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328 discussions

copying algorithms: GNU Scientific Library vs Numerical Recipes
by Boud Roukema 19 Nov '04

19 Nov '04

Witam, What can be legally (and morally) copied from a program under a restrictive copyright is "the algorithms, the ideas" but not the particular way of expressing them. So the practical question is: where is the borderline? In the GSL (GNU Scientific Library), http://www.gnu.org/software/gsl/, GNU provides, e.g. in Version 1.1.1, the version below of NR's ran0 routine. i'm sure most of us have access to a legal copy of the NR routine, or else a little googling shows e.g. http://cc.oulu.fi/~tf/tiedostot/pub/nrf/ran0.f Well, to me these look extremely similar to one another. Even the constants: static const long int m = 2147483647, a = 16807, q = 127773, r = 2836; static const unsigned long int mask = 123459876; are exactly identical to those in the NR routines, they even have the same names, except for the "i". Is this really a different "expression"? In any case, IMHO noone can deny that the authors of the GSL routines (there is also ran1, ran2, ran3) have very likely had access to the NR source code. Sure, they translated it to C and added some stuff, but it's the same algorithm, it's essentially the same sequence of steps. Anyway, GSL has lots of really cool stuff. :) Let's defend scientific software freedom! pozdr boud ---------------------------------------------------------------------- /* rng/ran0.c * * Copyright (C) 1996, 1997, 1998, 1999, 2000 James Theiler, Brian Gough * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. */ #include <config.h> #include <stdlib.h> #include <gsl/gsl_errno.h> #include <gsl/gsl_rng.h> /* This is an implementation of the algorithm used in Numerical Recipe's ran0 generator. It is the same as MINSTD with an XOR mask of 123459876 on the seed. The period of this generator is 2^31. Note, if you choose a seed of 123459876 it would give a degenerate series 0,0,0,0, ... I've made that into an error. */ static inline unsigned long int ran0_get (void *vstate); static double ran0_get_double (void *vstate); static void ran0_set (void *state, unsigned long int s); static const long int m = 2147483647, a = 16807, q = 127773, r = 2836; static const unsigned long int mask = 123459876; typedef struct { unsigned long int x; } ran0_state_t; static inline unsigned long int ran0_get (void *vstate) { ran0_state_t *state = (ran0_state_t *) vstate; const unsigned long int x = state->x; const long int h = x / q; const long int t = a * (x - h * q) - h * r; if (t < 0) { state->x = t + m; } else { state->x = t; } return state->x; } static double ran0_get_double (void *vstate) { return ran0_get (vstate) / 2147483647.0 ; } static void ran0_set (void *vstate, unsigned long int s) { ran0_state_t *state = (ran0_state_t *) vstate; if (s == mask) { GSL_ERROR_VOID ("ran0 should not use seed == mask", GSL_EINVAL); } state->x = s ^ mask; return; } static const gsl_rng_type ran0_type = {"ran0", /* name */ 2147483646, /* RAND_MAX */ 1, /* RAND_MIN */ sizeof (ran0_state_t), &ran0_set, &ran0_get, &ran0_get_double}; const gsl_rng_type *gsl_rng_ran0 = &ran0_type; ----------------------------------------------------------------------

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puzzled about healpix software and Numerical Recipes
by Boud Roukema 17 Nov '04

17 Nov '04

Witam, i am aware that at least one person felt that an earlier version of a package i released contained "expressions (particularly any arbitrary or stylistic choices)" identical to those in Numerical Recipes routines. My own judgment had been that the expression was different, only the "ideas, methodology and algorithm" were identical to the Numerical Recipes routines. In NR's own words, this is perfectly acceptable within the definition of copyright. And, of course, there were clear warnings that the code was inspired from NR. Nevertheless, i followed the concern, and stopped distribution. In order to avoid any ambiguity, i (and any other volunteers) will rework the code using routines from the GSL (GNU Scientific Library): http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/ComputerLanguages… which Michał Frąckowiak brought to our attention :)) and will reexpress any remaining algorithms, possibly changing the algorithms themselves, even though this is not necessary. However, you might want to note that there seems to be something curious about a certain non-free package called Healpix_1.20. i suggest to people with a copy of this package to have a look at two files, which, apparently, exist in this package: Healpix_1.20/src/f90/mod/num_rec.f90 and also at the copyright notice Healpix_1.20/READ_Copyrights_Licenses.txt and then to look at the Numerical Recipes guidelines for redistributing their routines, whether binary or as source code: http://www.numerical-recipes.com/com/info-permissions.html Apparently, the file Healpix_1.20/src/f90/mod/num_rec.f90 contains the source code for the routines: dsvbksb dpythag dsvdcmp isort A quick search on google on, e.g., "dsvbksb" shows that NR probably cannot control distribution of these files: http://www.google.pl/search?hl=pl&q=dsvbksb&btnG=Szukaj+z+Google&lr= Nevertheless, there *are*, apparently, NR routines provided as source code in the file Healpix_1.20/src/f90/mod/num_rec.f90 which is *claimed* to be NR code, including one-line copyright notices from NR. In principle, redistributing NR routines without permission from NR is a violation of copyright - stating the copyright notice is not enough to satisfy NR. Of course, it could, in principle, be the case that the Healpix collaboration have paid "a fixed fee" for this and have permission to redistribute. However, first note the cases in which NR provides permission: http://www.numerical-recipes.com/com/info-permissions.html > if you want to make available to your users a subset of Recipes in > object, or individually callable, form, but not including source > code. We consider such requests on a case-by-case basis, with > permission more likely when they are for fewer than 20 Recipes used in > this manner. > > * In most cases of specialized software, we charge only a nominal > flat fee per Recipe for each use (unlimited number of copies). > > * The copyright notice is required, as above, and we also request that > the printed manual contain words to the effect "the procedures [your > procedure identifiers] are based on routines in Numerical Recipes: The > Art of Scientific Computing, published by Cambridge University Press, > and are used by permission." Note: "not including source code". Also: the full copyright notice (not just one line, see "EXACT WORDING OF REQUIRED COPYRIGHT NOTICES" on http://www.numerical-recipes.com/com/info-permissions.html ) is required. However, for distributing *source code*: > Finally, there is the case where our source code, or source code > based in copyright on our code, is to be made available to users. We > consider these requests on a case-by-case basis, but the success > rate of these requests is not high. ... > # If permission is given, you will need to include a notice similar > to the sample below as a comment in each routine that is based on a > Numerical Recipes routine. So Healpix_1.20 could, in principle, redistribute NR source code (probably for a fixed fee). However, this is only considered "on a case-by-case basis" and "the success rate of these requests is not high". Moreover, there would need to be the full copyright notice, and, apparently, the file Healpix_1.20/READ_Copyrights_Licenses.txt does not contain any reference to Numerical Recipes. Also, the full copyright notice needs to be included "as a comment in each routine". (GNU recommends including a big copyright announcement at the top of each routine, not just one line.) There could be one way around this: since Healpix is non-free, and requires personal email between applicants and authors, the authors could restrict distribution to people who declare that they already have access to a legal copy of NR. i'm not sure if NR would be happy, but it might work. However, this is not our problem. But it does demonstrate why an open model of code development has advantages: people worried about copyright issues are more likely to speak up earlier in an open model compared to a non-free model. Now that Healpix is so widely used, the authors might have a problem negotiating with NR based on the large number of copies already distributed. It would seem to me that their options are either to negotiate with NR and pay whatever fee is required (i'm sure ESO could pay this), or else to rewrite the parts that need NR recipes. Of course, that is their problem, not ours. pozdr boud PS: It would also seem that Healpix has been using Mahatma Gandhi's "illegal civil disobedience" technique in protest against the patent on the LZW compression algorithm for making gif files. This file Healpix_1.20/src/f90/lib/gd.c apparently contains the ppmtogif.c code The code itself is freely redistributable. However, *usage* of the code was probably illegal, since the *algorithm* was patented. This is different from copyright, which only protects the expression of an algorithm and not the algorithm itself. See http://netpbm.sourceforge.net/doc/ppmtogif.html > If you use ppmtogif without the -nolzw option, you are using a > patent on the LZW compression method which is owned by Unisys, and > in all probability you do not have a license from Unisys to do > so. Unisys typically asks $5000 for a license for trivial use of the > patent. Unisys has never enforced the patent against trivial > users. The patent expired in the US in 2003 and is due to expire in > other countries in 2004. So the patent has now expired (e.g. http://news.bbc.co.uk/1/hi/technology/3007862.stm ) but for many years, more "conservative" GNU/Linux groups like GNU, Debian recommended using PNG instead of GIF, or else used a pseudo-GIF format. More radical software groups and probably millions and millions of users (probably including you!) simply used the algorithm despite the patent. A big battle is continuing against software patents in Europe. Go to http://kwiki.ffii.org/SwpatplEn to see info on what Polish poseł in the European parliament are doing or http://kwiki.ffii.org/FfiiprojEn or http://www.gnu.org/server/takeaction.pl.html for more on what you can do concretely.

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looking for hints on velocity distribution of electrons in relativistic jets
by Bartosz Lew 12 Nov '04

12 Nov '04

Hi everybody, I'm interested if anybody has some quick nice references or ideas regarding - as in the subject - what the velocities in relativistic jets can be - what this can depend on from theoretical considerations/modelling? The bottom line is, can we have some constrainst on these velocities from models, or models and ovservations (if so - what observables are needed) and what this can depend on ? Is it very bad to assume that these can span from say some arbitrary value to one in \beta space with flat statistical distribution ? Can we have some hints on this distribution ? Motyl, I could use your help here ? I don't have time for getting through tons of papers. Bartek

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Fw: mobcap
by Walker Albert 09 Nov '04

09 Nov '04

I noticed this email in my inbox, is this what you meant? http://www.yourrealworkscenter.com/info.html You can download full CD's, dvd's and games. Ive downloaded 6 dvd's so far. Once you've seen it get ahold of me, I want to hear your reaction - you'll go batty I know it. They walk you through the entire process of burning them to CD. I know this, the movie section has movies in it that are still in theates - I dont know about you but thats seriously impressive. See you this weekend. Candy

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isolat-0.1.10.tar.gz ready for testing and comments, feedback
by Boud Roukema 08 Nov '04

08 Nov '04

Witam, A GNU GPL (not GNU, just GNU GPL!) package which implements the algebra in A Solution to the Isolatitude, Equi-area, Hierarchical Pixel-Coordinate System http://de.arxiv.org/abs/astro-ph/0409533 is now ready. I've put it here: http://cosmo.torun.pl/GPLdownload/dodec/isolat-0.1.10.tar.gz It would be nice to have some precise, constructive comments regarding this. (Sure, negative criticisms are also welcome, but are most useful when accompanied by constructive suggestions...) Today is Mon 8 November. If there are no objections within a week, i.e. before Mon 15 November, then i will make a more formal proposal (with deadline two weeks later) for a formal consensus decision about continued distribution of the isolat package under the GNU GPL. i realise that this open method of communication means that we give a chance to "competitors"; however, i think it is best to trust in an open community. Most of us want to do good, free (as in speech) astronomy research, so IMHO we should trust our peers. In the long term, there will be more benefits than problems IMHO. BTW, just a reminder once again: http://cosmo.torun.pl/pipermail/cosmo-torun/2004-October/000269.html Numerical Recipes: http://www.library.cornell.edu/nr/bookfpdf/f0-1.pdf ; Copyright does not protect ideas, but only the expression of those ; ideas in a particular form. In the case of a computer program, the ideas ; consist of the program's methodology and algorithm, including the ; necessary sequence of steps adopted by the programmer. The expression of ; those ideas is the program source code (particularly any arbitrary or ; stylistic choices embodied in it), its derived object code, and any ; other derivative works. ; ; If you analyze the ideas contained in a program, and then express those ; ideas in your own completely different implementation, then that new ; program implementation belongs to you. That is what we have done for those ; programs in this book that are not entirely of our own devising. Isolat is *not* based on analysing the ideas in a certain non-free code which will remain unnamed here, though it *is* based on the algebraic solution to an electronically published sphere-pixelisation system. However, even if it *were* based on analysing the ideas in a certain non-free code, there would be no copyright problem, since to the best of my knowledge, the code is a "completely different implementation" to that non-free code. Of course, it must be more or less equivalent in the basic "ideas", even though the methodology and algorithm is almost certainly different, given the way the algebra is written in the paper inspired from our paper: http://de.arxiv.org/abs/astro-ph/0409513 Nevertheless, if anybody is concerned about this, please *look at the code*, don't just rely on rumours of A said that B said that C said that ... . The code is here: http://cosmo.torun.pl/GPLdownload/dodec/isolat-0.1.10.tar.gz The library part of the code is the part which codes the actual pixel number <-> spherical coordinate calculations. There is lib/getang.f pixel -> angular coordinates and lib/getpix.f angular coordinates -> pixel and lib/fr2pol.f converts a fraction in the square to phi/pi, sin(th) or inversely The total number of lines in these three routines, apart from comments and blank lines can be found by typing: cat lib/getang.f lib/getpix.f lib/fr2pol.f |grep -v "^[cC]" |grep -v "^$" |wc It is: 409 lines, 1240 words. That's not much. If anyone finds anything in these 409 lines which is considered to be "an expression (particularly any arbitrary or stylistic choices)" similar to that in any non-free software package, please say so and we can correct this. Simply making vague comments is not going to be constructive. The code is there and corrections can of course be made: this is the whole idea of GNU GPL, the idea of coming up with perfect code right from the beginning is not the way the system works. pozdr boud

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PROPOSED new list for skeptics discussion DEADLINE Thu 11 Nov 18:00
by Boud Roukema 04 Nov '04

04 Nov '04

Witam, Bartek is interested in opening a discussion list on adjani for something like a "sceptics' society". Sceptics' societies around the world are a mix of scientists and ordinary citizens curious about claims of events seen outside of the laboratory which seem to violate the known laws of physics, e.g. walking on hot coals and not having your feet burnt, UFOs, crop circles, etc. Have a look at http://www.skeptic.com and you'll see that even the aliens are convinced that the skeptics exist ;). The goal is to show to society that scientists are not just "dogmatic believers" who refuse to believe in events outside of our "narrow-minded" way of thinking, and to treat the claims seriously, and this way educate the public into the scientific method, maybe help develop better intuition of statistics and probability among ordinary people. There is a prize of Aus$100 000 (about 250 000 PLN) waiting since 1980 for someone able to prove they have psychic or paranormal powers: http://www.skeptics.com.au/features/challenge.htm There is also a US$1M prize (about 4 000 000 PLN): http://en.wikipedia.org/wiki/James_Randi#The_.241_million_challenge Some astronomers (e.g. Jayant Narlikar in India) are strongly supportive of skeptics' societies. And, who knows, a skeptics society might just possibly discover a real effect showing the next step beyond the Standard Models of physics and cosmology. (OK, personally i'm rather sceptical, but my mind is open, in principle...) Since this *could* be controversial, and i'm trying to implement consensus-method decision-making, here is the proposal: ###################################################################### PROPOSAL: new list for skeptics discussion DEADLINE Thu 11 Nov 18:00 We'll open a mailing list on adjani with a name like sceptyk-l at cosmo.torun.pl and Bartek will be the list admin. Purpose of list: discussion group to see if people in Toruń, especially scientists, are willing to spend the time setting up properly controlled experiments, writing them up properly, doing the proper statistical analyses, communicating them in public meetings etc., and communicating with other skeptics' groups around the world - especially if someone wants to try for the 250.000 PLN Australian prize money or the 4 000 000 PLN James Randi Foundation prize money. ###################################################################### Like any discussion group, IMHO it is most likely to be efficient if it is self-organising, and it will only work if there are enough people willing to spend enough time on it. But it can't hurt trying. pozdr boud

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wrapped space
by Bartosz Lew 28 Oct '04

28 Oct '04

interesting... http://edition.cnn.com/2004/TECH/space/10/21/warped.spaceII/index.html BL

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propozycji tematy licencjat/magister
by Boud Roukema 22 Oct '04

22 Oct '04

Witam, Propozycji dla licencjat/magister są tu: http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/LicMag Dzięki do Bartka dla komentarza :) Andrzej Strobel: Żeby możesz klejić do dokumenta tekstowy, treści jest tu, na dolę. pozdr boud ---------------------------------------------------------------------- Supervisor: B. Roukema (boud at astro.uni.torun.pl) Number of students: up to 3-4 students is possible Observational Cosmology Masters/Licencjat Project - General Outline Description: There are many possible projects which could be done as a master's thesis project, in using publicly available archival data from observational surveys to constrain one or more of the local or global cosmological parameters, either those related to shape (curvature, topology) or maybe also those unrelated to shape ("dark energy" or "dark matter"). The precise projects would be chosen in discussion with the masters students during Nov-Dec 2004. Please see http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/CosmoProjects for projects Boud is working on and http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/CosmoNews for ideas on the hottest topics in cosmology research - any of these would be appropriate if the student is sufficiently interested. Examples (1) Topology of the Universe Detection * In http://de.arxiv.org/abs/astro-ph/0402608, it seems that we may have measured the shape of the Universe, since certain parts of the cosmic microwave background seen by the WMAP satellite appear to be seen twice in different directions on the sky, due to topological lensing. The purpose of the masters/licencjat project is: * Aim: Propose and apply a further test using WMAP data which further tests the hypothesis. This requires: o Reading/writing/managing the WAMP data file with free software computer programs o Statistical analysis o Independently checking that the computer code does the algebraic and statistical analyses correctly (2) Dark Matter Detection * In http://de.arxiv.org/abs/astro-ph/0405282 the 7 year results of the DAMA/NaI dark matter direct detection experiment show a signal significant at 6.3? according to the authors. An explanation for why a signal from mirror-baryonic matter should be expected in this experiment but not in others with similar cross-section detection parameters is presented in http://de.arxiv.org/abs/0403043. * Aim: Check the experimental and theoretical claims and propose further tests o Try to find an alternative explanation for the DAMA/NaI results without going beyond the Standard Model of particle physics o Check whether the Foot et al. calculations of mirror matter properties are consistent with all the experimental data as the authors claim o Extend the Foot et al. calculations to find, e.g. a non-gravitational effect of mirror matter in stellar physics, e.g. symbiotic stars (gravitational effects of dark matter are already well studied) * More info: http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/NonBaryonicDarkMa… (3) Cosmic String Detection * In http://de.arxiv.org/abs/astro-ph/0410073 Kibble discusses the http://de.arxiv.org/abs/astro-ph/302547 possible detection of a cosmic string which seems to gravitationally lens a background galaxy (Sazhin et al.) In http://de.arxiv.org/abs/astro-ph/0406516 the extra pairs of lensed galaxies predicted by the hypothesis are discussed. * Aim: Understand the basics about (1) cosmic strings, (2) gravitational lensing versus cosmic string lensing, and test the hypothesis o Calculate the probability of seeing the original pair by chance o Check whether the statistics of expected numbers of lensed images are correct o Propose an independent test of the hypothesis, e.g. using radio observations and prepare an observing proposal General Requirements: * basic knowledge in astronomy, physics, mathematics, computing skills * desire to measure something about the shape of the Universe and/or dark matter or dark energy and/or cosmic strings * willingness both to learn from and to teach others interested in observational cosmology at TCfA * willingness to learn the following practical skills: touch-typing, emacs, \LaTeX, usage of wikis and/or mailing lists for communication, GPL compatible programming * participation in the "Shape of the Universe" monograph course and/or Bronek Rudak's semester 9 "Kosmologia" course: o http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/MonographCosmo o http://www.ncac.torun.pl/~bronek/KOS.html * Nie ma problemu jeśli student magistera lub licjencacki (jeszcze) nie dobrze mówi po angielsku, ale potrzeba znać czytać i rozumieć po angielski naukowcy ----------------------------------------------------------------------

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projects for licencjat/magister students
by Boud Roukema 21 Oct '04

21 Oct '04

witam, Apparently i should give this to Andrzej Strobel "before the end of the week" - i guess this means tomorrow (Friday) afternoon is OK. http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/LicMag i've including internal twiki links with the full URL so that Andrzej Strobel will (hopefully) include this in the text he distributes. Any comments (you could edit the twiki directly if you wish...)? pozdr boud

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cosmic string detection from close pairs of galaxies ?
by Boud Roukema 21 Oct '04

21 Oct '04

Witam, We have an interesting candidate for Dark Matter. It seems there is also an interesting candidate for cosmic string detection: http://adjani.astro.uni.torun.pl/cgi-bin/twiki/view/Cosmo/CosmoNews#cosmic_… (i've shifted CosmoNews to the twiki, so that it's easier to edit etc.) pozdr boud

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