Mailman 3 June 2015 - SciPy-Dev

signal.sosfilt filter representation
by Eric Quintero June 5, 2015

June 5, 2015

Hi All, I’m very happy that second order section filtering is being introduced in scipy! Looking at the implementation, I see that it was chosen to use the direct form 2 realization of a second order section, which has the advantage of speed. Looking at the code, this maybe was also chosen to simply use signal.lfilter for the actual filtering. However, in the LIGO project, we initially used this form in our digital control systems, and found that this form leads to high levels of quantization noise in floating point signals, especially when the signals have a high dynamic range. This is due to the fact that the signal is first propagated through the filter poles, before going through the zeros. We’ve now moved on to using the Biquad form, which has one additional summation step compared to DF2, but avoids large internal values. The noise introduced by filtering in this way can be hundreds of times less than the DF2 results, which for our purposes makes the modest increase in computational time definitely worth it. Also, as a point of reference, the sosfilt function in MATLAB also uses this form. Long story short, I think it would be to scipy’s benefit to include biquad SOS filtering, at the very least as a keyword argument option, if not the default. I am, of course, willing to work on this myself. I appreciate any feedback you all may have, thanks for your consideration, Eric Q.

3 3

Compiling/packaging SciPy on Windows with Visual Studio compilers
by Marcus D. Hanwell June 4, 2015

June 4, 2015

Hi, Big fan of SciPy, working on a project that would like to package it as part of our Python environment that is distributed with our desktop executable. It is an open source project called tomviz, reusing large pieces of ParaView and already bundling NumPy. As the second phase of the project we would like to offer the full SciPy suite, along with our wrapped code, in an integrated desktop application. We have run into issues packaging SciPy, and I was hoping to get advice on how could build a BLAS/LAPACK on Windows that could be packaged with the Python libraries we are linking to - existing build recipes would be extremely useful. We were hoping to use gfortran with Visual Studio, but that hasn't worked so far. I have searched and can't find anything, if my Google skills failed me please point me at any relevant pages. Thanks, Marcus

2 6

Update to stats.mannwhitneyu
by Alex Wagner June 2, 2015

June 2, 2015

Hello, I wrote up an exact test for the Mann-Whitney-Wilcoxon test, and also included alternative hypotheses (besides the current ambiguous one-sided test). Alongside this, I’ve developed unit tests corresponding to the enhanced features. I think that it would be a useful addition to the scipy module, and so I’ve proposed these changes on github, pull request #4933. Best, Alex -- Alex Wagner, PhD Postdoctoral Research Associate, McDonnell Genome Institute Washington University School of Medicine Campus Box 8501 4444 Forest Park Ave St. Louis, MO, 63108 P: (480) ALEX-PHD E: awagner(a)genome.wustl.edu

1 0

[scipy.stats improvements] Weekly Summary 2015/05/30
by Abraham Escalante June 1, 2015

June 1, 2015

Hello all, Today Ralf and I had our second weekly meeting and we decided to adopt (or you know, shamelessly copy) the weekly status approach from Jaime and Aman. Here is the first one: *Week 1* - [closed] statistics review: masked_var - [closed] statistics review: ss - [closed] statistics review: square_of_sums - [WIP] Add 'alternative' keyword to hypothesis tests in stats - [WIP] Trimmed statistics functions have inconsistent API *Plan for week 2* - Trimmed statistics functions have inconsistent API - statistics review: trim_mean - statistics review: trim1 - statistics review: trimboth - statistics review: ppcc_max - statistics review: find_repeats - statistics review: _chk_asarray Since there's quite a few items, I will refrain from going into much detail. If anyone is interested in knowing more, please feel free to contact me and I will gladly provide more info. Regards, Abraham.

2 1