Mailman 3 March 2018 - SciPy-Dev

SciPy : GSoC Proposal [Seeking Feedback] on Rotation Formalism in 3 Dimension
by Anubhav Patel March 24, 2018

March 24, 2018

Hi everyone, I am want to contribute to SciPy through GSoC 2018. I am currently seeking feedback on my proposal ( https://docs.google.com/document/d/1ylzugkvVYI7m3IXsWVLD4EkE6zQd8B9YDPKtTno… ). I would appreciate any advice regarding the proposal. Considering Ralf advice to look for existing implementation, I am currently looking into few implementation for conversions between rotation representations, for reuse and inspiration. One of the issues I felt with almost all of them is that they are designed to work on single rotation at a time. The API they use sort of suggest towards it. Consider the example of transforms3d ( http://matthew-brett.github.io/transforms3d/ ), due to it's API accepting a single rotation at a time, not a array of rotations, they tend not to utilise numpy vector operations and miss out on the speed improvement that comes with it. I decided to reach out to you regarding how useful would the support for multiple conversions among rotation formalism at once be. It is even worth considering? How frequent does such a scenario occurs where you have to convert a sequence of rotation from one formalism to another. I create a test (code at https://gist.github.com/anubhavp28/e79645a544c6e7b16b408a172e522134 ) to see possible improvement with vector operations. I implemented rotation matrix to quaternion conversion using vector operations and timed it against what a user would have to do to achieve the same result with transforms3d. My code took about 0.009185953000269365 while the one with transform3d took about 0.022295135000604205, for 100 iterations with sample matrices provided in the code. I would appreciate any suggestions. Anubhav Patel

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Review GSoC-2018 Proposal
by sudheer achary March 24, 2018

March 24, 2018

I am Sudheer Achary, 3rd year B.Tech computer science student from International Institute of Information technology, Hyderabad. Iam interested in contributing to SciPy through GSoC-2k18. i kindly request to review my proposal and suggest me appropriate changes need to me made, I have little more to add and here i share my google doc. thanks. [image: Google Document] Scipy-Proposal GSoC 2018 Sudheer Achary <https://docs.google.com/document/d/13U4feVYTJJfGFgSHA37p_JxpexBKZJ2-VSjs4z7…>

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Moving slow parts of find_peaks to Cython
by Lars G. March 23, 2018

March 23, 2018

Hello, I'm currently working on 3 PRs that move slow parts in `find_peaks`, `peak_prominences` and `peak_widths` to Cython. * ENH: Speed-up peak distance filtering with Cython https://github.com/scipy/scipy/pull/8523 * ENH: Cythonize peak_prominences https://github.com/scipy/scipy/pull/8541 * ENH: Cythonize peak_widths https://github.com/scipy/scipy/pull/8594 I quite happy with the first two PRs and think they have left the "work in progress" state and are ready for some final polishing. I might still tweak the third one here or there but nothing too drastic. Because these 3 modify the same files I'd propose to merge in the given order (if desired) so that I can rebase and resolve the arising merge conflicts. If any of you guys with more experience in Cython have tips to improve the performance even further I'd be especially happy to learn. :D As always, thank you for your time and feedback. Best regards, Lars

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Fast Walsh–Hadamard transform for SciPy ?
by Chaman Agrawal March 23, 2018

March 23, 2018

Hello, Thanks, please send the link ,it would be good to have multiple references. However the important part is where to implement this ,in fftpack or signal as Ralf Gommers <https://github.com/rgommers> mentioned in the issue page. Cheers, Chaman I have my own code for FHT if you are interested On Thu, Mar 22, 2018 at 2:52 PM Chaman Agrawal <chaman.ag at gmail.com <https://mail.python.org/mailman/listinfo/scipy-dev>> wrote: >* Issue #8590 https://github.com/scipy/scipy/issues/8590 <https://github.com/scipy/scipy/issues/8590> *>>* Currently there is no implementation of Fast Walsh–Hadamard transform in *>* SciPy. Although it seems that FWHT is not as general as FFT but it is *>* pretty ubiquitous ,it is there is other maths and science softwares like *>* MATLAB etc. .I would like to contribute towards it. Following are the *>* details about it. *>* Fast Walsh–Hadamard transform *>>* Hadamard transform is an example of a generalized class of Fourier *>* transforms. It performs an orthogonal, symmetric, involutive, linear *>* operation on 2^(m) numbers. It is equivalent to a multidimensional DFT. *>* Time Complexity: *>>* O(nlogn) with Fast Walsh-Hadamard transform (FWHT) *>* Comparison with FFT: *>>* FWHT is very useful for reducing bandwidth storage requirements and *>* spread-spectrum analysis. Compared to the FFT, the FWHT requires less *>* storage space and is faster to calculate because it uses only real *>* additions and subtractions, while the FFT requires complex values. The FWHT *>* is able to represent signals with sharp discontinuities more accurately *>* using fewer coefficients than the FFT. *>* Some Usage examples: *>>* The Hadamard transform is used in data encryption, as well as many signal *>* processing and data compression algorithms, such as JPEG XR and MPEG-4 AVC. *>* It is also a crucial part of Grover's algorithm and Shor's algorithm in *>* quantum computing. The Hadamard transform is also applied in scientific *>* methods such as NMR, mass spectroscopy and crystallography. *>

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GSoC Rotation Formalism Proposal
by Vishal Gupta March 23, 2018

March 23, 2018

Hey, I am a 3rd CSE undergrad at SSNCE, Chennai, India. I'd like to work on Rotation Formalism in 3 Dimensions as a part of this year's GSoC . https://docs.google.com/document/d/1y5OalGAvYkk8UvLtFjQ2-xhRj_NTwq0fV3GvlCB… Thanks, Vishal Gupta ‌ <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…>

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Feedback for the proposal
by Samyak Jain March 23, 2018

March 23, 2018

Hi all, I am a 2nd-year student contributing towards SciPy's Rotation Formalism in 3 dimensions project as a part of GSOC'18. I have drafted a proposal here. <https://docs.google.com/document/d/12cP0LTFa0H3aQqJfb1WAmr5A_KU6bN3qZ17LbKd…> I would appreciate any feedback on this so that I can improve my proposal. Thanks, Samyak Jain Link : https://docs.google.com/document/d/12cP0LTFa0H3aQqJfb1WAmr5A_KU6bN3qZ17LbKd…

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regarding issue #8589
by sudheer achary March 23, 2018

March 23, 2018

I would like to refactor the code as mentioned in https://github.com/scipy/scipy/issues/8589 are there any issues with the given changes made ?

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Re: [SciPy-Dev] Contributing to SciPy through GSoC
by Nikolay Mayorov March 22, 2018

March 22, 2018

Hi, Anybhev! I think getting Rotation right is a top priority and so far unfortunately nobody dig into technical details of it. I would like to see that from students. As for the algorithms. I believe that Wahba's problem can be generalized by adding a translation vector, but the interpretation will be different (search for "absolute orientation problem"). As for methods to solve Wahba's problem --- probably SVD based is the easiest to understand and implement, but if we decide to use quaternions as the base representation, then we can go with "Q-method". "Cubic spline" for orientation is also a very cool algorithm which wasn't promoted anywhere, but this is the best idea I found on the subject (i.e. interpolation with continuous angular rates and acceleration). Other algorithms are quite small, they can be added quickly. I would say it is more of a question of what we should include. If you have some ideas outside (mostly) "aerospace" field --- they are welcome. For all parts I would like to see more concrete and technical details. For example, if we want SLERP interpolation --- what will it be (class or function), what it will accept, what will be the most difficult part to implement it correctly. The same for all other things. Best, Nikolay ---- On Sat, 03 Mar 2018 16:26:28 +0500 anubhavp28(a)gmail.com wrote ---- Hi, I wanted feedback regarding whether a combination of rotation class and implementation of quaternion SLERP algorithm and Davenport's Q-method solving Wahba's Problem, will be enough for GSoC? Should I include more rotation related algorithm for implementation? Any suggestions what more I could do? On Mon, Feb 26, 2018 at 9:30 PM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: Hi Anubhev, On Mon, Feb 26, 2018 at 2:12 AM, Anubhav Patel <anubhavp28(a)gmail.com> wrote: Hi everyone, I want to work on SciPy as part of GSoC and I have few queries. 1. On the Ideas Page, there was a mention of scipy.spatial.transform module. I want to know what will be the exact purpose of this module? Did you read the whole idea? There's a lot of detail. It says for example "The aim of this project is to create a module which will allow to conveniently describe, apply and compose rotations. ". That answer your question I think. 2. Whether the idea for a module for numerical differentiation was dropped completely? Yes, for now that's off the table - at least not feasible for a GSoC we've concluded after several attempts. 3. Apart from those ideas listed on ideas page, are there any other area where you guys would like to see contribution on? Ideas for new features on http://scipy.github.io/devdocs/roadmap.html are of interest, or ones you may have yourself. But given that they're not on the ideas page, it's not guaranteed we can find mentors for those. Cheers, Ralf _______________________________________________ SciPy-Dev mailing list SciPy-Dev(a)python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev(a)python.org https://mail.python.org/mailman/listinfo/scipy-dev

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Benchmark for scalar Newton
by Mark Alexander Mikofski March 21, 2018

March 21, 2018

Hi all, I've added to the airspeed velocity benchmarks. There were only benchmarks for the pure C methods, so I added one for the scalar Newton method in scipy.optimize.zeros. if you want to compare it with the other zeros use "f1", a parabola, which is equivalent to "f2" for the other zeros. If it's convenient for you please consider reviewing scipy PR #8587 . I look forward to your comments. Best regards, Mark Mikofski

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SciPy dependencies
by Peter Balazovic March 21, 2018

March 21, 2018

Dears, I am trying to get installed SciPy under Yocto. I encounter compile error: ERROR: scipy-1.0.0-r0 do_compile: Function failed: do_compile (log file is located at ../tmp/work/cortexa9hf-neon-poky-linux-gnueabi/scipy/1.0.0-r0/temp/log.do_compile.5023) Log data follows:| DEBUG: Executing shell function do_compile | ERROR: python setup.py build execution failed.| ../tmp/sysroots/x86_64-linux/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'| warnings.warn(msg)| lapack_opt_info:| openblas_lapack_info:| libraries openblas not found in ['../tmp/sysroots/x86_64-linux/usr/lib']| NOT AVAILABLE The SciPy install setup.py looks for openBLAS in different directory *x86_64-linux* instead of *target-arm* directory. I have already installed openBLAS and it is located at *target-arm* sysroot. ./tmp/sysroots/target-arm/usr/lib/libopenblas.so ./tmp/sysroots/target-arm/usr/lib/libopenblas.a ./tmp/sysroots/target-arm/usr/include/openblas_config.h With building Yocto there are three "build" directories *target-arm* (target sysroot), *target-arm-tcbootstrap* (intermediate directory for the compiler bootstrap), and *x86_64-linux* (host tools and libraries). The openBLAS is installed within *target-arm* sysroot. My question is how to tell and redirect SciPy installer to look for openBLAS (and other dependencies) at *target-arm* directory ( *./tmp/sysroots/target-arm/*)? Thanks you. Sent from Mailspring <https://getmailspring.com/>, the best free email app for work

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