Mailman 3 February 2013 - SciPy-Dev

Bootstrap confidence limits code
by Constantine Evans 05 Oct '14

05 Oct '14

Hello everyone, A few years ago I implemented a scikit for bootstrap confidence limits (https://github.com/cgevans/scikits-bootstrap). I didn’t think much about it after that until recently, when I realized that some people are actually using it, and that there’s apparently been some talk about implementing this functionality in either scipy.stats or statsmodels (I should thank Randal Olson for discussing this and bringing it to my attention). As such I’ve rewritten most of the code, and written up some docstrings. The current code can do confidence intervals with basic percentile interval, bias-corrected accelerated, and approximate bootstrap confidence methods, and can also provide bootstrap and jackknife indexes. Most of it is implemented from the descriptions in Efron and Tibshirani’s Introduction to the Bootstrap, but the ABC code at the moment is a port from the modified-BSD-licensed bootstrap package for R (not the boot package) as I’m not entirely confident in my understanding of the method. And so, I have a few questions for everyone: * Is there any interest in including this sort of code in either scipy.stats or statsmodels? If so, where do people think would be the better place? The code is relatively small; at the moment it is less than 200 lines, with docstrings probably making up 100 of those lines. * Also, if so, what would need to be changed, added, and improved beyond what is mentioned in the Contributing to Scipy part of the reference guide? I’m never a fan of my own code, and imagine quite a bit would need to be fixed; I know tests will need to be added too. In addition, I have a few questions about what would be better practice for the API, and I haven’t really found a guide on best practices for Scipy: * When I started writing the code, I wrote a single function ci for confidence intervals, with a method argument to choose the method. This is easy for users, especially so that they don’t have to look through documentation to realize that BCA is the most generally useful method (at least from everything I’ve read) and that there really isn’t any reason to use many of the simpler methods. However, ABC takes different paramenters, and needs a statistic function that takes weights, which makes this single-function organization trickier. At the moment, I have a separate function for ABC. Would it be better to split up all the methods to their own functions? * ABC requires a statistic function that takes weights. I’ve noticed that things like np.average takes a weights= argument. Would it be better to require input of a stat(data,weights) function, or input of a stat(data,weights=) with weights as a named argument? The latter would be nice in terms of allowing the same function to be used for all methods, but would make it impossible to use a lambda for the function. Is there some other method of doing this entirely? * Are there any missing features that anyone thinks should be added? I apologize if much of this is answered elsewhere, I just haven’t found any of it; I also apologize if this is far too long-winded and confusing! Regards, Constantine Evans

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SLSQP Constrained Optimizer Status
by Rob Falck 25 Nov '13

25 Nov '13

I'm currently implementing the Sequential Least Squares Quadratic Programming (SLSQP) optimizer, by Dieter Kraft, for use in Scipy. The Fortran code being wrapped with F2PY is here: http://www.netlib.org/toms/733 (its use within Scipy has been cleared) SLSQP provides for bounds on the independent variables, as well as equality and inequality constraint functions, which is a capability that doesn't exist in scipy.optimize. Currently the code works, although the constraint normals are being generated by approximation. I'm working on a way to pass these in. I think the most elegant way will be a single function that returns the matrix of constraint normals. For a demonstration of what the code can do, here is an optimization of f(x,y) = 2xy + 2x - x**2 - 2y**2 Example 14.2 in Chapra & Canale gives the maximum as x=2.0, y=1.0. The unbounded optimization tests find this solution. As expected, its faster when derivatives are provided rather than approximated. Unbounded optimization. Derivatives approximated. Elapsed time: 1.45792961121 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] Unbounded optimization. Derivatives provided. Elapsed time: 1.03211402893 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] The following example uses an equality constraint to find the optimal when x=y. Bound optimization. Derivatives approximated. Elapsed time: 1.384973526 ms Results [[0.99999996845920858, 0.99999996845920858], -0.99999999999999889, 4, 0, 'Optimization terminated successfully.'] I've tried to conform to the syntax used by the other optimizers in scipy.optimize. The function definition and doc string are below. If anyone is interested in testing it out, let me know. def fmin_slsqp( func, x0 , eqcons=[], f_eqcons=None, ieqcons=[], f_ieqcons=None, bounds = [], fprime = None, fprime_cons=None,args = (), iter = 100, acc = 1.0E-6, iprint = 1, full_output = 0, epsilon = _epsilon ): """ Minimize a function using Sequential Least SQuares Programming Description: Python interface function for the SLSQP Optimization subroutine originally implemented by Dieter Kraft. Inputs: func - Objective function (in the form func(x, *args)) x0 - Initial guess for the independent variable(s). eqcons - A list of functions of length n such that eqcons[j](x0,*args) == 0.0 in a successfully optimized problem f_eqcons - A function of the form f_eqcons(x, *args) that returns an array in which each element must equal 0.0 in a successfully optimized problem. If f_eqcons is specified, eqcons is ignored. ieqcons - A list of functions of length n such that ieqcons[j](x0,*args) >= 0.0 in a successfully optimized problem f_ieqcons - A function of the form f_ieqcons(x0, *args) that returns an array in which each element must be greater or equal to 0.0 in a successfully optimized problem. If f_ieqcons is specified, ieqcons is ignored. bounds - A list of tuples specifying the lower and upper bound for each independent variable [ (xl0, xu0), (xl1, xu1), ...] fprime - A function that evaluates the partial derivatives of func fprime_cons - A function of the form f(x, *args) that returns the m by n array of constraint normals. If not provided, the normals will be approximated. Equality constraint normals precede inequality constraint normals. args - A sequence of additional arguments passed to func and fprime iter - The maximum number of iterations (int) acc - Requested accuracy (float) iprint - The verbosity of fmin_slsqp. iprint <= 0 : Silent operation iprint == 1 : Print summary upon completion (default) iprint >= 2 : Print status of each iterate and summary full_output - If 0, return only the minimizer of func (default). Otherwise, output final objective function and summary information. epsilon - The step size for finite-difference derivative estimates. Outputs: ( x, { fx, gnorm, its, imode, smode }) x - The final minimizer of func. fx - The final value of the objective function. its - The number of iterations. imode - The exit mode from the optimizer, as an integer. smode - A string describing the exit mode from the optimizer. Exit modes are defined as follows: -1 : Gradient evaluation required (g & a) 0 : Optimization terminated successfully. 1 : Function evaluation required (f & c) 2 : Number of equality constraints larger than number of independent variables 3 : More than 3*n iterations in LSQ subproblem 4 : Inequality constraints incompatible 5 : Singular matrix E in LSQ subproblem 6 : Singular matrix C in LSQ subproblem 7 : Rank-deficient equality constraint subproblem HFTI 8 : Positive directional derivative for linesearch 9 : Iteration limit exceeded -- - Rob Falck

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Vector Strength function
by Todd 22 Nov '13

22 Nov '13

I am interested in implementing a function for scipy. The function is called "vector strength". It is basically a measure of how reliably a set of events occur at a particular phase. It was originally developed for neuroscience research, to determine how well a set of neural events sync up with a periodic stimulus like a sound waveform. However, it is useful for determining how periodic a supposedly periodic set of events really are, for example: 1. Determining whether crime is really more common during a full moon and by how much 2. Determining how concentrated visitors to a coffee shop are during rush hour 3. Determining exactly how concentrated hurricanes are during hurricane season My thinking is that this could be implemented in stages: First would be a Numpy function that would add a set of vectors in polar coordinates. Given a number of magnitude/angle pairs it would provide a summed magnitude/angle pair. This would probably be combined with a cartesian<->polar conversion functions. Making use of this function would be a scipy function that would actually implement the vector strength calculation. This is done by treating each event as a unit vector with a phase, then taking the average of the vectors. If all events have the same phase, the result will have an amplitude of 1. If they all have a different phases, the result will have an amplitude of 0. It may even be worth having a dedicated polar dtype, although that may be too much. What does everyone think of this proposal?

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Multilinear interpolation
by Pablo Winant 10 May '13

10 May '13

Hi, Continuing a series of thread about interpolation, I have an almost ready implementation of multilinear implementation, that is linear interpolation in each dimension. I have been toying with several implementations - in pure numpy (quite memory hungry) - in cython - using pycuda Obviously, if there is some interest for it in scipy, it would be a good motivation to finish it. There are two main differences with respect to the existing interp routine : - it is independent of fitpack - it extrapolates linearly while the existing routine returns a constant (or NaN) Now I have some questions about it: - in this case I several implementations, in the same library that can potentially be enabled on different systems (with a compiler, with a gpu). I made a python file that tries to import one version after all shadowing slower ones by faster ones. It is meant to replicate the .m/.mex file behavior of Matlab. Is there a better approach ? - the cython code is meant to operate on double* inputs, and is limited to 4 dimensions. It is however very easy to generate single or higher order code. What would you use for that purpose ? Best, Pablo

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Status of Migrating Issues to Github?
by Skipper Seabold 17 Apr '13

17 Apr '13

Hi, Just curious what the status of migrating the issues to github for scipy is? I think this was on the table right? Thanks, Skipper

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OSError with Cookbook
by Frank Breitling 10 Apr '13

10 Apr '13

Hi, I have been trying to create a new page for the SciPy cookbook via http://www.scipy.org/Cookbook/Matplotlib/Histograms?action=edit but received the error below. Who can solve this? Frank --- OSError [Errno 31] Too many links: '/home/scipy/wiki/data/pages/Cookbook(2f)Matplotlib(2f)Histograms' If you want to report a bug, please save this page and attach it to your bug report. Show debugging information Report bug Visit MoinMoin wiki Traceback A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred. /usr/lib/python2.4/site-packages/MoinMoin/request.py in run (self=<MoinMoin.request.RequestFastCGI object>) 1149 from MoinMoin.wikiaction import getHandler 1150 handler = getHandler(self, action) 1151 handler(self.page.page_name, self) 1152 1153 # generate page footer (actions that do not want this footer use handler = <function do_edit> self = <MoinMoin.request.RequestFastCGI object> self.page = <MoinMoin.Page.Page instance> self.page.page_name = u'Cookbook/Matplotlib/Histograms' /usr/lib/python2.4/site-packages/MoinMoin/wikiaction.py in do_edit (pagename=u'Cookbook/Matplotlib/Histograms', request=<MoinMoin.request.RequestFastCGI object>) 580 # is invoked without savetext start editing 581 if savetext is None: 582 pg.sendEditor() 583 return 584 pg = <MoinMoin.PageEditor.PageEditor instance> pg.sendEditor = <bound method PageEditor.sendEditor of <MoinMoin.PageEditor.PageEditor instance>> /usr/lib/python2.4/site-packages/MoinMoin/PageEditor.py in sendEditor (self=<MoinMoin.PageEditor.PageEditor instance>, **kw={}) 176 except OSError, err: 177 if err.errno != errno.ENAMETOOLONG: 178 raise err 179 msg = _("Page name is too long, try shorter name.") 180 err = <exceptions.OSError instance> OSError [Errno 31] Too many links: '/home/scipy/wiki/data/pages/Cookbook(2f)Matplotlib(2f)Histograms' args = (31, 'Too many links') errno = 31 filename = '/home/scipy/wiki/data/pages/Cookbook(2f)Matplotlib(2f)Histograms' strerror = 'Too many links' System Details Date: Mon, 04 Feb 2013 10:25:58 +0000 Platform: Linux scipy.org 2.6.32-4-pve #1 SMP Thu Oct 21 09:35:29 CEST 2010 i686 Python: Python 2.4.3 (/usr/bin/python) MoinMoin: Release 1.5.6 (release)

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Splines
by Charles R Harris 29 Mar '13

29 Mar '13

Hi All, There have been several threads on the list about splines and consolidation of splines. For instance, there are several uniform spline implementations for images and signal processing, various low level functions in fitlib that are unexposed, and perhaps useful altenatives to b-splines for some applications like straight interpolation. For myself, I've started implementing several functions in pure Python with an eye to converting them to Cython once the interface and documentation is in place, mostly for doing things that fitpack doesn't do because it is very integrated, as opposed to supplying a basic toolset. As part of this project, I'd like to get some feedback on which functions people use most and what features they would like to see. I'm not interested in the high level classes at this point, either the current classes or combo functions like fpcurf, but rather a collection of good lower level function that could be used to implement the higher level functions in a more flexible way. Thoughts? Chuck

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2D histogram: request for plotting variable bin size
by Frank Breitling 28 Mar '13

28 Mar '13

Hello, http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogram2d.html explains the usage of 2D histograms. Although it is possible to construct 2D histograms with a variable bin size, there is no simple way to plot them. Therefore I would like to request an implementation to imshow that allows the visualization of 2D histograms with variable bin size. I imagine a syntax like imshow(historgram2d, xedges=xedges, yedges=yedges) where xedges and yedges are the bin edges along the x- and y-axis. I have attached a short program and its output which constructs a numpy.historgram2d with variable bin width (xedges=[0,1,3]) and shows its bin content with imshow. I would highly appreciate if imshow would be extended to represent the histogram correctly. If there is an alternative solution, I would be interested to learn about it as well. Kind regards Frank

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ANN: SciPy 0.12.0 beta 1 release
by Ralf Gommers 22 Mar '13

22 Mar '13

Hi, I am pleased to announce the availability of the first beta release of SciPy 0.12.0. This is shaping up to be another solid release, with some cool new features (see highlights below) and a large amount of bug fixes and maintenance work under the hood. The number of contributors also keeps rising steadily, we're at 74 so far for this release. Sources and binaries can be found at http://sourceforge.net/projects/scipy/files/scipy/0.12.0b1/, release notes are copied below. A Python 3.3 Windows installer will follow soon. Please try this release and report any problems on the mailing list. Cheers, Ralf ========================== SciPy 0.12.0 Release Notes ========================== .. note:: Scipy 0.12.0 is not released yet! SciPy 0.12.0 is the culmination of 7 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Moreover, our development attention will now shift to bug-fix releases on the 0.12.x branch, and on adding new features on the master branch. Some of the highlights of this release are: - Completed QHull wrappers in scipy.spatial. - cKDTree now a drop-in replacement for KDTree. - A new global optimizer, basinhopping. - Support for Python 2 and Python 3 from the same code base (no more 2to3). This release requires Python 2.6, 2.7 or 3.1-3.3 and NumPy 1.5.1 or greater. Support for Python 2.4 and 2.5 has been dropped as of this release. New features ============ ``scipy.spatial`` improvements ------------------------------ cKDTree feature-complete ^^^^^^^^^^^^^^^^^^^^^^^^ Cython version of KDTree, cKDTree, is now feature-complete. Most operations (construction, query, query_ball_point, query_pairs, count_neighbors and sparse_distance_matrix) are between 200 and 1000 times faster in cKDTree than in KDTree. With very minor caveats, cKDTree has exactly the same interface as KDTree, and can be used as a drop-in replacement. Voronoi diagrams and convex hulls ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ `scipy.spatial` now contains functionality for computing Voronoi diagrams and convex hulls using the Qhull library. (Delaunay triangulation was available since Scipy 0.9.0.) Delaunay improvements ^^^^^^^^^^^^^^^^^^^^^ It's now possible to pass in custom Qhull options in Delaunay triangulation. Coplanar points are now also recorded, if present. Incremental construction of Delaunay triangulations is now also possible. Spectral estimators (``scipy.signal``) -------------------------------------- The functions ``scipy.signal.periodogram`` and ``scipy.signal.welch`` were added, providing DFT-based spectral estimators. ``scipy.optimize`` improvements ------------------------------- Callback functions in L-BFGS-B and TNC ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A callback mechanism was added to L-BFGS-B and TNC minimization solvers. Basin hopping global optimization (``scipy.optimize.basinhopping``) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A new global optimization algorithm. Basinhopping is designed to efficiently find the global minimum of a smooth function. ``scipy.special`` improvements ------------------------------ Revised complex error functions ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The computation of special functions related to the error function now uses a new `Faddeeva library from MIT <http://ab-initio.mit.edu/Faddeeva>`__ which increases their numerical precision. The scaled and imaginary error functions ``erfcx`` and ``erfi`` were also added, and the Dawson integral ``dawsn`` can now be evaluated for a complex argument. Faster orthogonal polynomials ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Evaluation of orthogonal polynomials (the ``eval_*`` routines) in now faster in ``scipy.special``, and their ``out=`` argument functions properly. ``scipy.sparse.linalg`` features -------------------------------- - In ``scipy.sparse.linalg.spsolve``, the ``b`` argument can now be either a vector or a matrix. - ``scipy.sparse.linalg.inv`` was added. This uses ``spsolve`` to compute a sparse matrix inverse. - ``scipy.sparse.linalg.expm`` was added. This computes the exponential of a sparse matrix using a similar algorithm to the existing dense array implementation in ``scipy.linalg.expm``. Listing Matlab(R) file contents in ``scipy.io`` ----------------------------------------------- A new function ``whosmat`` is available in ``scipy.io`` for inspecting contents of MAT files without reading them to memory. Documented BLAS and LAPACK low-level interfaces (``scipy.linalg``) ------------------------------------------------------------------ The modules `scipy.linalg.blas` and `scipy.linalg.lapack` can be used to access low-level BLAS and LAPACK functions. Polynomial interpolation improvements (``scipy.interpolate``) ------------------------------------------------------------- The barycentric, Krogh, piecewise and pchip polynomial interpolators in ``scipy.interpolate`` accept now an ``axis`` argument. Deprecated features =================== `scipy.lib.lapack` ------------------ The module `scipy.lib.lapack` is deprecated. You can use `scipy.linalg.lapack` instead. The module `scipy.lib.blas` was deprecated earlier in Scipy 0.10.0. `fblas` and `cblas` ------------------- Accessing the modules `scipy.linalg.fblas`, `cblas`, `flapack`, `clapack` is deprecated. Instead, use the modules `scipy.linalg.lapack` and `scipy.linalg.blas`. Backwards incompatible changes ============================== Removal of ``scipy.io.save_as_module`` -------------------------------------- The function ``scipy.io.save_as_module`` was deprecated in Scipy 0.11.0, and is now removed. Its private support modules ``scipy.io.dumbdbm_patched`` and ``scipy.io.dumb_shelve`` are also removed. Other changes ============= Authors ======= * Anton Akhmerov + * Alexander Eberspächer + * Anne Archibald * Jisk Attema + * K.-Michael Aye + * bemasc + * Sebastian Berg + * François Boulogne + * Matthew Brett * Lars Buitinck * Steven Byrnes + * Tim Cera + * Christian + * Keith Clawson + * David Cournapeau * Nathan Crock + * endolith * Bradley M. Froehle + * Matty G * Christoph Gohlke * Ralf Gommers * Robert David Grant + * Yaroslav Halchenko * Charles Harris * Jonathan Helmus * Andreas Hilboll * Hugo + * Oleksandr Huziy * Jeroen Demeyer + * Johannes Schönberger + * Steven G. Johnson + * Chris Jordan-Squire * Jonathan Taylor + * Niklas Kroeger + * Jerome Kieffer + * kingson + * Josh Lawrence * Denis Laxalde * Alex Leach + * Lorenzo Luengo + * Stephen McQuay + * MinRK * Sturla Molden + * Eric Moore + * mszep + * Matt Newville + * Vlad Niculae * Travis Oliphant * David Parker + * Fabian Pedregosa * Josef Perktold * Zach Ploskey + * Alex Reinhart + * richli + * Gilles Rochefort + * Ciro Duran Santillli + * Jan Schlueter + * Jonathan Scholz + * Anthony Scopatz * Skipper Seabold * Fabrice Silva + * Scott Sinclair * Jacob Stevenson + * Sturla Molden + * Julian Taylor + * thorstenkranz + * John Travers + * trueprice + * Nicky van Foreest * Jacob Vanderplas * Patrick Varilly * Daniel Velkov + * Pauli Virtanen * Stefan van der Walt * Warren Weckesser A total of 74 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

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The New Scipy Central Home page
by Surya Kasturi 05 Mar '13

05 Mar '13

Hey, As discussed before, I want to start my first contribution to SciPy by make Scipy Central new design. So, my idea is to make the site look "clean and simple". However, lots of things needed to be done, I just want to share this small piece. http://ksurya.github.com/scipycentral/ The whole point of sharing at this early is that I need some suggestions regarding some major design-changes in the code. 1. Remove "Tag cloud" from its current position and place on the background of "Heading: Scipy Central" 2. Submit Code, Submit Lib files, Submit Link.. part, I don't want to comment on it now. May be we don't need to change but can change some design! However, we can as well put them on on nav-bar Fundamentally, I want to hear some suggestions regarding these things.. Hope you like the page. Also, What about the "color". Is black okay? How about regular "scipy blue"? Not sure? Need some suggestion on it?

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