From sebastian.walter at gmail.com Wed Aug 5 07:48:17 2015 From: sebastian.walter at gmail.com (Sebastian Walter) Date: Wed, 5 Aug 2015 13:48:17 +0200 Subject: [SciPy-User] [ANN] HCO Challenge Workshop "Parameter and State Estimation: Methods - Software - Applications", Nov. 10-11, 2015, Heidelberg, Germany Message-ID: Dear SciPy community, There seems to be a significant interest in nonlinear optimization and parameter estimation methods in the SciPy community (numerous discussions on the mailing list, the ongoing GSoC project by Evgeni Burovski and Nikolay Mayorov, etc.). I am myself a regular user of the NumPy/SciPy stack, and maintainer of some humble Python packages (AlgoPy, PyAdolc). The Heidelberg Collaboratory for Industrial Optimization (HCO) is hosting a Challenge Workshop on "Parameter and State Estimation: Methods - Software - Applications", Nov. 10-11, 2015, Heidelberg. I believe this workshop could be of interest to the SciPy developers and community. Here is the official announcement: --------------- start announcement ---------------------- We cordially invite you to participate in the *HCO Challenge Workshop**?Parameter and State Estimation: Methods - Software - Applications?* November 10-11, 2015 International Academic Forum Heidelberg *Hauptstr. 42, 69117 Heidelberg, Germany* *Homepage*: *http://hco.iwr.uni-heidelberg.de * *Scope of the workshop:* Model-based simulation and optimization methods become increasingly important for the development of new products and more efficient processes. Fundamental requirement to leverage the full potential of model-based methods is the development of *predictive mathematical models* and their quantitative validation. This complex task requires robust and efficient numerical methods for parameter estimation. Furthermore, advanced control of processes in real time needs fast and reliable numerical methods for state estimation. Industrial practice shows that in order to realize the full potential of modelling complex processes we have to deal with a number of new challenges. Because of the high relevance of *parameter and state estimation* methods for current and future research and development, the Heidelberg Collaboratory for Industrial Optimization (HCO) invites decision makers, researchers and practitioners from academia and industry to participate in this workshop. Primary goals: - present an overview of state-of-the-art methods for parameter and state estimation - discuss current challenges from industry and academia - identify requirements for the next generation of parameter and state estimation methods and software - foster synergies and collaborations We kindly invite your contribution and participation. Note that the number of participants and remaining presentation slots is limited. *Please register at* *http://hco.iwr.uni-heidelberg.de* . *Workshop Fee:* Early Bird: 100 EUR Normal: 150 EUR *Important Deadlines*: Abstract Submission: Sept. 30, 2015 Registration (early bird): Sept. 30, 2015 *Confirmed speakers include representatives of:* Austrian Institute of Technology, BASF SE, Deutsche ACCUmotive GmbH & Co. KG, Daimler AG, HSKA Karlsruhe, TU Berlin, TU Dortmund, SAS Institute GmbH *The event is kindly supported by: *Committee for Mathematical Modeling, Simulation and Optimization (KoMSO) Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp) Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Mathematics Center Heidelberg (MATCH) --------------- end announcement ---------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From evgeny.burovskiy at gmail.com Thu Aug 6 12:08:42 2015 From: evgeny.burovskiy at gmail.com (Evgeni Burovski) Date: Thu, 6 Aug 2015 17:08:42 +0100 Subject: [SciPy-User] [ANN] HCO Challenge Workshop "Parameter and State Estimation: Methods - Software - Applications", Nov. 10-11, 2015, Heidelberg, Germany In-Reply-To: References: Message-ID: Hi, > There seems to be a significant interest in nonlinear optimization and > parameter estimation methods in the SciPy community (numerous discussions on > the mailing list, the ongoing GSoC project by Evgeni Burovski and Nikolay > Mayorov, etc.). I am myself a regular user of the NumPy/SciPy stack, and > maintainer of some humble Python packages (AlgoPy, PyAdolc). Just a small bit of attribution: the original idea for the GSoC project is (I believe) by Pauli Virtanen and the project itself is co-mentored by Chuck Harris and me. Evgeni PS Big thank you for making AlgoPy! From sebastian.walter at gmail.com Mon Aug 10 04:58:07 2015 From: sebastian.walter at gmail.com (Sebastian Walter) Date: Mon, 10 Aug 2015 10:58:07 +0200 Subject: [SciPy-User] [ANN] HCO Challenge Workshop "Parameter and State Estimation: Methods - Software - Applications", Nov. 10-11, 2015, Heidelberg, Germany In-Reply-To: References: Message-ID: Hello Evgeni, thanks for setting the record straight! It's great to see that the project is going smoothly and that state of the art methods are being made available to a large audience. Sebastian On Thu, Aug 6, 2015 at 6:08 PM, Evgeni Burovski wrote: > Hi, > > > There seems to be a significant interest in nonlinear optimization and > > parameter estimation methods in the SciPy community (numerous > discussions on > > the mailing list, the ongoing GSoC project by Evgeni Burovski and Nikolay > > Mayorov, etc.). I am myself a regular user of the NumPy/SciPy stack, and > > maintainer of some humble Python packages (AlgoPy, PyAdolc). > > Just a small bit of attribution: the original idea for the GSoC > project is (I believe) by > Pauli Virtanen and the project itself is co-mentored by Chuck Harris and > me. > > > > Evgeni > > PS Big thank you for making AlgoPy! > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alec.kalinin at gmail.com Tue Aug 11 06:54:50 2015 From: alec.kalinin at gmail.com (Alexander Kalinin) Date: Tue, 11 Aug 2015 10:54:50 +0000 Subject: [SciPy-User] Examples how to call NumPy from C++ Message-ID: Dear SciPy users, I have some software in C++. A want to call NumPy python procedures from C++, for example some matrix multiplication procedures. Does anybody know some examples how to pass arrays from C++ to NumPy and call procedure like matrix multiplication? Sincerely, Alexander -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Aug 11 17:23:08 2015 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 11 Aug 2015 15:23:08 -0600 Subject: [SciPy-User] ANN: Numpy 1.10.0b1 release Message-ID: Hi All, give this release a whirl and report any problems either on the numpy-discussion list or by opening an issue on github. I'm pleased to announce the first beta release of Numpy 1.10.0. There is over a year's worth of enhancements and bug fixes in the 1.10.0 release, so please give this release a whirl and report any problems either on the numpy-discussion list or by opening an issue on github. Tarballs, installers, and release notes may be found in the usual place at Sourceforge . Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.barker at noaa.gov Wed Aug 12 16:58:54 2015 From: chris.barker at noaa.gov (Chris Barker) Date: Wed, 12 Aug 2015 13:58:54 -0700 Subject: [SciPy-User] Examples how to call NumPy from C++ In-Reply-To: References: Message-ID: On Tue, Aug 11, 2015 at 3:54 AM, Alexander Kalinin wrote: > Dear SciPy users, > > I have some software in C++. A want to call NumPy python procedures from > C++, for example some matrix multiplication procedures. > > Does anybody know some examples how to pass arrays from C++ to NumPy and > call procedure like matrix multiplication? > Step one -- figure out how to call Python from C++ -- look for "embedding" -- though you may be better off hosting the process with Python, and and callig teh C++ code from there, it's generally easier. Step two-- figure out how to get C+= and Python (numpy) to "talk" to each other. This can be done with the C API and numpy's C API -- and it is not too hard, but most of us find it easier and less error-prone to use a tool for the interface. I think Cython is the best option, but as C++ person, you may prefer boost-python Have fun! -CHB -- 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 at noaa.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From sturla.molden at gmail.com Wed Aug 12 18:28:43 2015 From: sturla.molden at gmail.com (Sturla Molden) Date: Wed, 12 Aug 2015 22:28:43 +0000 (UTC) Subject: [SciPy-User] Examples how to call NumPy from C++ References: Message-ID: <213502131461110918.763161sturla.molden-gmail.com@news.gmane.org> Alexander Kalinin wrote: > I have some software in C++. A want to call NumPy python procedures from > C++, for example some matrix multiplication procedures. If you want matrix multiplication in C++ you are better off using CBLAS (e.g. Intel MKL, OpenBLAS, Apple Accelerate Framework), Eigen or BLISS. If you need more linear algebra there is LAPACKE. That said, to call NumPy from C++ you must either embed the Python interpreter in your C++ program or extend Python with C++. The most relevant options are Python C API, PyCXX, Boost.Python, SIP, Swig, or Cython. Personally I prefer PyCXX or Cython, but it is a matter of taste. Sturla From alec.kalinin at gmail.com Thu Aug 13 04:40:38 2015 From: alec.kalinin at gmail.com (Alexander Kalinin) Date: Thu, 13 Aug 2015 08:40:38 +0000 Subject: [SciPy-User] Examples how to call NumPy from C++ In-Reply-To: <213502131461110918.763161sturla.molden-gmail.com@news.gmane.org> References: <213502131461110918.763161sturla.molden-gmail.com@news.gmane.org> Message-ID: Thank you very much for answers! I have a little bit more complicated algorithm in NumPy than simple matrix multiplication. I have a big software in C++ and want to integrate some new math. First idea was to prototype algorithm in NumPy and next rewrite it on C++. But in NumPy implementation suddenly becomes very clear and it works pretty fast! So my idea now to embed this algorithm in C++ directly. Yes, I known Swig, Cython and other tools. But all of them mostly do the reverse task: embed C++ into Python. I did now found any detailed examples how to solve my task: embed Python into C++. So I found only two candidates: Python C API and boost.python with pretty new addon boot.numpy. But also there is a lack of examples how to pass and return complex numpy structures to C++. But I believe I am not a first one who what to call NumPy from C++. May be somebody already played with such tasks. Sincerely, Alexander On Thu, Aug 13, 2015 at 1:29 AM Sturla Molden wrote: > Alexander Kalinin wrote: > > > I have some software in C++. A want to call NumPy python procedures from > > C++, for example some matrix multiplication procedures. > > If you want matrix multiplication in C++ you are better off using CBLAS > (e.g. Intel MKL, OpenBLAS, Apple Accelerate Framework), Eigen or BLISS. If > you need more linear algebra there is LAPACKE. > > That said, to call NumPy from C++ you must either embed the Python > interpreter in your C++ program or extend Python with C++. The most > relevant options are Python C API, PyCXX, Boost.Python, SIP, Swig, or > Cython. Personally I prefer PyCXX or Cython, but it is a matter of taste. > > Sturla > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at seefeld.name Thu Aug 13 04:54:08 2015 From: stefan at seefeld.name (Stefan Seefeld) Date: Thu, 13 Aug 2015 04:54:08 -0400 Subject: [SciPy-User] Examples how to call NumPy from C++ In-Reply-To: References: <213502131461110918.763161sturla.molden-gmail.com@news.gmane.org> Message-ID: <55CC5B30.3060908@seefeld.name> On 13/08/15 04:40 AM, Alexander Kalinin wrote: > Thank you very much for answers! > > I have a little bit more complicated algorithm in NumPy than simple > matrix multiplication. I have a big software in C++ and want to > integrate some new math. First idea was to prototype algorithm in > NumPy and next rewrite it on C++. But in NumPy implementation suddenly > becomes very clear and it works pretty fast! So my idea now to embed > this algorithm in C++ directly. > > Yes, I known Swig, Cython and other tools. But all of them mostly do > the reverse task: embed C++ into Python. I did now found any detailed > examples how to solve my task: embed Python into C++. > > So I found only two candidates: Python C API and boost.python with > pretty new addon boot.numpy. But also there is a lack of examples how > to pass and return complex numpy structures to C++. > > But I believe I am not a first one who what to call NumPy from C++. > May be somebody already played with such tasks. Alexander, I have been using Boost.Python to bridge C++ and Python successfully. (I'm actually the maintainer of Boost.Python, and I have mentored some GSoC work on Boost.NumPy in the past.) I do know from my own experience that it's possible to share arrays between the C++ and Python runtimes (in both directions) without copies, so creating a C++ array and then expose that as a NumPy array to the Python runtime definitely works. For a more in-depth technical discussion I suggest the Boost.Python mailing list. Regards, Stefan -- ...ich hab' noch einen Koffer in Berlin... From njs at pobox.com Thu Aug 13 07:45:05 2015 From: njs at pobox.com (Nathaniel Smith) Date: Thu, 13 Aug 2015 11:45:05 +0000 Subject: [SciPy-User] Examples how to call NumPy from C++ In-Reply-To: References: <213502131461110918.763161sturla.molden-gmail.com@news.gmane.org> Message-ID: On Aug 13, 2015 1:44 AM, "Alexander Kalinin" wrote: > > Thank you very much for answers! > > I have a little bit more complicated algorithm in NumPy than simple matrix multiplication. I have a big software in C++ and want to integrate some new math. First idea was to prototype algorithm in NumPy and next rewrite it on C++. But in NumPy implementation suddenly becomes very clear and it works pretty fast! So my idea now to embed this algorithm in C++ directly. > > Yes, I known Swig, Cython and other tools. But all of them mostly do the reverse task: embed C++ into Python. I did now found any detailed examples how to solve my task: embed Python into C++. In general, embedding python in c/c++ is very similar to going the other way. Basically you just have to call a few functions to set up the python interpreter and then it's just the usual problems of calling python from C or vice versa, and you can use all the usual tools like cython or boost.python or whatever you like: https://docs.python.org/2/extending/embedding.html You might also want to seriously think turning things around and embedding your C++ library in python instead. It's a bit more work of you're starting from an existing C++ program, but there are a lot of advantages as well. This essay is very opinionated but does do a good job of explaining why this is worth considering: https://twistedmatrix.com/users/glyph/rant/extendit.html -n -------------- next part -------------- An HTML attachment was scrubbed... URL: From joferkington at gmail.com Sun Aug 16 20:03:47 2015 From: joferkington at gmail.com (Joe Kington) Date: Sun, 16 Aug 2015 19:03:47 -0500 Subject: [SciPy-User] ANN: mpldatacursor v0.6 - Interactive annotation boxes for Matplotlib Message-ID: Hi folks, mpldatacursor version 0.6 has been released (it's long overdue). mpldatacursor provides interactive ?data cursors? (clickable annotation boxes) for matplotlib. Major Changes in v0.6 Version 0.6 adds: - Better handling of date-formatted axes. - ?Popup? text boxes can be interactively hidden by right-clicking (controllable through the hide_button and display_button kwargs). - Proper support for twinned axes. - Better unicode support for the formatter function. Note that this makes mpldatacursor incompatibile with early 3.x versions (3.0, 3.1, and 3.2). However, it remains compatible with Python >= 3.3 (e.g. 3.3, 3.4, and 3.5) as well as 2.6 and 2.7. - Annotation boxes will now try to stay visible inside the figure by default. Specify keep_inside=False to disable this. - Added basic support for extracting the z-value of 3D artists. - Made the precision of the default x & y formatting depend on the range of the axes. - Full support for interactive IPython notebooks through the nbagg backend. Note that the performance on the nbagg may be very poor. - Workarounds for annotation issues in Matplotlib v1.4.3 - Numerous bugfixes (Thanks to everyone for the reports!). Basic Usage mpldatacursor offers a few different styles of interaction through the datacursor function. As an example, this displays the x, y coordinates of the selected artist in an annotation box: import matplotlib.pyplot as plt import numpy as np from mpldatacursor import datacursor data = np.outer(range(10), range(1, 5)) fig, ax = plt.subplots() lines = ax.plot(data) ax.set_title('Click somewhere on a line') datacursor(lines) plt.show() Installation mpldatacursor can be installed from PyPi using easy_install/pip/etc. (e.g. pip install mpldatacursor) or you may download the source and install it directly with python setup.py install. Thanks, -Joe -------------- next part -------------- An HTML attachment was scrubbed... URL: From gb.gabrielebrambilla at gmail.com Fri Aug 21 10:50:20 2015 From: gb.gabrielebrambilla at gmail.com (Gabriele Brambilla) Date: Fri, 21 Aug 2015 10:50:20 -0400 Subject: [SciPy-User] numpy.lexsort Message-ID: Hi I want to order a numpy.array using lexsort. >>> import numpy as np >>> surnames = ['Hertz', 'Galilei', 'Hertz'] >>> names = ['Heinrich', 'Galilao', 'Gustav'] >>> ind = np.lexsort((names,surnames)) >>> ind array([1, 2, 0]) But how can I have an array ordered according to this indexes? I would do surnames2 = surnames.copy() for i, a in enumerate(ind): surnames2[i] = surnames[a] But I think there should be another way without writing the cycle by myself. Thanks GB -------------- next part -------------- An HTML attachment was scrubbed... URL: From guziy.sasha at gmail.com Fri Aug 21 11:53:12 2015 From: guziy.sasha at gmail.com (Oleksandr Huziy) Date: Fri, 21 Aug 2015 11:53:12 -0400 Subject: [SciPy-User] numpy.lexsort In-Reply-To: References: Message-ID: Hi: Here's a way I found in documentation (tested on py3): In [1]: import numpy as np In [2]: surnames = ['Hertz', 'Galilei', 'Hertz'] In [3]: names = ['Heinrich', 'Galilao', 'Gustav'] In [4]: arr = np.fromiter(zip(surnames, names), dtype=[("lastname", "S100"), ("firstname", "S100")]) In [5]: arr Out[5]: array([(b'Hertz', b'Heinrich'), (b'Galilei', b'Galilao'), (b'Hertz', b'Gustav')], dtype=[('lastname', 'S100'), ('firstname', 'S100')]) In [6]: arr.sort() In [7]: surnames2 = arr["lastname"]; names2 = arr["firstname"] In [8]: surnames2 Out[8]: array([b'Galilei', b'Hertz', b'Hertz'], dtype='|S100') In [9]: names2 Out[9]: array([b'Galilao', b'Gustav', b'Heinrich'], dtype='|S100') Cheers 2015-08-21 10:50 GMT-04:00 Gabriele Brambilla < gb.gabrielebrambilla at gmail.com>: > Hi I want to order a numpy.array using lexsort. > > >>> import numpy as np > > >>> surnames = ['Hertz', 'Galilei', 'Hertz'] > > >>> names = ['Heinrich', 'Galilao', 'Gustav'] > > >>> ind = np.lexsort((names,surnames)) > > >>> ind > > array([1, 2, 0]) > > But how can I have an array ordered according to this indexes? > > I would do > > surnames2 = surnames.copy() > > for i, a in enumerate(ind): > > surnames2[i] = surnames[a] > > But I think there should be another way without writing the cycle by > myself. > > Thanks > > GB > > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > -- Sasha -------------- next part -------------- An HTML attachment was scrubbed... URL: From woshi1984lian at 163.com Mon Aug 24 11:29:12 2015 From: woshi1984lian at 163.com (=?GBK?B?xdPQobfm?=) Date: Mon, 24 Aug 2015 23:29:12 +0800 (CST) Subject: [SciPy-User] cross-compile support In-Reply-To: <551fee5c.1514d.14f5f06e434.Coremail.woshi1984lian@163.com> References: <551fee5c.1514d.14f5f06e434.Coremail.woshi1984lian@163.com> Message-ID: <34622c30.18b2d.14f6053dabb.Coremail.woshi1984lian@163.com> Hi: I am a scipy user who needs scipy ,pandas and numpy to resolve a problem related to calssification.The algorithm used is SVM. My question is as follows: scipy and other related project can support cross-compiling with mips64-octeon or not ? If yes,what should i do ? Many thanks! Xiaofeng ???????????1? ???????????1? ???????????1? -------------- next part -------------- An HTML attachment was scrubbed... URL: From cournape at gmail.com Tue Aug 25 21:03:22 2015 From: cournape at gmail.com (David Cournapeau) Date: Wed, 26 Aug 2015 02:03:22 +0100 Subject: [SciPy-User] cross-compile support In-Reply-To: <34622c30.18b2d.14f6053dabb.Coremail.woshi1984lian@163.com> References: <551fee5c.1514d.14f5f06e434.Coremail.woshi1984lian@163.com> <34622c30.18b2d.14f6053dabb.Coremail.woshi1984lian@163.com> Message-ID: Hi Xiaofeng, I am afraid there is no support for cross compiling numpy, scipy and pandas, so you are on your own there. David On Mon, Aug 24, 2015 at 4:29 PM, ??? wrote: > Hi: > > I am a scipy user who needs scipy ,pandas and numpy to resolve a problem > related to calssification.The algorithm used is SVM. > My question is as follows: > scipy and other related project can support cross-compiling > with mips64-octeon or not ? > If yes,what should i do ? > > Many thanks! > > Xiaofeng > > > ???????????1? > > > > ???????????1? > > > > > ???????????1? > > > > ???????????1? > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: