Mailman 3 April 2015 - SciPy-User

Number of input partitions
by Wenlei Xie April 18, 2015

April 18, 2015

Hi, I am wondering the mechanism that determines the number of partitions created by SparkContext.sequenceFile ? For example, although my file has only 4 splits, Spark would create 16 partitions for it. Is it determined by the file size? Is there any way to control it? (Looks like I can only tune minPartitions but not maxPartitions) Thank you! Best, Wenlei

1 1

Non-constant timesteps in scipy.signal.lsim
by Clancy Rowley April 13, 2015

April 13, 2015

The current behavior of scipy.signal.lsim is that it accepts input signals with non-constant timesteps. We are considering a non-backward-compatible change in implementation that would break this, and require constant timesteps: https://github.com/scipy/scipy/pull/4675 Does anybody rely on the current behavior, and if so, could you work around such a change in behavior? Some background: - The current implementation of scipy.signal.lsim has a number of problems. For instance, for a linear system with a pole at the origin, it throws an exception; for systems with repeated poles, it gives incorrect results. - There is a workaround, a routine scipy.signal.lsim2, that fixes these problems (and also accepts non-uniform timesteps), but it is typically hundreds or even thousands of times slower than the (broken) implementation in lsim. (It calls a generic ODE integrator instead of a specialized solver for linear systems.) - An efficient implementation of lsim requires constant time steps. - Matlab's version of lsim also requires constant time steps. ===== Clancy Rowley Professor, Mechanical and Aerospace Engineering Affiliated faculty, Program in Applied and Computational Math Princeton University http://www.princeton.edu/~cwrowley

1 0

Julia and SciPy -- will they ever be married yet?
by Brian Merchant April 12, 2015

April 12, 2015

In one of his blog posts <https://jakevdp.github.io/blog/2012/09/20/why-python-is-the-last/> titled "Why Python is the last language you'll have to learn", Jake Vanderplas mentioned that a potential merger/collaboration between Julia and SciPy seemed to be just on the horizon based on the mood of this discussion <https://groups.google.com/forum/?fromgroups=#!topic/julia-dev/YftOOEfcwrk%5…> on the julia-dev boards. It has been a long time since 2012 now, and I wonder, what is the status of all of that happy-talk?

2 1

1-norm estimation via Hager's algorithm in SCIPY
by Wenlei Xie April 11, 2015

April 11, 2015

Hi, I would like to estimate the 1-norm of matrix A*B, where A is n*k and B is k*n. n is around 1 million while k is around 100. So I cannot materialize it directly. I am wondering if there is anything similar to condest in Matlab to estimate the matrix 1-norm via Hager's algorithm? Would scipy.sparse.linalg.onenormest be a good choice? (It seems to be working for Sparse matrices?) Thank you! Best, Wenlei

2 1

Python benchmarks project
by Todd April 8, 2015

April 8, 2015

Although not strictly scipy-related, I was wondering if anyone was aware of a project containing basic python benchmarks. I don't mean a project with benchmark tools, but rather a project with measurements of common python operations. For example, it used to be the case that list comprehensions were faster than for loops. The sort of project I am looking for would have benchmarks showing how long those took to do the same thing. Does anyone know if such a thing exists? Thanks.

3 2

Research position in the Brazilian Research Institute for Science and Neurotechnology – BRAINN
by Thiago Franco de Moraes April 8, 2015

April 8, 2015

Research position in the Brazilian Research Institute for Science and Neurotechnology – BRAINN Postdoc researcher to work with software development for medical imaging The Brazilian Research Institute for Neuroscience and Neurotechnology (BRAINN) (www.brainn.org.br) focuses on the investigation of basic mechanisms leading to epilepsy and stroke, and the injury mechanisms that follow disease onset and progression. This research has important applications related to prevention, diagnosis, treatment and rehabilitation and will serve as a model for better understanding normal and abnormal brain function. The BRAINN Institute is composed of 10 institutions from Brazil and abroad and hosted by State University of Campinas (UNICAMP). Among the associated institutions is Renato Archer Information Technology Center (CTI) that has a specialized team in open-source software development for medical imaging (www.cti.gov.br/invesalius) and 3D printing applications for healthcare. CTI is located close the UNICAMP in the city of Campinas, State of São Paulo in a very technological region of Brazil and is looking for a postdoc researcher to work with software development for medical imaging related to the imaging analysis, diagnosis and treatment of brain diseases. The postdoc position is for two years with the possibility of being renovated for more two years. Education - PhD in computer science, computer engineering, mathematics, physics or related. Requirements - Digital image processing (Medical imaging) - Computer graphics (basic) Benefits 6.143,40 Reais per month free of taxes (about US$ 2.800,00); 15% technical reserve for conferences participation and specific materials acquisition; Interested Send curriculum to: jorge.silva(a)cti.gov.br with subject “Postdoc position” Applications reviews will begin April 30, 2015 and continue until the position is filled.

1 0

Windows 64bits support
by Jerome Kieffer April 4, 2015

April 4, 2015

Hi, I am wondering why there is no "official" packages for scipy on windows 64 bits ? The same is True for NumPy and even Python which systematically suggests the 32-bits version. After the nice move from Microsoft for provide compiler, is it still an issue ? Cheers, -- Jérôme Kieffer Data analysis unit - ESRF PS: I know the wonderful work of Christopher Gohlke, but his work is "unofficial"

8 13

SciPy 2015 Conference Updates - LAST CALL for talks - 4/10 extension, registration open, keynotes announced, John Hunter Plotting Contest
by Courtenay Godshall (Enthought) April 3, 2015

April 3, 2015

--------------------------------------------------------------------------- **LAST CALL FOR SCIPY 2015 TALK AND POSTER SUBMISSIONS - EXTENSION TO 4/10* --------------------------------------------------------------------------- SciPy 2015 will include 3 major topic tracks and 7 mini-symposia tracks. Submit a proposal on the SciPy 2015 website: http://scipy2015.scipy.org. If you have any questions or comments, feel free to contact us at: scipy-organizers(a)scipy.org. You can also follow @scipyconf on Twitter or sign up for the mailing list on the website for the latest updates! Major topic tracks include: - Scientific Computing in Python (General track) - Python in Data Science - Quantitative Finance and Computational Social Sciences Mini-symposia will include the applications of Python in: - Astronomy and astrophysics - Computational life and medical sciences - Engineering - Geographic information systems (GIS) - Geophysics - Oceanography and meteorology - Visualization, vision and imaging -------------------------------------------------------------------------- **SCIPY 2015 REGISTRATION IS OPEN** Please register ASAP to help us get a good headcount and open the conference to as many people as we can. PLUS, everyone who registers before May 15 will not only get early bird discounts, but will also be entered in a drawing for a free registration (via refund or extra)! Register on the website at http://scipy2015.scipy.org -------------------------------------------------------------------------- **SCIPY 2015 KEYNOTE SPEAKERS ANNOUNCED** Keynote speakers were just announced and include Wes McKinney, author of Pandas; Chris Wiggins, Chief Data Scientist for The New York Times; and Jake VanderPlas, director of research at the University of Washington's eScience Institute and core contributor to a number of scientific Python libraries including sci-kit learn and AstroML. -------------------------------------------------------------------------- **ENTER THE SCIPY JOHN HUNTER EXCELLENCE IN PLOTTING CONTEST - DUE 4/13** In memory of John Hunter, creator of matplotlib, we are pleased to announce the Third Annual SciPy John Hunter Excellence in Plotting Competition. This open competition aims to highlight the importance of quality plotting to scientific progress and showcase the capabilities of the current generation of plotting software. Participants are invited to submit scientific plots to be judged by a panel. The winning entries will be announced and displayed at the conference. John Hunter's family is graciously sponsoring cash prizes up to $1,000 for the winners. We look forward to exciting submissions that push the boundaries of plotting! See details here: http://scipy2015.scipy.org/ehome/115969/276538/ Entries must be submitted by April 13, 2015 via e-mail to plotting-contest(a)scipy.org -------------------------------------------------------------------------- **CALENDAR AND IMPORTANT DATES** --Sprint, Birds of a Feather, Financial Aid and Talk submissions OPEN NOW --Apr 10, 2015: Talk and Poster submission deadline --Apr 13, 2015: Plotting contest submissions due --Apr 15, 2015: Financial aid application deadline --Apr 17, 2015: Tutorial schedule announced --May 1, 2015: General conference speakers & schedule announced --May 15, 2015 (or 150 registrants): Early-bird registration ends --Jun 1, 2015: BoF submission deadline --Jul 6-7, 2015: SciPy 2015 Tutorials --Jul 8-10, 2015: SciPy 2015 General Conference --Jul 11-12, 2015: SciPy 2015 Sprints

1 0

Array indexing question
by Joseph C Slater, PhD, PE April 1, 2015

April 1, 2015

On http://wiki.scipy.org/NumPy_for_Matlab_Users, under Linear Algebra Equivalents, the following row is given: a(1:5,:) a[0:5] or a[:5] or a[0:5,:] the first five rows of a I'm quite confused as I thought since the first row is indexed as zero, the fifth would be as 5. Indeed, a[5,5] provides the value in the 6th row and 6th column. However, it seems that 0:5 means 0, 1, 2, 3, 4 . So, when used with a colon, the 5 no longer means the same value as when used without. Am I missing something? Why this peculiar behavior, and how does one avoid errors with this inconsistency? (What's the logic to help me understand why it works this way?) Thank you for any guidance. Joe

5 4