Mailman 3 September 2006 - SciPy-User

cobyla help
by joe stano 01 Oct '06

01 Oct '06

Hi there I am very new to python but have found myself in way over my head. I am trying to perform a constrained optimization using fmin_cobyla and am running into some problems. I was wondering if you may have some examples that I could review. Especially examples that use a list of constraint functions that take inputs from the function that is being optimized. I am a novice who is just trying to learn about python and programming in general. I am working with numpy arrays and when I run my program without the optimization everything seems to run ok. However, when I include the optimization, when I multiply 2 arrays together (element wise not using dot()), I get a (ValueError: shape mismatch: objects cannot be broadcast to a single shape) error message that confuses me as I don't get it when I simply run the program and print out the results. When I exclude the optimization, and print just the array that I pass to the function, it looks like how I define it (N x N array). But when I include the optimization and print what I pass from the function before the code crashes, it no longer looks like how I define it (i.e., 1 x more then N array). Which is why I think I get the shape error. I know that I am calling the optimization wrong so I figured I would give you a snapshot of what I am trying to do, and maybe you can tell what I am doing wrong in calling the optimization. I have attached some of the code with a description of the arrays. Any advice or help you could give would be greatly appreciated. Thanks either way, joe

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Debian Sarge and Python
by Seweryn Kokot 29 Sep '06

29 Sep '06

Hello, I've started reading this group for 5 days and I find the discussions really interesting. For some time I also started with Python and looking forward to replacing Matlab with SciPy/Matplotlib and friends. The problem is that I'm using Debian Sarge and the packages are so outdated especially in the case of SciPy and Matplotlib which are in continous and fast progress. Of course I could compile all the packages myself but I'm wondering if there are some other Debian Sarge users and how they cope with the problem? Any suggestions? Regards, Seweryn Kokot

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Debug console - Re: Pros and Cons of Python verses other array environments
by Bill Baxter 29 Sep '06

29 Sep '06

On 9/29/06, Ryan May <rmay(a)ou.edu> wrote: > Bill Baxter wrote: > > 2) integration of debugging is not as good as matlab. In matlab when > > you stop at a breakpoint in your code, you get an interactive console > > where you can probe current values in your program, or create new ones > > etc. The Wing IDE has this, but I couldn't find any open source IDEs > > that did this. > > > You might try the Eric IDE: > http://www.die-offenbachs.de/detlev/eric3.html > > The GUI is a little complicated/full, but now that I've started to get > the hang of it, I really like it. Instead of a console, it gives you a > list of locals and globals while in debug mode. Thanks. A number of free IDEs provied a list of watch variables or locals&globals (Wing included). But a list of variables isn't quite the same as being able to interactively test out functions and expressions on the values in question. That's what the debug console is great for. Oops! Got an error. Bad syntax, huh? Hmm, is this right? No, what about this? Nope. This? yeh that's it! Ok great. Fix code. Rerun. I think the PyDev eclipse plugin actually has this now, but didn't when I was shopping around. Either way, Eclipse has a pretty steep learning curve. Anyway, I went ahead and bought a license for Wing. I think it was well worth it. Far cheaper than a license for Matlab, anyway. :-) The only thing it seems to lack that I would expect from a commercial IDE is tooltips to show the values of variables. --bb

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malloc incorrect checksum for freed object error using delaunay module
by Aaron Hoover 29 Sep '06

29 Sep '06

Hi all, I'm using SciPy 0.5.1 with the delaunay module built from source on OS X (Intel Mac). I'm also using iPython 0.7.2, NumPy 1.0.5b, and matplotlib 0.87.5 (all built from source). I'm having the strangest problem - I've been able to use the delaunay function in delaunay.triangulate just fine up until recently when I triangulated a fairly large data set (2M points). The triangulation succeeded (but took a while, of course), but now whenever I attempt to use the delaunay function again, I get the following error: Python(288,0xa000cf60) malloc: *** error for object 0x1b47e00: incorrect checksum for freed object - object was probably modified after being freed, break at szone_error to debug Python(288,0xa000cf60) malloc: *** set a breakpoint in szone_error to debug Then, iPython dies with a "Bus error." Rebooting does not help My question is twofold. Does anyone know what causes this error? (Google turned up an enormous variety of sources for this error in just about all software that uses malloc.h). And, is it possible to fix this without rebuilding SciPy. Rebuilding isn't really *that* big of a deal, but I'd like to know if there's an easier solution in case this thing rears its ugly head in the future. Thanks, Aaron

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Webpage
by Travis Oliphant 29 Sep '06

29 Sep '06

Oh yeah! Here's the link: http://www.scipy.org/NumPyProConPage

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python crash in leastsq
by djf＠pdx.edu 29 Sep '06

29 Sep '06

I receive a segmentation fault from the following code: from scipy.optimize import * from scipy import * # Fit Mean of A*x to Mean of B---------- #-------------------------------------- def fit(x): d=mean(x*A)-mean(B) return d #-------------------------------------- A=[1,2] B=[3,4] x0=[1] (x,msg)=leastsq(fit,x0) print x Any advice? thanks, djoefish

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Does scipy have a function to...?
by Bill Dandreta 28 Sep '06

28 Sep '06

What I want is a smooth curve that serves as an upper limit for a data plot. I would like it to be close to the data at the local maxima. Does such a function exist? Bill

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Bilinear Interpolation
by Ryan May 28 Sep '06

28 Sep '06

Hi, Is there function for doing a simple bilinear interpolation in scipy? I tried the interpolate.interp2d routines, but it appears that it uses B-splines even when kind='linear' is specified. (I wouldn't otherwise care except that my class assignment explicitly says to use bilinear.) I know I can do this using a series of interp1d calls, but I wanted to see if there was a simpler way I was missing. Thanks Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma (405)325-3791 rmay(a)rossby.ou.edu

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Re: [SciPy-user] Interpolation using splines -> possible solution
by Ewald Zietsman 27 Sep '06

27 Sep '06

Hi, Thank you for trying this out on your computers. The code I posted works on my computer at home but not on my office computer. I noticed that at home matplotlib uses numpy ( Numerix = numpy ) and at the office it is numarray I think. I recompiled matplotlib with numpy as numerix and the problem disappeared. Hope this can help someone. Cheers -Ewald

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Interpolation using splines
by Ewald Zietsman 26 Sep '06

26 Sep '06

Hi all, I'm trying to fit a cubic spline to a data set. I can't seem to get the functions in scipy.interpolate (splrep and splev) to work correctly ( I'm probably being stupid). When I do the following, #! /usr/bin/python from scipy import interpolate from pylab import * x = arange(0.0,2.0*pi+pi/4.0,2.0*pi/8.0) y = sin(x) tck = interpolate.splrep(x,y,s=0.0) xnew = arange(0.0,2.0*pi+pi/4.0,pi/50.0) ynew = interpolate.splev(xnew,tck,der=0.0) plot(x,y,'x') plot(xnew,ynew,'r-') show() I should get a plot showing a sin curve made of blue x's and a smooth red line which is the spline. However, the spline seems to be zero except for one place where it spikes. I'm using scipy 0.5.0 and matplotlib 0.87.3 with python 2.4.3 on Fedora Core 5. Any help on this will be appreciated. -Ewald

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