[SciPy-user] 2d interpolation (Michael Hearne)
Alex Liberzon
alex.liberzon at gmail.com
Wed Aug 1 17:43:00 EDT 2007
It doesn't fit because xi and yi are 1:.5:4 in Matlab but 0:.5:3 in Python
I tested it with
outgrid(arange(1,4.1,.5),arange(1,4.1,.5)) and the result is the same
as in Matlab.
Best
Alex
On 8/2/07, scipy-user-request at scipy.org <scipy-user-request at scipy.org> wrote:
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> Today's Topics:
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> 1. Re: Ant Colony Optimization (Alan G Isaac)
> 2. Re: General Python Question: nested function calls (Ryan Krauss)
> 3. Re: General Python Question: nested function calls
> (Gael Varoquaux)
> 4. Re: Finding Neighboors (Barry Wark)
> 5. Re: Finding Neighboors (jelle)
> 6. Re: Testing BOF at scipy'07? (Fernando Perez)
> 7. 2d interpolation (Michael Hearne)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Aug 2007 15:58:34 -0400
> From: Alan G Isaac <aisaac at american.edu>
> Subject: Re: [SciPy-user] Ant Colony Optimization
> To: scipy-user at scipy.org
> Message-ID: <Mahogany-0.67.0-1600-20070801-155834.00 at american.edu>
> Content-Type: TEXT/PLAIN; CHARSET=UTF-8
>
> On Wed, 01 Aug 2007, "Brandon C. Nuttall" apparently wrote:
> > Is there an implementation of the Ant Colony Optimization
> > routines available in Python? See
> > http://www.aco-metaheuristic.org/
>
> You could wrap the C code at:
> http://www.aco-metaheuristic.org/aco-code/public-software.html
>
> fwiw,
> Alan Isaac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Aug 2007 14:56:59 -0500
> From: "Ryan Krauss" <ryanlists at gmail.com>
> Subject: Re: [SciPy-user] General Python Question: nested function
> calls
> To: "SciPy Users List" <scipy-user at scipy.org>
> Message-ID:
> <c5b438120708011256x2d0ebbeaw79d2514b285f21b at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> That would have been a better solution in this case - I have done that
> before and don't know why I didn't here.
>
> Any thoughts on the same situation with calling a parent class's
> method. I just wrote code that did this:
> def __init__(self, pathin=None, dialect=spreadsheet.tabdelim):
> ....
> spreadsheet.SpreadSheet.__init__(self, pathin=pathin,
> skiprows=0, collabels=collabels, colmap=colmap, datafunc=float,
> picklekeys=['t','lg','a','v0'])
>
> Basically, I do a few other things and then call the parent's __init__
> somewhere in the middle.
>
> On 8/1/07, Robert Kern <robert.kern at gmail.com> wrote:
> > Ryan Krauss wrote:
> > > I often write code something like this:
> > >
> > > def TruncatePickleFile(pathin, trigname='a', trigtype='sw',
> > > savepath=None, threshlevel=None, duration=0.05, backup=0.01):
> > > """Trunate the pickleddatafile whose path is pathin. If
> > > trigtype=='lg', use a DropDownLightGateTrigger, else use a
> > > standard Trigger."""
> > > untrunc = pickleddatafiles.PickledDataFile(pathin)
> > > mytrunc = pickleddatafiles.TruncateDataObj(untrunc,
> > > threshlevel=threshlevel, backup=backup, duration=duration)
> > > mytrunc.chname = trigname
> > > if trigtype == 'lg':
> > > mytrunc.SetupTrigger(DataProcMixins.DropDownLightGateTrigger)
> > > else:
> > > mytrunc.SetupTrigger()
> > > mytrunc.SetupTruncChannel()
> > > mytrunc.Truncate()
> > > pathout = mytrunc.Pickle(savepath)
> > > return pathout
> > >
> > > def TruncatePickleFiles(listin, trigname='a', trigtype='sw',
> > > threshlevel=None, duration=0.05, backup=0.01):
> > > listout = []
> > > for item in listin:
> > > print item
> > > curpath = TruncatePickleFile(item, trigname=trigname,
> > > trigtype=trigtype, threshlevel=threshlevel, duration=duration,
> > > backup=backup)
> > > listout.append(curpath)
> > > return listout
> > >
> > > where TruncatePickleFiles is sort of just a vectorization of
> > > TruncatePickleFile, but with some of the keyword args set. My problem
> > > is not that this might not be the fastest way to execute the code, but
> > > that I get tired of doing this kind of stuff:
> > >
> > > curpath = TruncatePickleFile(item, trigname=trigname,
> > > trigtype=trigtype, threshlevel=threshlevel, duration=duration,
> > > backup=backup)
> > >
> > > but I also don't want to just do
> > >
> > > def TruncatePickleFiles(listin, **kwargs):
> > >
> > > because I like to see the defaults and know what keyword arguments are legal.
> > >
> > > Does anyone else have this problem or have an elegant solution to it?
> > > The problem comes up for me also when I want a derived class to call a
> > > parent class's method in some partially overwritten method of the
> > > derived class.
> > >
> > > Ideally, I think I would like to pass **kwargs to the nested function,
> > > but without using **kwargs in the definition of the top function, if
> > > that makes any sense.
> >
> > There isn't really a straightforward solution.
> >
> > However, for something like this, you may want to consider just implementing one
> > version of the function which can take either a list of filenames or a single
> > filename.
> >
> > --
> > Robert Kern
> >
> > "I have come to believe that the whole world is an enigma, a harmless enigma
> > that is made terrible by our own mad attempt to interpret it as though it had
> > an underlying truth."
> > -- Umberto Eco
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 1 Aug 2007 22:22:32 +0200
> From: Gael Varoquaux <gael.varoquaux at normalesup.org>
> Subject: Re: [SciPy-user] General Python Question: nested function
> calls
> To: SciPy Users List <scipy-user at scipy.org>
> Message-ID: <20070801202232.GB29 at clipper.ens.fr>
> Content-Type: text/plain; charset=iso-8859-1
>
> On Wed, Aug 01, 2007 at 02:56:59PM -0500, Ryan Krauss wrote:
> > That would have been a better solution in this case - I have done that
> > before and don't know why I didn't here.
>
> > Any thoughts on the same situation with calling a parent class's
> > method. I just wrote code that did this:
> > def __init__(self, pathin=None, dialect=spreadsheet.tabdelim):
> > ....
> > spreadsheet.SpreadSheet.__init__(self, pathin=pathin,
> > skiprows=0, collabels=collabels, colmap=colmap, datafunc=float,
> > picklekeys=['t','lg','a','v0'])
>
> > Basically, I do a few other things and then call the parent's __init__
> > somewhere in the middle.
>
> I had a similar problem recently and resolved it using a complex
> machinery (my requirements where a bit more complex than only this). I
> used traits, but you could do this without traits (though it would be
> harder).
>
> The thread concerning this problem and its solution can be found at
> https://mail.enthought.com/pipermail/enthought-dev/2007-August/007820.html
>
> This is heavy machinery, but there are some ideas to steal.
>
> Ga?l
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 1 Aug 2007 13:31:58 -0700
> From: "Barry Wark" <barrywark at gmail.com>
> Subject: Re: [SciPy-user] Finding Neighboors
> To: "SciPy Users List" <scipy-user at scipy.org>
> Message-ID:
> <cd7634ce0708011331pee2ede1y39e2e03fbb0a31bf at mail.gmail.com>
> Content-Type: text/plain; charset=WINDOWS-1252
>
> Hi all,
>
> Catching this conversation late. As jelle points out, BioPython has a
> k-d tree implemetation, but it hasn't been converted to numpy yet (I
> think it still uses Numeric). I've written a SWIG (with numpy type
> maps) wrapper around the Approximate Nearest Neighbor library
> (http://www.cs.umd.edu/~mount/ANN/), which includes both exact and
> approximate k-d tree searches. Email me off list if you would like a
> copy of the swig definition files. If there's interest, I will send it
> on to the ANN writers for inclusion in the library itself.
>
> Barry
>
> On 7/31/07, Emanuele Zattin <emanuelez at gmail.com> wrote:
> > Hi, you might want to take a look at kd-trees. No implementation in
> > scipy, but it should not be too hard to achieve. As far as i can
> > remember its definition in wikipedia includes some python code. Just
> > my 2 cents :)
> >
> > On 8/1/07, Matthieu Brucher <matthieu.brucher at gmail.com> wrote:
> > > Hi,
> > >
> > > I have an implementation, but it depends on my own matrix library... That's
> > > a stopper... But it works.
> > > I do not know the other templated matrix libraries very well, but I'd say I
> > > do not need much to make it work with another library.
> > >
> > > Matthieu
> > >
> > > 2007/8/1, Alan G Isaac <aisaac at american.edu>:
> > > > On Tue, 17 Apr 2007, Matthieu Brucher apparently wrote:
> > > > > I wanted to know if there was a module in scipy that is able to find the
> > > > > k-neighboors of a point ?
> > > > > If so, is there an optimized one - tree-based search - ?
> > > > > If not, I'm doing the optimized version.
> > > >
> > > > Hi Matthieu,
> > > >
> > > > Where did you go with this?
> > > >
> > > > Thanks!
> > > > Alan
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > SciPy-user mailing list
> > > > SciPy-user at scipy.org
> > > > http://projects.scipy.org/mailman/listinfo/scipy-user
> > > >
> > >
> > >
> > > _______________________________________________
> > > SciPy-user mailing list
> > > SciPy-user at scipy.org
> > > http://projects.scipy.org/mailman/listinfo/scipy-user
> > >
> > >
> >
> >
> > --
> > Emanuele Zattin
> > ---------------------------------------------------
> > -I don't have to know an answer. I don't feel frightened by not
> > knowing things; by being lost in a mysterious universe without any
> > purpose ? which is the way it really is, as far as I can tell,
> > possibly. It doesn't frighten me.- Richard Feynman
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 1 Aug 2007 21:06:22 +0000 (UTC)
> From: jelle <jelleferinga at gmail.com>
> Subject: Re: [SciPy-user] Finding Neighboors
> To: scipy-user at scipy.org
> Message-ID: <loom.20070801T230532-760 at post.gmane.org>
> Content-Type: text/plain; charset=us-ascii
>
> Terrific!
> ANN seems like a very useful module Barry!
> Thanks for pointing out!
>
> Cheers,
>
> -jelle
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 1 Aug 2007 15:14:25 -0600
> From: "Fernando Perez" <fperez.net at gmail.com>
> Subject: Re: [SciPy-user] Testing BOF at scipy'07?
> To: "SciPy Users List" <scipy-user at scipy.org>
> Message-ID:
> <db6b5ecc0708011414n6545fe0fx359fe3615db310ee at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On 8/1/07, Karl Young <Karl.Young at ucsf.edu> wrote:
> >
> > Sounds great to me; I need to learn a lot more about developing good
> > testing practices (given that it doesn't conflict with the planned 3D
> > visualization BOF on Thursday evening as I've already agreed to be
> > counted for that).
>
> No worries, I also said I'd go to the Thursday viz one as well.
>
> I wonder if we could plan on 2 bofs a night. Titus is already signed
> up as moderator for one on Thursday:
>
> http://scipy.org/SciPy2007/BoFs
>
> and I'd like to have him in for the testing one as well. If we could
> plan something like
>
> bof1 bof2
>
> 7-8 vis3d bio
> 8-9 testing astronomy
>
> then we could have Titus available for both and those of us who said
> yes to the vis3d one could also go to testing.
>
> Else we put the other bofs on Wednesday night, at the risk of getting
> less people in. Friday is probably out, since a lot of people leave
> then...
>
> Opinions?
>
> f
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 1 Aug 2007 15:15:22 -0600
> From: Michael Hearne <mhearne at usgs.gov>
> Subject: [SciPy-user] 2d interpolation
> To: scipy-user at scipy.org
> Message-ID: <6F6365AF-B63F-4D6D-99BA-39D47179DA31 at usgs.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> All: I'm trying to use interp2d to replicate behavior in Matlab.
>
> The Matlab script:
> x = reshape(1:16,4,4)';
> xi = 1:0.5:4;
> yi = [1:0.5:4]';
> z = interp2(x,xi,yi,'linear')
>
> which results in the matrix:
> z =
>
> 1.0000 1.5000 2.0000 2.5000 3.0000 3.5000 4.0000
> 3.0000 3.5000 4.0000 4.5000 5.0000 5.5000 6.0000
> 5.0000 5.5000 6.0000 6.5000 7.0000 7.5000 8.0000
> 7.0000 7.5000 8.0000 8.5000 9.0000 9.5000 10.0000
> 9.0000 9.5000 10.0000 10.5000 11.0000 11.5000 12.0000
> 11.0000 11.5000 12.0000 12.5000 13.0000 13.5000 14.0000
> 13.0000 13.5000 14.0000 14.5000 15.0000 15.5000 16.0000
>
> I had thought the following Python/numpy script would be equivalent,
> but it is not:
> from scipy.interpolate import interpolate
> from numpy.random import randn
> from numpy import *
>
> data = arange(16)
> data = data+1
> data = data.reshape(4,4)
> xrange = arange(4)
> yrange = arange(4)
> X,Y = meshgrid(xrange,yrange)
>
> outgrid = interpolate.interp2d(X,Y,data,kind='linear')
> xi = array([0,0.5,1,1.5,2,2.5,3])
> yi = xi
>
> z = outgrid(xi,yi)
>
> This results in the matrix:
> [[ 1. 1.10731213 2. 2.89268787 3.
> 3.25045605
> 4. ]
> [ 3. 2.57118448 4. 5.42881552 5.
> 4.90975947
> 6. ]
> [ 5. 4.03505682 6. 7.96494318 7.
> 6.56906289
> 8. ]
> [ 7. 5.49892917 8. 10.50107083 9.
> 8.22836631
> 10. ]
> [ 9. 6.96280152 10. 13.03719848 11.
> 9.88766973
> 12. ]
> [ 11. 8.42667386 12. 15.57332614 13.
> 11.54697315
> 14. ]
> [ 13. 9.89054621 14. 18.10945379 15.
> 13.20627657
> 16. ]]
>
> (Incidentally, is there a way to pretty-print arrays in numpy? The
> above is kind of ugly and hard to read)
>
> Is this some kind of spline interpolation that I don't understand?
>
> Thanks,
>
> Mike Hearne
>
>
>
>
>
>
> ------------------------------------------------------
> Michael Hearne
> mhearne at usgs.gov
> (303) 273-8620
> USGS National Earthquake Information Center
> 1711 Illinois St. Golden CO 80401
> Senior Software Engineer
> Synergetics, Inc.
> ------------------------------------------------------
>
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