Mailman 3 March 2011 - SciPy-User

hello
by DARK Cyrus 08 Mar '11

08 Mar '11

http://_dark_slave_code1.enmatch.com/forum/2008/05/medicines-to-neglect-the… Herewith the shortest version you'll ever see of what every chief executive of every technology company needs to know about running the business.Microsoft wants to buy startups. It just better make sure the price is right.For more than 100 years, the Rocky Mountain Collegian has been run by the students at Colorado State University without any corporate masters. On Tuesday, the school administration met with staff from the Gannett publication, The Coloradoan in Fort Collin

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[ANN] Bottleneck 0.4.0
by Keith Goodman 08 Mar '11

08 Mar '11

Bottleneck is a collection of fast NumPy array functions written in Cython. It contains functions like median, nanmedian, nanargmax, move_mean. The fourth release of Bottleneck contains new functions and bug fixes. Separate source code distributions are now made for 32 bit and 64 bit operating systems. New functions: - rankdata() - nanrankdata() Enhancements: - Optionally specify the shapes of the arrays used in benchmark - Can specify which input arrays to fill with one-third NaNs in benchmark Breaks from 0.3.0: - Removed group_nanmean() function - Bump dependency from NumPy 1.4.1 to NumPy 1.5.1 - C files are now generated with Cython 0.14.1 instead of 0.13 Bug fixes: - #6 Some functions gave wrong output dtype for some input dtypes on 32 bit OS - #7 Some functions choked on size zero input arrays - #8 Segmentation fault with Cython 0.14.1 (but not 0.13) download http://pypi.python.org/pypi/Bottleneck docs http://berkeleyanalytics.com/bottleneck code http://github.com/kwgoodman/bottleneck mailing list http://groups.google.com/group/bottle-neck mailing list 2 http://mail.scipy.org/mailman/listinfo/scipy-user

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fitting a 2D rotated gauss
by Robert Robert 08 Mar '11

08 Mar '11

Hello all, I was looking at the scipy cookbook and found a code for fitting 2D gauss. The code I found in the cookbook was for a not rotated 2D gauss. It points to another code which could be found through the following link http://code.google.com/p/agpy/source/browse/trunk/agpy/gaussfitter.py This code found at the link, says to be able to fit a rotated 2D Gauss. What I don't understand of the code found at the given link is that when it calculates the guess parameters for the 2D rotated gauss it always returns 0.0 degrees. How is this possible. I tried out the code myself, generated a rotated gauss and then let the function moments() in the code calculate the guess parameters. I don't seem to get the correct sigma x , sigma y and the rotation back. The rotation seems to be 0.0, as I expected, looking at the code. I was wondering if this is an error in the code or that the guess rotation is always zero ?? I hope someone can please help me out with this question. regards, pim

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Possible to integrate an ODE in until the solution reaches a certain value?
by Randy Williams 07 Mar '11

07 Mar '11

Greetings, I'm trying to model the dynamics of a catapult-like mechanism used to launch a projectile, and have a system of ODEs which I need to numerically integrate over time. I am trying to solve for the position of the projectile as well as the other components in my mechanism. At some point in time, the projectile separates from the mechanism, and becomes airborne. The equations governing the system change at that point in time, but because it's a function of position (which i'm solving for), I don't know up front what timespan I need to integrate over. I would like the ODE solver to stop integrating once the the solution reaches this certain value, and I will use the states at that point to compute the initial conditions to another ODE describing the motion from that time onward. Is there an ODE solver in Python/SciPy which will integrate from the initial t until the solution reaches a certain value, or until a specific condition is met? The ODE solvers in Matlab have "events" which will do this, but I'm trying my best to stick with Python. Thanks, Randy

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Scientific Software developer wanted in Seattle.
by Christopher Barker 07 Mar '11

07 Mar '11

Scientific Software Developer NOAA Emergency Response Division Help us develop our next-generation oil spill transport model. Background: The Emergency Response Division (ERD) of NOAA's Office of Response and Restoration (OR&R) provides scientific expertise to support the response to oil and chemical spills in the coastal environment. We played a major role in the recent Deepwater Horizon oil spill in the Gulf of Mexico. In order to fulfill our mission, we develop many of the software tools and models required to support a response to hazardous material spills. In the wake of the Deepwater horizon incident, we are embarking on a program to develop our next-generation oil spill transport model, taking into account lessons learned from years of response and this major incident. General Characteristics: The incumbent of this position will provide software development services to support the mission of the Emergency Response Division of NOAA's Office of Response and Restoration. As part of his/her efforts, independent evaluation and application of development techniques, algorithms, software architecture, and programming patterns will be required. The incumbent will work with the staff of ERD to provide analysis on user needs and software, GUI, and library design. He/she will be expect to work primarily on site at NOAA's facility in Seattle. Knowledge: The incumbent must be able to apply modern concepts of software engineering and design to the development of computational code, desktop applications, web applications, and libraries. The incumbent will need to be able to design, write, refactor, and implement code for a complex desktop and/or web application and computational library. The incumbent will work with a multi-disciplinary team including scientists, users, and other developers, utilizing software development practices such as usability design, version control, bug and issue tracking, and unit testing. Good communication skills and the knowledge of working as part of a team are required. Direction received: The incumbent will participate on various research and development teams. While endpoints will be identified through Division management and some direct supervision will be provided, the incumbent will be responsible for progressively being able to take input from team meetings and design objectives and propose strategies for reaching endpoints. Typical duties and responsibilities: The incumbent will work with the oil and chemical spill modeling team to improve and develop new tools and models used in fate and transport forecasting. Different components of the project will be written in C++, Python, and Javascript. Education requirement, minimum: Bachelor's degree in a technical discipline. Experience requirement, minimum: One to five years experience in development of complex software systems in one or more full-featured programming languages (C, C++, Java, Python, Ruby, Fortran, etc.) The team requires experience in the following languages/disciplines. Each incumbent will need experience in some subset: * Computational/Scientific programming * Numerical Analysis/Methods * Parallel processing * Desktop GUI * Web services * Web clients: HTML/CSS/Javascript * Python * wxPython * OpenGL * C/C++ * Python--C/C++ integration * Software development team leadership While the incumbent will work on-site at NOAA, directly with the NOAA team, this is a contract position with General Dynamics Information Technology: http://www.gdit.com/default.aspx For more information and to apply, use the GDIT web site: https://secure.resumeware.net/gdns_rw/gdns_web/job_detail.cfm?key=59436&sho… if that long url doesn't work, try: http://www.resumeware.net/gdns_rw/gdns_web/job_search.cfm and search for job ID: 179178 NOTE: This is a potion being hired by GDIT to work with NOAA, so any questions about salary, benefits, etc, etc should go to GDIT. However, feel free to send me questions about our organization, working conditions, more detail about the nature of the projects etc. -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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help stats module to determine the type of distribution
by vineeth 04 Mar '11

04 Mar '11

Hello all, I am looking forward to determine the type of distribution my data set follows. Is there any way in stats module of python to do this kind of operation? or is there any round about way? Thank You Vineeth

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Parallel processing
by Nils Wagner 04 Mar '11

04 Mar '11

Hi all, my question is a bit off-topic. However, I hope that I will get an answer I would like to parallelize a number of calls to mycmd nproc denotes the number of processes . for i in range(nproc): try: retcode = call("mycmd" + " myarg", shell=True) if retcode < 0: print >>sys.stderr, "Child was terminated by signal", -retcode else: print >>sys.stderr, "Child returned", retcode except OSError, e: print >>sys.stderr, "Execution failed:", e How can I manage that with python ? Any pointer would be appreciated. Thanks in advance Nils

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Strange behaviour from corrcoef when calculating correlation-matrix in SciPy/NumPy.
by Rajeev Raizada 04 Mar '11

04 Mar '11

Dear SciPy users, I have a matrix (or, more strictly speaking, an array), and I want to calculate the correlation between each column and every other column, i.e. to make a standard correlation matrix. In Matlab, this is pretty straightforward, and the results also reflect the mathematical convention that corr(m) is just an abbreviated way of saying corr(m,m). >> m = [ 1 2; -1 3; 0 4] m = 1 2 -1 3 0 4 >> corr(m) ans = 1.0000 -0.5000 -0.5000 1.0000 >> corr(m,m) ans = 1.0000 -0.5000 -0.5000 1.0000 However, the behaviour of SciPy/NumPy is quite different from what I had expected. In those modules, corrcoeff(m) is *not* the same as corrcoeff(m,m). Apparently, corrcoeff(x,y) produces the result corrcoef(vstack(x,y)), which strikes me as rather weird, and inconsistent with standard mathematical usage. Here are some examples, below. Raj ------------------ In [1]: import scipy In [2]: m = scipy.array([[ 1, 2],[ -1, 3],[ 0, 4]]) In [3]: m Out[3]: array([[ 1, 2], [-1, 3], [ 0, 4]]) In [4]: m.T Out[4]: array([[ 1, -1, 0], [ 2, 3, 4]]) In [5]: scipy.corrcoef(m) Out[5]: array([[ 1., 1., 1.], [ 1., 1., 1.], [ 1., 1., 1.]]) In [6]: scipy.corrcoef(m.T) Out[6]: array([[ 1. , -0.5], [-0.5, 1. ]]) # Note from Raj: that answer above, at least, matches what we'd want. # But it still gives a different result from corrcoef(m.T,m.T) ! In [7]: scipy.corrcoef(m,m) Out[7]: array([[ 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1.]]) In [8]: scipy.corrcoef(m.T,m.T) Out[8]: array([[ 1. , -0.5, 1. , -0.5], [-0.5, 1. , -0.5, 1. ], [ 1. , -0.5, 1. , -0.5], [-0.5, 1. , -0.5, 1. ]])

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Re: [SciPy-User] error: command 'swig' failed with exit status 1
by franck kalala 03 Mar '11

03 Mar '11

Hey all, I was install new release of scipy as describe here http://www.scipy.org/Installing_SciPy/Linux When I run the command python setup.py build I get at the end this error message swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i swig -python -I/usr/include/suitesparse -o build/src.linux-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.linux-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i unable to execute swig: No such file or directory error: command 'swig' failed with exit status 1 Any help with this? Cheers Maziba -- ********** ++++ --- *

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[SciPy-user] mgrid format from unstructured data
by Spiffalizer 03 Mar '11

03 Mar '11

Hi I am trying to write some code to find the interpolated value of some specified points. My input is x,y,z values. Where the x,y value is the coordinates in 2d and z is the value I am interested in. My input is sort of unstructured. I get it from looping over some data that I have. It is however constructed from a grid pattern to begin with. But i am not certain in what order the points are in the loop. example: 1: 0,0,1 2: 1,0,5 3: 2,0,12 4: 0,1,0 5: 1,1,10 6: 2,1,25 7: 0,3,9 8: 1,3,20 9: 2,3,11 the order point 1-9 comes is unknown to me. I have found some examples that looks like this x,y = np.mgrid[-1:1:10j,-1:1:10j] z = (x+y)*np.exp(-6.0*(x*x+y*y)) xnew,ynew = np.mgrid[-1:1:3j,-1:1:3j] tck = interpolate.bisplrep(x,y,z,s=0) znew = interpolate.bisplev(xnew[:,0],ynew[0,:],tck) So my question really is how to sort/convert my input to a format that can be used by the interpolate function? Thanks Joakim -- View this message in context: http://old.nabble.com/mgrid-format-from-unstructured-data-tp30993544p309935… Sent from the Scipy-User mailing list archive at Nabble.com.

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