Mailman 3 December 2015 - NumPy-Discussion

Numpy 1.10.2rc2 released
by Charles R Harris 09 Dec '15

09 Dec '15

Hi All, I'm pleased to announce the release of Numpy 1.10.2rc2. After two months of stomping bugs I think the house is clean and we are almost ready to put it up for sale. However, bugs are persistent and may show up at anytime, so please inspect and test thoroughly. Windows binaries and source releases can be found at the usual place on Sourceforge <https://sourceforge.net/projects/numpy/files/NumPy/1.10.2rc2/>. If there are no reports of problems in the next week I plan to release the final. Further bug squashing will be left to the 1.11 release except possibly for regressions. The release notes give more detail on the changes. *bon appétit,* Chuck

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Memory mapping and NPZ files
by Mathieu Dubois 09 Dec '15

09 Dec '15

Dear all, If I am correct, using mmap_mode with Npz files has no effect i.e.: f = np.load("data.npz", mmap_mode="r") X = f['X'] will load all the data in memory. Can somebody confirm that? If I'm correct, the mmap_mode argument could be passed to the NpzFile class which could in turn perform the correct operation. One way to handle that would be to use the ZipFile.extract method to write the Npy file on disk and then load it with numpy.load with the mmap_mode argument. Note that the user will have to remove the file to reclaim disk space (I guess that's OK). One problem that could arise is that the extracted Npy file can be large (it's the purpose of using memory mapping) and therefore it may be useful to offer some control on where this file is extracted (for instance /tmp can be too small to extract the file here). numpy.load could offer a new option for that (passed to ZipFile.extract). Does it make sense? Thanks in advance, Mathieu

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array of random numbers fails to construct
by DAVID SAROFF (RIT Student) 08 Dec '15

08 Dec '15

This works. A big array of eight bit random numbers is constructed: import numpy as np spectrumArray = np.random.randint(0,255, (2**20,2**12)).astype(np.uint8) This fails. It eats up all 64GBy of RAM: spectrumArray = np.random.randint(0,255, (2**21,2**12)).astype(np.uint8) The difference is a factor of two, 2**21 rather than 2**20, for the extent of the first axis. -- David P. Saroff Rochester Institute of Technology 54 Lomb Memorial Dr, Rochester, NY 14623 david.saroff(a)mail.rit.edu | (434) 227-6242

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Re: [Numpy-discussion] Q: Use of scipy.signal.bilinear
by R Schumacher 08 Dec '15

08 Dec '15

Sorry - I'll join there. - Ray At 10:00 AM 12/8/2015, you wrote: >On Tue, Dec 8, 2015 at 9:30 AM, R Schumacher ><<mailto:rays@blue-cove.com>rays(a)blue-cove.com> wrote: >We have a function which describes a frequency >response correction to piezo devices we use. To >flatten the FFT, it is similar to: >Cdis_t = .5 >N = 8192 >for n in range(8192): >Â B3 = n * 2560 / N >Â Fc(n) = 1 / >((B3/((1/(Cdis_t*2*pi))**2+B3**2)**0.5)*(-0.01*log(B3) + 1.04145)) > >In practice it really only matters for low frequencies. > >I suggested that we might be able to do a time >domain correction as a forward-reverse FFT >filter using the function, but another said it >can also be applied in the time domain using a bilinear transform. >So, can one use ><http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.signal.bil…>http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.signal.bil… >and, how does one generate b,a from the given >Fourrier domain flattening function? > > >This should go to either ><mailto:scipy-user@scipy.org>scipy-user(a)scipy.org > or <mailto:scipy-dev@scipy.org>scipy-dev(a)scipy.org > >Chuck >_______________________________________________ >NumPy-Discussion mailing list >NumPy-Discussion(a)scipy.org >https://mail.scipy.org/mailman/listinfo/numpy-discussion

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Q: Use of scipy.signal.bilinear
by R Schumacher 08 Dec '15

08 Dec '15

We have a function which describes a frequency response correction to piezo devices we use. To flatten the FFT, it is similar to: Cdis_t = .5 N = 8192 for n in range(8192): B3 = n * 2560 / N Fc(n) = 1 / ((B3/((1/(Cdis_t*2*pi))**2+B3**2)**0.5)*(-0.01*log(B3) + 1.04145)) In practice it really only matters for low frequencies. I suggested that we might be able to do a time domain correction as a forward-reverse FFT filter using the function, but another said it can also be applied in the time domain using a bilinear transform. So, can one use http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.signal.bil… and, how does one generate b,a from the given Fourrier domain flattening function? I'd guess someone here has done this... - Ray

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Re: [Numpy-discussion] Where is Jaime?
by Peter Creasey 08 Dec '15

08 Dec '15

>> > >> > Is the interp fix in the google pipeline or do we need a workaround? >> > >> >> Oooh, if someone is looking at changing interp, is there any chance >> that fp could be extended to take complex128 rather than just float >> values? I.e. so that I could write: >> >> >>> y = interp(mu, theta, m) >> rather than >> >>> y = interp(mu, theta, m.real) + 1.0j*interp(mu, theta, m.imag) >> >> which *sounds* like it might be simple and more (Num)pythonic. > > That sounds like an excellent improvement and you should submit a PR > implementing it :-). > > "The interp fix" in question though is a regression in 1.10 that's blocking > 1.10.2, and needs a quick minimal fix asap. > Good answer - as soon as I hit 'send' I wondered how many bugs get introduced by people trying to attach feature requests to bug fixes. I will take a look at the code later and pm you if I get anywhere... Peter

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Where is Jaime?
by Charles R Harris 07 Dec '15

07 Dec '15

Anyone hear from Jaime lately? He seems to have gone missing. Chuck

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Re: [Numpy-discussion] NumPy-Discussion Digest, Vol 111, Issue 9
by Sydney Shall 07 Dec '15

07 Dec '15

On 07/12/2015 09:38, numpy-discussion-request(a)scipy.org wrote: > Message: 4 > Date: Sun, 06 Dec 2015 22:01:40 -0500 > From: "DAVID SAROFF (RIT Student)"<dps7802(a)rit.edu> > To: Discussion of Numerical Python<numpy-discussion(a)scipy.org> > Cc: Stefi Baum<stefibaumodea(a)gmail.com> > Subject: Re: [Numpy-discussion] array of random numbers fails to > construct > Message-ID: > <CABMftcSkX9kL=G2sepOn80YCKQygFGHa7WBdmAxy3_1iVAtJcw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Allan, > > I see with a google search on your name that you are in the physics > department at Rutgers. I got my BA in Physics there. 1975. Biological > physics. A thought: Is there an entropy that can be assigned to the dna in > an organism? I don't mean the usual thing, coupled to the heat bath. > Evolution blindly explores metabolic and signalling pathways, and tends > towards disorder, as long as it functions. Someone working out signaling > pathways some years ago wrote that they were senselessly complex, branched > and interlocked. I think that is to be expected. Evolution doesn't find > minimalist, clear, rational solutions. Look at the amazon rain forest. What > are all those beetles and butterflies and frogs for? It is the wrong > question. I think some measure of the complexity could be related to the > amount of time that ecosystem has existed. Similarly for genomes. Dear David, You are mistaken in this remark in your message; > Evolution blindly explores metabolic and signalling pathways, and > tends towards disorder, as long as it functions. In fact, biological evolution does just the opposite. It overcomes disorder and creates complexity at the expense of 'pulling in' energy from the outside, from the environemnt. Of course you are correct that biological evolution does NOT look for nor does it achieve optimum solutions. It merely replaces current mechanism with another mechanism biologically derived from the current mechanism, provided only that the replacement mechanism is marginally, fractionally superior in the totality of the life of the ecosystem. Have a good day, Sydney -- Sydney

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Re: [Numpy-discussion] Where is Jaime?
by Peter Creasey 06 Dec '15

06 Dec '15

> > Is the interp fix in the google pipeline or do we need a workaround? > Oooh, if someone is looking at changing interp, is there any chance that fp could be extended to take complex128 rather than just float values? I.e. so that I could write: >>> y = interp(mu, theta, m) rather than >>> y = interp(mu, theta, m.real) + 1.0j*interp(mu, theta, m.imag) which *sounds* like it might be simple and more (Num)pythonic. Peter

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Travis is busted.
by Charles R Harris 05 Dec '15

05 Dec '15

Just to note that travis is broken at the moment, it can't find the whitelisted gfortran package.

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