Mailman 3 January 2002 - SciPy-User

problem with using scipy.io.mio on Windows
by Herb Schilling 17 Jan '02

17 Jan '02

Hello, I am using scipy.io.mio to read in binary PLOT3D files. Everything works fine when I run my code on an SGI but when I run it under Windows 98 I have problems. ( I am using Windows native, not-cygwin Python 2.1 ). Here is the basic code I am using import scipy.io.mio # open the file fileHandle = scipy.io.mio.fopen( filePath, 'r' , format = 'b' ) # read in the total number of blocks in this file numberOfBlocks = fileHandle.fread( 1 , 'l' ) # Read in the size of each block imaxes = [] jmaxes = [] for iBlock in range( numberOfBlocks ) : imax = fileHandle.fread( 1 , 'l' ) jmax = fileHandle.fread( 1 , 'l' ) imaxes.append( imax ) jmaxes.append( jmax ) # Read in the X,Y coordinates of the points in the grids for iBlock in range( numberOfBlocks ) : imax = imaxes[ iBlock ] jmax = jmaxes[ iBlock ] # Note that we do want the transposed form xGrid = fileHandle.fread( ( jmax, imax ) , 'f' , 'f' ) yGrid = fileHandle.fread( ( jmax, imax ) , 'f' , 'f' ) The number of blocks, and the size of each block is read in just fine. When I start to read the X,Y coordinates things go bad. In the case where the file has 5 blocks, I get the following errors and the values for the xGrid and yGrid are, as you would expect, zeros after reading in the first xGrid. numpyio: Warning: 30060 bytes requested, 12 bytes read. numpyio: Warning: 30060 bytes requested, 0 bytes read. numpyio: Warning: 11084 bytes requested, 0 bytes read. numpyio: Warning: 11084 bytes requested, 0 bytes read. numpyio: Warning: 36816 bytes requested, 0 bytes read. numpyio: Warning: 36816 bytes requested, 0 bytes read. numpyio: Warning: 34160 bytes requested, 0 bytes read. numpyio: Warning: 34160 bytes requested, 0 bytes read. numpyio: Warning: 34160 bytes requested, 0 bytes read. numpyio: Warning: 34160 bytes requested, 0 bytes read. I am using the same code and the same file on both the PC and the SGI and I can use "od" to see that there is more data to be read. Even fileHandle.size() returns 292604. Why can't the rest of the bytes be read ? What's different under Windows? Thanks in advance! -- --------------------------------- Herb Schilling NASA Glenn Research Center Cleveland, OH 44135 Herbert.W.Schilling(a)grc.nasa.gov It is not enough to run, one must start in time. - teabag

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Unit tests for compile_code.py returns ImportError
by Louis Luangkesorn 17 Jan '02

17 Jan '02

Hello When I ran the scipy.test_all() after installing everything, I get the failure at the bottom of this message. [ImportError: DLL load failed: Invalid access to memory location.] When I had MINGW installed incorrectly, the compile tests actually succeded (although it did not compile the code and ran those tests as straight python), so the problem is probably with how it interacts with gcc. I'm using gcc 2.95.3-4 (mingw special) which is from mingw-1.0-20010608 Am I missing anything? Thanks Louis <'No test suite found' and 'creating test suite' messages snipped> No test suite found for scipy.special No test suite found for scipy.stats ...................................................................................................... Expression: result[1:-1,1:-1] = (b[1:-1,1:-1] + b[2:,1:-1] + b[:-2,1:-1]+ b[1:-1,2:] + b[1:-1,:-2]) / 5. Run: (10, 10) f Compiling code. This may take a few minutes running build_ext building 'sc_1184ec2786fc765046a8e2929d8c9a2642' extension c:\apps\gccmingw\bin\gcc.exe -mno-cygwin -mdll -O2 -w -IC:\apps\Python\scipy\compiler\blitz-20001213 -IC:\apps\Python\scipy\compiler\scxx -IC:\APPS\Python\Include -c C:\DOCUME~1\kll560\LOCALS~1\Temp\sc_1184ec2786fc765046a8e2929d8c9a2642.cpp -o C:\DOCUME~1\kll560\LOCALS~1\Temp\Release\sc_1184ec2786fc765046a8e2929d8c9a2642.o writing C:\DOCUME~1\kll560\LOCALS~1\Temp\Release\sc_1184ec2786fc765046a8e2929d8c9a2642.def c:\apps\gccmingw\bin\dllwrap.exe --driver-name g++ -mno-cygwin -mdll -static -s C:\DOCUME~1\kll560\LOCALS~1\Temp\Release\sc_1184ec2786fc765046a8e2929d8c9a2642.o C:\DOCUME~1\kll560\LOCALS~1\Temp\Release\sc_1184ec2786fc765046a8e2929d8c9a2642.def -LC:\APPS\Python\libs -lpython21 -o C:\DOCUME~1\kll560\LOCALS~1\Temp\sc_1184ec2786fc765046a8e2929d8c9a2642.pyd finished compiling (sec): 43.7829999924 E..................................................................................... ====================================================================== ERROR: result[1:-1,1:-1] = (b[1:-1,1:-1] + b[2:,1:-1] + b[:-2,1:-1] ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\apps\Python\scipy\compiler\tests\test_compile_code.py", line 280, in check_5point_avg_2d self.generic_2d(expr) File "C:\apps\Python\scipy\compiler\tests\test_compile_code.py", line 256, in generic_2d standard,compiled = self.generic_test(expr,arg_dict,type,size) File "C:\apps\Python\scipy\compiler\tests\test_compile_code.py", line 217, in generic_test scipy.compiler.compile_code.compiled_exec(expr,arg_dict,module_location=None) File "C:\apps\Python\scipy\compiler\compile_code.py", line 134, in compiled_exec exec ('import ' + module_name) File "<string>", line 1, in ? ImportError: DLL load failed: Invalid access to memory location. ---------------------------------------------------------------------- Ran 188 tests in 46.688s FAILED (errors=1) ===== When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place, what is man that you are mindful of him, the son of man that you care for him? Psalm 8:3-4 Y!M, AOL, jabber.com: lluang __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/

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Unit tests for compile_code.py returns ImportError
by Louis Luangkesorn 17 Jan '02

17 Jan '02

Hello I solved my own problem. It seems that it is only an issue with the latest mingw. When I use the older version (19991024) which is on Mumit Khan's site (and is linked to on the scipy.org site) the unit tests pass OK. I'll add a comment on the Installation page. Louis ===== When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place, what is man that you are mindful of him, the son of man that you care for him? Psalm 8:3-4 Y!M, AOL, jabber.com: lluang __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/

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comparisions of fft / inverse fft algorithms
by Michael.Biester＠t-online.de 14 Jan '02

14 Jan '02

Hello , its good to know that a bug in fft.FFT2.ifft(x) has been fixed. However updated modules in the CVS are currently of little use to me. I don't have the tools to compile the source for WIN32. The binary distribution for WIN32 is still version 0.10 and dates back to August 2001. Could anybody indicate, when an update of the binary release will be available ? Best regards Michael mailto:michael.biester@t-online.de

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comparisions of fft / inverse fft algorithms
by Michael.Biester＠t-online.de 14 Jan '02

14 Jan '02

For filter design program I experimented with Fast Fourier Tranforms ( and their inverse). I used algorithms from the Numeric module and from Scipy.fft . It seems, that FFT.fft from Numeric and fft.FFT2.fft perform similar (except for speed of execution and round off errors) However when applying the inverse transformations FFT.inverse_fft(...) from Numeric and fft.FFT2.ifft to the same sequence, results are not the same. While FFT.inverse_fft(...) from Numeric performs as expected ( compared with MATLABs ifft() ) fft.FFT2.ifft gives a sequence which is somehow shifted ... I used this sample script : ------ sample script --------------------------------------------------------- #--- test different versions of fft and its inverse from Numeric import * import FFT from scipy import * import win32com.client L = 500 N = 512 # create sequences with L complex 1's x1 = ones(L)*(1+1j) # use fft from Numeric y1 = FFT.fft(x1,N) # since x1 has L samples transform x1 with zero padding x1i = FFT.inverse_fft(y1) # transform back #-- except for round off errors we expect x1i[0:L] = x1[0:L] # (indeed they are ...) # now use fft and inverse fft from Scipy.fft y2 = fft.FFT2.fft(x1,N) # transform x1 with zero padding x2i = fft.FFT2.ifft(y2) # transform back #-- except for round off errors we expect x2i[0:L] = x1[0:L] # this time however the samples differ; plotting them reveals that # these sequences are similar but shifted versions of each other -------------------------------------------------------------------------------------------- Regards Michael

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New F2PY snapshot available
by Pearu Peterson 13 Jan '02

13 Jan '02

Hi! I made a new snapshot of F2PY available. It is beta version of the 5th F2PY release. It includes many updates, bug fixes, the latest scipy_distutils etc. See NEWS.txt for details. The most important new feature is *** New -c switch that will run the Fortran wrapping process from Alpha to Omega. For example, if foo.f contains subroutine bar, then running f2py -c foo.f -m car will create car.so in the current directory that can be readily imported to Python: >>> import car >>> print car.bar.__doc__ <snip> The snapshot is available for download in http://cens.ioc.ee/projects/f2py2e/2.x/ Regards, Pearu

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New tarballs for weave
by eric 12 Jan '02

12 Jan '02

Hello group, New weave tarballs available on: http://www.scipy.org/site_content/weave These tarballs include some attempts at fixes for Prabhu on Debian. They have been tested on Solaris (2.95.1), W2K (gcc 2.95.2), and RH 7.1 (gcc 2.96) and all tests pass. I still haven't found any reason for the "Abort" error reported on Mandrake (bummer). I'd been interested in reports of success or failure of weave.test() on any and all architectures. Instructions for testing are on the page. There is one minor change likely tomorrow and then I'll announce on comp.python.lang on Monday to get a wider testing audience. Thanks to those who have already spent time testing. eric

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Re: [SciPy-user] Kmeans help and C source
by Costas Malamas 11 Jan '02

11 Jan '02

Thanks Eric, this will help. I do need to modify the distance metric. However, I am now stuck way before kmeans so it will be a coupla weeks before I attempt it. At some point, I will probably need this in C... I know I am looking too far ahead, but probably my vector-space will not fit into RAM. Does anybody know any tricks for clustering "pages" of the v-space or otherwise fit an 1e8 observations cube into a kmeans algorithm? Thanks, C. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp.

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Re: [SciPy-user] Kmeans help and C source
by Costas Malamas 10 Jan '02

10 Jan '02

Eric, This is more lucid than anything I've read so far on the Web. Seriously, this should be in the docstring :-)... I still need to grok where and what to modify, but at least now I know that I don't have to look outside of SciPy ;-) Many thanks, Costas _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx

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Nonlinear Constraint Optimization.
by H Jansen 10 Jan '02

10 Jan '02

I've a nonlinear optimal (trajectory) control problem to solve and have looked around for public domain (C++) code. The best I could find was Omuses (time-continuous front end) that is based on HQP ("Huge" sequential "Quadratic" "Program"/solver that can directly be used for time-discrete problems; it employes sparsity using the sparse meschach code which is in C). Solving a system with Omuses/HQP involves writing a class (that inherits from Omuses_Problem or HQP_Problem) with a set of differential (or difference) equations in C++, linking them with the library; the solution process is initialized/controled with Tcl scripts. Wouldn't it be wonderful if this all could be done from within a Python environment? To that end, the following Python interfaces should be available: 1. One to meschach, and the partially implemented C++ interface, meschach++, may work as a start; 2. One to the Hqp_Program class; 3. One to the Hqp_SeqProgram class; 4. One to the Omuses_Program class; I've tried to make a start with meschach using SWIG which is geared towards C, creating functions that can be wrapped by shadow classes in Python. However, the boost.python library also provides an "interface builder" which provides a tighter coupling between C/C++ and Python. After a while, I had to give up, because I feel I'm lacking the experience to make the correct decisions. Preferably, I would team up with other people that may be interested and join into a shared project in which we can share ideas and build things quicker. Are there people interested? I'm open to all ideas. Kind regards, Henk Jansen. HQP link: http://www.systemtechnik.tu-ilmenau.de/~fg_opt/omuses/hqp.html Omuses link: http://www.systemtechnik.tu-ilmenau.de/~fg_opt/omuses/omuses.html Other links to Optimization Software: http://www-fp.mcs.anl.gov/otc/Guide/SoftwareGuide/index.html

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