Mailman 3 May 2005 - SciPy-User

gplt.plot problem with float data
by Rosa Ruiloba May 17, 2005

May 17, 2005

Hello, my data are not correctly plotted with plot command of gplt. Values are float with 10-4 precision. I'm giving you in attached file the result of the plot for the next values (see below). My command line is : gplt.plot(date,h,'with points') Do you know how to resolve the problem? Xplt plot data correctly. 17663.41597 2.767 17663.41944 2.764 17663.42292 2.756 17663.42639 2.758 17663.42986 2.751 17663.43333 2.753 17663.43681 2.749 17663.44028 2.744 17663.44375 2.744 17663.44722 2.743 17663.45069 2.739 17663.45417 2.739 17663.45764 2.735 17663.46111 2.728 17663.46458 2.730 17663.46806 2.726 17663.47153 2.722 17663.47500 2.715 17663.47847 2.716 17663.48194 2.711 17663.48542 2.706 17663.48889 2.709 17663.49236 2.701 17663.49583 2.700 17663.49931 2.697 17663.50278 2.694 17663.50625 2.695 17663.50972 2.692 17663.51319 2.690 17663.51667 2.688 17663.52014 2.685 17663.52361 2.687 17663.52708 2.684 17663.53056 2.679 17663.53403 2.677 17663.53750 2.676 17663.54097 2.670 17663.54444 2.670 17663.54792 2.668 17663.55139 2.664 17663.55486 2.659 17663.55833 2.658 17663.56181 2.659 17663.56528 2.658 17663.56875 2.658 17663.57222 2.659 17663.57569 2.661 17663.57917 2.653 17663.58264 2.652 17663.58611 2.655 17663.58958 2.652 17663.59306 2.651 17663.59653 2.650 17663.60000 2.652 17663.60347 2.645 17663.60694 2.647 17663.61042 2.644 17663.61389 2.644 17663.61736 2.645 17663.62083 2.651 17663.62431 2.652 17663.62778 2.658 17663.63125 2.656 17663.63472 2.653 17663.63819 2.653 17663.64167 2.651 17663.64514 2.661 17663.64861 2.660 17663.65208 2.664 17663.65556 2.666 17663.65903 2.673 17663.66250 2.678 17663.66597 2.684 17663.66944 2.680 17663.67292 2.684 17663.67639 2.682 17663.67986 2.692 17663.68333 2.698 17663.68681 2.699 17663.69028 2.703 17663.69375 2.705 17663.69722 2.714 -- -- NOVELTIS Parc Technologique du Canal 2, avenue de l'Europe 31526 RAMONVILLE SAINT AGNE CEDEX Tel: +(33) (0)5.62.88.11.23

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slow fft time
by Ryan Krauss May 15, 2005

May 15, 2005

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cephesmodule build problem
by Stephen Walton May 13, 2005

May 13, 2005

I'm having a very strange and annoyingly intermittent problem building Scipy 0.3.4613 from CVS. Specifically, if I do "python setup.py build" all is well. If I do "python setup.py bdist_rpm" I get the following error: > gcc: Lib/special/_cephesmodule.c > Lib/special/_cephesmodule.c:17:30: _nc_cephesmodule.c: No such file or > directory > Lib/special/_cephesmodule.c:17:30: _nc_cephesmodule.c: No such file or > directory > error: Command "gcc -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -m32 > -march=i386 -mtune=pentium4 -D_GNU_SOURCE -fPIC -O2 -g -pipe -m32 > -march=i386 -mtune=pentium4 -fPIC -DUSE_MCONF_LE > -DNUMERIC_VERSION="\"24.0b2\"" -DNUMERIC -I/usr/include/python2.3 > -I/usr/include/python2.3 -c Lib/special/_cephesmodule.c -o > build/temp.linux-i686-2.3/Lib/special/_cephesmodule.o" failed with > exit status 1 If I copy the above gcc command and paste it into a terminal window, it succeeds fine. As far as I can tell, the gcc commands for both build and bdist_rpm are the same. I do 'rm -rf build dist MANIFEST' in the root scipy directory before the build in all cases. This is on FC3.

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structure arrays in SciPy
by Ryan Krauss May 13, 2005

May 13, 2005

I have some data that I was storing in structure arrays in Matlab. It seems like I can do everything I need to do with mat_struct in SciPy, but I am wondering if there is a better way. Basically, I have some experimental data I need to turn into Bode plots and then store with some describing information. Each test would have a magnitude vector, a phase vector, and then some miscellanious information such as the input and output (which would be strings), and raw data filenames (a list of strings), and maybe a date and a description blurb. A group of these tests with different inputs and outputs would be one set that I would save as a datafile. In Matlab, each test was an element of a structure array. Each element of the structure array had unique magnitude and phase vectors and input and output labels. The rest of the data was the same but got repeated for each element in the structure array (I want to keep it all together in one structure and what was repeated was small compared to the data vectors). I think I can do all of this with a list of mat_struct's and I seem to be able to pickle and unpickle them with io.pickler.objload and objsave, but I didn't know if there is some more elegant way of doing this in SciPy. Any thoughts? Thanks, Ryan

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No module named xplt
by Rosa Ruiloba May 13, 2005

May 13, 2005

Hello I have installed Scipy with python2.4.1 and Numeric23.5. I van import xplt module (see below). My PYTHONPATH seems ok. Do I set other variables? echo $PYTHONPATH /home/ruiloba/my_libs/Python-2.4.1/lib/python2.4/site-packages ls /home/ruiloba/my_libs/Python-2.4.1/lib/python2.4/site-packages dateutil matplotlib Numeric.pth pytz scipy_distutils f2py2e numarray pylab.py scipy scipy_test gui_thread Numeric pylab.pyc scipy_base weave ------------ import scipy from xplt import * Traceback (most recent call last): File "<stdin>", line 1, in ? ImportError: No module named xplt -- -- NOVELTIS Parc Technologique du Canal 2, avenue de l'Europe 31526 RAMONVILLE SAINT AGNE CEDEX Tel: +(33) (0)5.62.88.11.23

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Installing problems
by Rosa Ruiloba May 13, 2005

May 13, 2005

Hello, I'm trying to install Scipy-0.3.2 from sources on RedHat 8.0. I've installed ATLAS, LAPACK and BLAS as it's explained in Scipy web pages. But I have a problem when I build Scipy. I'm giving you some results of the building below. Do you know what is missing? Thank you, Rosa ----------------- blas_opt_info: atlas_blas_threads_info: scipy_distutils.system_info.atlas_blas_threads_info NOT AVAILABLE atlas_blas_info: scipy_distutils.system_info.atlas_blas_info FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/home/ruiloba/my_libs/src/ATLAS/lib/Linux_P4SSE2'] language = c ----------- ATLAS version 3.6.0 creating build/temp.linux-i686-2.2/config_pygist ============= begin top level configuration ============= compiling '_configtest.c': /* check whether libm is broken */ #include <math.h> int main(int argc, char *argv[]) { return exp(-720.) > 1.0; /* typically an IEEE denormal */ } gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc _configtest.o -o _configtest _configtest.o: In function `main': /home/ruiloba/my_libs/SCIPY/SciPy_complete-0.3.2/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status _configtest.o: In function `main': /home/ruiloba/my_libs/SCIPY/SciPy_complete-0.3.2/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o ----------------------------- building extension "scipy.linalg.atlas_version" sources building extension "scipy.linalg._iterative" sources Traceback (most recent call last): File "setup.py", line 111, in ? setup_package(ignore_packages) File "setup.py", line 98, in setup_package url = "http://www.scipy.org", File "scipy_core/scipy_distutils/core.py", line 73, in setup return old_setup(**new_attr) File "/usr/src/build/143041-i386/install/usr/lib/python2.2/distutils/core.py", line 138, in setup File "/usr/src/build/143041-i386/install/usr/lib/python2.2/distutils/dist.py", line 893, in run_commands File "/usr/src/build/143041-i386/install/usr/lib/python2.2/distutils/dist.py", line 913, in run_command File "/usr/src/build/143041-i386/install/usr/lib/python2.2/distutils/command/build.py", line 107, in run File "/usr/lib/python2.2/cmd.py", line 330, in run_command print "\n" File "/usr/src/build/143041-i386/install/usr/lib/python2.2/distutils/dist.py", line 913, in run_command File "scipy_core/scipy_distutils/command/build_src.py", line 81, in run self.build_sources() File "scipy_core/scipy_distutils/command/build_src.py", line 88, in build_sources self.build_extension_sources(ext) File "scipy_core/scipy_distutils/command/build_src.py", line 124, in build_extension_sources sources = self.template_sources(sources, ext) File "scipy_core/scipy_distutils/command/build_src.py", line 197, in template_sources outstr = process_str(fid.read()) File "scipy_core/scipy_distutils/from_template.py", line 197, in process_str writestr += fix_capitals(newstr[oldend:sub[0]]) File "scipy_core/scipy_distutils/from_template.py", line 182, in fix_capitals astr = maxre.sub(r"MAX(\g<1>,\g<2>)",astr) File "/usr/lib/python2.2/pre.py", line 344, in sub return self.subn(repl, string, count)[0] File "/usr/lib/python2.2/pre.py", line 366, in subn repl = pcre_expand(_Dummy, repl) TypeError: 'NoneType' object is not callable -- -- NOVELTIS Parc Technologique du Canal 2, avenue de l'Europe 31526 RAMONVILLE SAINT AGNE CEDEX Tel: +(33) (0)5.62.88.11.23

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Possible bug wrt bmat
by Nils Wagner May 13, 2005

May 13, 2005

Hi all, >>> from scipy import * numerix Numeric 24.0b2 >>> I = identity(2) >>> I array([[1, 0], [0, 1]]) >>> bmat(r_[c_[I,I],c_[I,I]]) Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.4/site-packages/scipy_base/matrix_base.py", line 136, in bmat return Matrix.Matrix(obj) File "/usr/local/lib/python2.4/site-packages/scipy_base/ppimport.py", line 102, in __getattr__ return getattr(attr, name) AttributeError: class Matrix has no attribute 'Matrix' I guess it's a bug. Am I missing something ? Nils

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scipy.test(1,verbosity=10) failed
by Nils Wagner May 12, 2005

May 12, 2005

Hi all, A scipy.test(1,verbosity=10) using >> import scipy numerix Numeric 24.0b2 >>> scipy.__version__ '0.3.3_304.4613' check_random_complex (scipy.linalg.decomp.test_decomp.test_qr) ... ok check_simple (scipy.linalg.decomp.test_decomp.test_qr) ... ok check_simple_complex (scipy.linalg.decomp.test_decomp.test_qr) ... ok check_simple (scipy.linalg.decomp.test_decomp.test_schur) ... ok failed with check_random (scipy.linalg.decomp.test_decomp.test_svd) ** On entry to DGESDD parameter number 12 had an illegal value Any idea ? Nils

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weave and large arrays
by Ryan Krauss May 12, 2005

May 12, 2005

Does anyone have an example of using weave to read in large ASCII arrays? Is it possible to use weave to read large *.mat Matlab binary files? I have *.mat files that contain 10-15 column vectors that are 25000 rows long. For now I have written a Matlab script to convert them to ASCII. Thanks, Ryan

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Fwd: Re: [SciPy-user] weave and large arrays
by Francesc Altet May 12, 2005

May 12, 2005

A Dimecres 11 Maig 2005 21:16, Ryan Krauss va escriure: > I don't know anything about PyTables. The data is now in tab delimited > ASCII files where each column is on data vector. Can PyTables quickly read > that and give me either a matrix of 11 different column vectors? No, PyTables doesn't support importing ASCII files directly. However, you can use a tool on the HDF5 distribution called h5import [1] that can read ASCII files and convert them into HDF5 files. [1] http://hdf.ncsa.uiuc.edu/HDF5/doc/Tools.html#Tools-Import > The student version of Matlab R13 does not seem to support hdf5. It can > read hdf, but doesn't seem to be able to write at all. Ops. Well, now that you have solved your problem I suppose that it does not matter anymore. Cheers, -- Francesc Altet

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