurial repository is now publicly available here: http://code.google.com/p/guidata/source/checkout The `guidata` documentation with examples, API reference, etc. is available here: http://packages.python.org/guidata/ Python package index page: http://pypi.python.org/pypi/guidata/ Documentation, screenshots: http://packages.python.org/guidata/ Downloads (source + Windows installers): http://guidata.googlecode.com -- Dr. Pierre Raybaut CEA - Commissariat à l'Energie Atomique et aux Energies Alternatives

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Re[SciPy-user] binning to polar coordinates
by arsbbr Aug. 31, 2012

Aug. 31, 2012

Hi, I'm trying to rebin some uniform gridded data to polar coordinates. The original data (Z) is noisy but on a fine grid. ### snip # define grid in cartesian coordinates x = arange(-500, 500) y = arange(-500, 500) X, Y = meshgrid(x, y) Z = X**2 + Y**2 Z += uniform(-5000, 5000, size=Z.shape)) # transform to polar coordinates def cart2pol(x, y): theta = arctan2(y, x) rho = sqrt(x**2 + y**2) return (theta, rho) THETA_xy, RHO_xy = cart2pol(X, Y) # define new polar grid theta = arange(-pi, pi, 0.1) rho = arange(0.1 ,500, 2.0) THETA, RHO = meshgrid(theta, rho) # Tried to use griddata, but it gives of course very jumpy results, because it # does not take the average over the pixels in a patch (dTHETA, dRHO) but an interpolation at the # exact new point. interpolate.griddata((THETA_xy.ravel(), RHO_xy.ravel()), Z.ravel(), (THETA, RHO), method='linear') ### snip Is there a method that rebins the data to a new grid, possibly taking the average of the Z-values inside a patch (dTHETA, dRHO)? Thanks for any hints! -- View this message in context: http://old.nabble.com/Rebinning-to-polar-coordinates-tp34348219p34348219.ht… Sent from the Scipy-User mailing list archive at Nabble.com.

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Re: [SciPy-User] Tensioned Spline interpolation
by Jonathan Stickel Aug. 31, 2012

Aug. 31, 2012

Gary I am not familiar with the "tension" terminology, but it sounds like a smoothing parameter. scipy.interpolate.UnivariateSpline provides splines with smoothing. You might also try the scikit "datasmooth" http://pypi.python.org/pypi/scikits.datasmooth/0.61 While not exactly a spline implementation, it computes a trend-line through 1D data with user-specified or automatically determined smoothing. HTH, Jonathan On 8/30/12 10:08 , scipy-user-request(a)scipy.org wrote: > Date: Thu, 30 Aug 2012 17:22:21 +1000 > From: gary ruben > Subject: [SciPy-User] Tensioned Spline interpolation > > Hi, > > I'm rewriting some IDL code in Python. The original code uses IDL's > spline function to interpolate a 1D ungridded data series onto a > regular grid. Unfortunately, I can't find a close enough equivalent in > scipy. I'm guessing the IDL spline function implements a "tensioned > spline." > > The signature of the IDL spline function is > Result = SPLINE(X, Y, T [, Sigma]) > where Sigma is 'The amount of "tension" that is applied to the curve. > If sigma is close to 0, (e.g., .01), then effectively there is a cubic > spline fit. If sigma is large, (e.g., greater than 10), then the fit > will be like a polynomial interpolation.' > > In the code I'm trying to reproduce, the author has set sigma=15 so > the result is quite different to a simple cubic spline. > Scipy's pchip algorithm gives a similar result, but is unfortunately > too slow for my application. Can anyone confirm that IDL's spline is a > tensioned spline routine? Does anyone know of a BSD-licensed Python > module that implements a tensioned spline. Failing that any > suggestions for a good routine I should look at wrapping (maybe Alan > Cline's fitpack on netlib?) > > thanks, > Gary

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