Mailman 3 September 2008 - SciPy-User

[numerical optimization] OpenOpt release v 0.19
by dmitrey Sept. 15, 2008

Sept. 15, 2008

Hi all, I'm glad to inform you about new OpenOpt release: v 0.19. http://openopt.blogspot.com/2008/09/openopt-release-019.html OpenOpt is free (license: BSD) numerical optimization with lots of 3rd party solvers connected (some are C or Fortran written) and some own ones, graphic output and lots of other numerical optimization "MUST HAVE" features. For more details see OpenOpt's - homepage: http://scipy.org/scipy/scikits/wiki/OpenOpt - foreword: http://scipy.org/scipy/scikits/wiki/OOForeword Regards, Dmitrey.

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How to give a name to a figure?
by Mathieu Dubois Sept. 15, 2008

Sept. 15, 2008

Hi, I'm a beginner in scipy and I have a small problem with figures. Let me explain. I have to plot complicated data so I have a lot of figures. I have set title and axes names. My problem is that the windows are titled with things like 'Figure 1', 'Figure 2' etc. Is it possible to set this name to something more understable? Apparently title() changes the name of the plots inside the figure. My goal is to save (with savefig()) them with a nice name say 'title.png' (where title would be replaced by the title of my figure). Any help would be appreciated. Thanks in advance, Mathieu

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trouble building scipy on mac os 10.5 intel
by George Dahl Sept. 15, 2008

Sept. 15, 2008

Hi everyone. I get the following result when I run python setup.py build for scipy 0.6.0. I have numpy and it works in python2.5, which is the version of python I want to use scipy from. I have gcc 4.0.1 and gfortran 4.2.1. I have pasted some of the output of python setup.py build below. I don't really know what I am doing, but I would really like to get scipy working and I would appreciate any help anyone can give me! I looked around in the archives with google a bit, but nothing seemed to deal with my situation exactly, hopefully I didn't miss anything. - George scipy-0.6.0$ python setup.py build . . . bnrm2,resid,info = dstoptest2(r,b,bnrm2,tol,info) Constructing wrapper function "cstoptest2"... bnrm2,resid,info = cstoptest2(r,b,bnrm2,tol,info) Constructing wrapper function "zstoptest2"... bnrm2,resid,info = zstoptest2(r,b,bnrm2,tol,info) Wrote C/API module "_iterative" to file "build/src.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/scipy/linalg/iterative/_iterativemodule.c" adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.5' to include_dirs. building extension "scipy.linsolve._zsuperlu" sources building extension "scipy.linsolve._dsuperlu" sources building extension "scipy.linsolve._csuperlu" sources building extension "scipy.linsolve._ssuperlu" sources building extension "scipy.linsolve.umfpack.__umfpack" sources creating build/src.macosx-10.3-fat-2.5/scipy/linsolve creating build/src.macosx-10.3-fat-2.5/scipy/linsolve/umfpack adding 'scipy/linsolve/umfpack/umfpack.i' to sources. swig: scipy/linsolve/umfpack/umfpack.i swig -python -o build/src.macosx-10.3-fat-2.5/scipy/linsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.3-fat-2.5/scipy/linsolve/umfpack scipy/linsolve/umfpack/umfpack.i scipy/linsolve/umfpack/umfpack.i:192: Error: Unable to find 'umfpack.h' scipy/linsolve/umfpack/umfpack.i:193: Error: Unable to find 'umfpack_solve.h' scipy/linsolve/umfpack/umfpack.i:194: Error: Unable to find 'umfpack_defaults.h' scipy/linsolve/umfpack/umfpack.i:195: Error: Unable to find 'umfpack_triplet_to_col.h' scipy/linsolve/umfpack/umfpack.i:196: Error: Unable to find 'umfpack_col_to_triplet.h' scipy/linsolve/umfpack/umfpack.i:197: Error: Unable to find 'umfpack_transpose.h' scipy/linsolve/umfpack/umfpack.i:198: Error: Unable to find 'umfpack_scale.h' scipy/linsolve/umfpack/umfpack.i:200: Error: Unable to find 'umfpack_report_symbolic.h' scipy/linsolve/umfpack/umfpack.i:201: Error: Unable to find 'umfpack_report_numeric.h' scipy/linsolve/umfpack/umfpack.i:202: Error: Unable to find 'umfpack_report_info.h' scipy/linsolve/umfpack/umfpack.i:203: Error: Unable to find 'umfpack_report_control.h' scipy/linsolve/umfpack/umfpack.i:215: Error: Unable to find 'umfpack_symbolic.h' scipy/linsolve/umfpack/umfpack.i:216: Error: Unable to find 'umfpack_numeric.h' scipy/linsolve/umfpack/umfpack.i:225: Error: Unable to find 'umfpack_free_symbolic.h' scipy/linsolve/umfpack/umfpack.i:226: Error: Unable to find 'umfpack_free_numeric.h' scipy/linsolve/umfpack/umfpack.i:248: Error: Unable to find 'umfpack_get_lunz.h' scipy/linsolve/umfpack/umfpack.i:272: Error: Unable to find 'umfpack_get_numeric.h' error: command 'swig' failed with exit status 1

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Help: building scipy+numpy locally on x86_64 running Centos
by Francis Drossaert Sept. 15, 2008

Sept. 15, 2008

Hi everybody, I am trying to install python2.5/scipy/numpy/sympy/matplotlib locally, because of various reasons. I am not root. At home I am using Ubuntu and I am root and everything works as it should. So far I managed to make python2.5, sympy and ipython to run fine on my computer at work, but I am struggling to make numpy+scipy since I am trying to install it locally. The problem is likely the lapack+atlas build. I have followed the build by hand instructions on http://www.scipy.org/Installing_SciPy/Linux. I am not getting any errors during the build and install. However after installing I tried to import numpy in python and received to following error: ImportError: /users/francisd/local/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_ Googling this error, it seems that the error is caused by having a wrong lapack version. I am running Centos 5 (basically Red Hat Enterprise Linux 5) on a x86_64 machine. Does anybody know how I can get the right version, by changing some flags, or whatever? FYI I have added the -m64 flag for the lapack build, but no change. Cheers, Francis

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Breaking up an array of indices into contiguous/ strided chunks
by Anand Patil Sept. 15, 2008

Sept. 15, 2008

Hi all, I have an array of indices that I want to use as a slice, but cvxopt sparse matrices don't seem to take fancy slices so I need to take the slice manually. If I just do it element-by-element in a for-loop it's extremely slow. I know that the array of indices is in ascending order, but that's all. Does anyone know an easy way to break it up into strided chunks that are as big as possible? Thanks, Anand

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2-D interpolation of irregularly spaced data
by Emmanuelle Gouillart Sept. 15, 2008

Sept. 15, 2008

Hello, I have an irregular 2-D mesh, and 1-D data measured at the vertices of the mesh (the mesh is finer where the data vary more rapidly), and I need to interpolate the data at other (also irregularly spaced) points. To do so, I use the delaunay scikit and its NNInterpolator which can take an iregular mesh. The problem is that I cannot call the interpolator with irregularly spaced points, so that my code is running very slowly now. Here is a minimal example of what I do now (with regular grids and few points for clarity): *** import scikits.delaunay as d def evolve(positions, mesh, values): tri = d.Triangulation(mesh[0], mesh[1]) interpolator = d.NNInterpolator(tri, values) return array([interpolator(x,y) for (x,y) in positions.T]).ravel() #Mesh X, Y = mgrid[-1:1:20j, -1:1:20j] #regular grid for clarity X = X.flatten() Y = Y.flatten() mesh = array([X,Y]) #Values values = Y**2 #Positions positions = mgrid[-0.5:0.5:20j, -0.5:0.5:20j] positions = array([positions[0].flatten(), positions[1].flatten()]) new_values = evolve(positions, mesh, values) *** Any hints about I could accelerate the interpolation? (Usually, I work with meshes of size ~1.e4 and positions of size ~1.e6). Any help will be very welcome! Cheers, Emmanuelle

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ipython install: egg not python 2.4 compatible
by joep Sept. 14, 2008

Sept. 14, 2008

Sorry for wrong group: I'm not subscribed to ipython-user: ipython-0.9-py2.4.egg uses features from python 2.5: error messages with easy_install:: C:\Programs\Python24\Scripts\easy_install-script.py -U C:\Josef\work- oth\sort\pypi\ipython-0.9-py2.4.egg Processing ipython-0.9-py2.4.egg creating c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg Extracting ipython-0.9-py2.4.egg to c:\programs\python24\lib\site- packages File "c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg \IPython\con fig\config.py", line 49 with raw(self): ^ SyntaxError: invalid syntax File "c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg \IPython\fro ntend\linefrontendbase.py", line 192 finally: ^ SyntaxError: invalid syntax File "c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg \IPython\fro ntend\prefilterfrontend.py", line 207 finally: ^ SyntaxError: invalid syntax SyntaxError: ('future feature with_statement is not defined',) File "c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg \IPython\ker nel\tests\test_contexts.py", line 28 with parallel as pr: ^ SyntaxError: invalid syntax File "c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg \share\doc\i python\examples\kernel\nwmerge.py", line 48 toadd = (key(item), i, item, itr) if key else (item, i, itr) ^ SyntaxError: invalid syntax Adding ipython 0.9 to easy-install.pth file Installing iptest-script.py script to C:\Programs\Python24\Scripts Installing iptest.exe script to C:\Programs\Python24\Scripts Installing ipythonx-script.py script to C:\Programs\Python24\Scripts Installing ipythonx.exe script to C:\Programs\Python24\Scripts Installing ipcluster-script.py script to C:\Programs\Python24\Scripts Installing ipcluster.exe script to C:\Programs\Python24\Scripts Installing ipython-script.py script to C:\Programs\Python24\Scripts Installing ipython.exe script to C:\Programs\Python24\Scripts Installing pycolor-script.py script to C:\Programs\Python24\Scripts Installing pycolor.exe script to C:\Programs\Python24\Scripts Installing ipcontroller-script.py script to C:\Programs \Python24\Scripts Installing ipcontroller.exe script to C:\Programs\Python24\Scripts Installing ipengine-script.py script to C:\Programs\Python24\Scripts Installing ipengine.exe script to C:\Programs\Python24\Scripts Installed c:\programs\python24\lib\site-packages\ipython-0.9-py2.4.egg Processing dependencies for ipython==0.9 Finished processing dependencies for ipython==0.9

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step size using optimize.fmin
by SimonPalmer Sept. 14, 2008

Sept. 14, 2008

Hi, I have a weird and lumpy N-D function that I am trying to minimize using optimize.fmin. The problem I am having is that the step size that fmin uses is fixed and not quite big enough to move the function value sufficiently far to examine a different "state", so the function terminates (cleanly) presuming it is on a flat surface. I have been looking through the code and I can't see a way of adjusting the step size, which seem to be magic numbers in the code: nonzdelt = 0.05 zdelt = 0.00025 I guess what I am looking for is one of: a) a way to set these to be a slightly larger value b) a callback to be able to adjust them if the convergence criteria are met but nothing has changed (i.e. a flat surface) c) a different minimmisation algorithm which has momentum I am also contemplating d) change my function so that it is somewhat more continuous in nature e) hack a local copy of fmin but I would rather not do either unless I have to. Anyone have any recommendations? Am I reading fmin right? tia Simon

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Re: [SciPy-user] scale arrays with interpolation
by Alex Liberzon Sept. 14, 2008

Sept. 14, 2008

Hi Fabian Fortunately, I'm from the same field so I think I understand what you're talking about :-) If I translate your wish is:: a) find the location and the value of the maximum of the y_array => local_max b) half_width is the x_array value at the position of the maximum of y_array If this is true, then you'd better use numpy arrays and not lists: # starting from your lists: x_array = asarray(x_array).astype('f') # array of floats y_array = asarray(y_array).astype('f') half_width = x_array[argmax(y_array)] scaled_x_array = x_array/half_width scaled_y_array = y_array/max(y_array) plot(scaled_x_array,scaled_y_array,'o') Hope it helps, Alex

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scale arrays with interpolation
by Fabian Braennstroem Sept. 13, 2008

Sept. 13, 2008

Hi, in fluid dynamics one often plots velocity distribution scaled by some reference to take a look at self-similarity. E.g. for free jets one can extract the velocity across the plot, which gives two different arrays; an x_array and an y_array, where the x_array corresponds to the position and the y_array to the velocity at this position. So one would get two arrays of the same size: x_array=[ 1,2,3,4,5,6,7,8,9,10] y_array=[ 0,1,1,2,5,2,1,1,1,1] For the visualization of self-similar behavior one scales the y_array with the local maximum (in this case 5) and the x_array with the position, where the velocity is the half of the maximum. This means one has to calculate the half velocity (5/2=2.5) and has to interpolate the position of this value to get the position (in this case it is somewhere between 4 and 5). This half-width position would be used to scale the x_array. At the end one gets: x_array_scaled= [1/half_width_position, 2/half_with_position,...,10/half_width_position] y_array_scaled= [0/local_max,1/local_max,...,1/local_max] Does anyone have a suggestion how to do this? The major problem is how to get the 'half_width_position'. Would be nice, if anyone has an idea! Greetings! Fabian

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