Mailman 3 December 2004 - SciPy-Dev

Feature request : Comparison of sparse matrices is not implemented.
by Nils Wagner Dec. 3, 2004

Dec. 3, 2004

Hi all, I tried to visualize the structure of large and sparse matrices using from matplotlib.colors import LinearSegmentedColormap from matplotlib.matlab import * from scipy import * import IPython def spy2(Z): """ SPY(Z) plots the sparsity pattern of the matrix S as an image """ #binary colormap min white, max black cmapdata = { 'red' : ((0., 1., 1.), (1., 0., 0.)), 'green': ((0., 1., 1.), (1., 0., 0.)), 'blue' : ((0., 1., 1.), (1., 0., 0.)) } binary = LinearSegmentedColormap('binary', cmapdata, 2) Z = where(Z>0,1.,0.) imshow(transpose(Z), interpolation='nearest', cmap=binary) rows, cols, entries, rep, field, symm = io.mminfo('k0.mtx') print 'number of rows, cols and entries', rows, cols, entries print 'Start reading matrix - this may take a minute' ma = io.mmread('k0.mtx') print 'Finished' flag = 1 if flag == 1: spy2(ma) show() It failed. Is it somehow possible to visualize sparse matrices ? Any suggestion would be appreciated. Thanks in advance Nils number of rows, cols and entries 67986 67986 4222171 Start reading matrix - this may take a minute Finished Traceback (most recent call last): File "spy.py", line 29, in ? spy2(ma) File "spy.py", line 19, in spy2 Z = where(Z>0,1.,0.) File "/usr/lib/python2.3/site-packages/scipy/sparse/Sparse.py", line 145, in __cmp__ raise TypeError, "Comparison of sparse matrices is not implemented." TypeError: Comparison of sparse matrices is not implemented.

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Problems with building scipy
by Nils Wagner Dec. 2, 2004

Dec. 2, 2004

Hi all, Finally, I decided to use FORTRAN LAPACK/BLAS libraries instead of ATLAS. The environmental variables are set as follows vs/scipy> echo $ATLAS None cvs/scipy> echo $BLAS None cvs/scipy> echo $LAPACK None cvs/scipy> echo $LAPACK_SRC /var/tmp/src/lapack cvs/scipy> echo $BLAS_SRC /var/tmp/src/blas Now python2.3 setup.py build yields Traceback (most recent call last): File "setup.py", line 112, in ? setup_package(ignore_packages) File "setup.py", line 99, 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/lib/python2.3/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib/python2.3/distutils/dist.py", line 907, in run_commands self.run_command(cmd) File "/usr/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "/usr/lib/python2.3/distutils/command/build.py", line 107, in run self.run_command(cmd_name) File "/usr/lib/python2.3/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() 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 122, in build_extension_sources sources = self.generate_sources(sources, ext) File "scipy_core/scipy_distutils/command/build_src.py", line 164, in generate_sources source = func(extension, build_dir) File "Lib/lib/blas/setup_blas.py", line 94, in get_cblas_source f = open(source,'w') NameError: global name 'source' is not defined Nils

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IPYthon's who() and sparse matrices
by Nils Wagner Dec. 2, 2004

Dec. 2, 2004

Hi all, from scipy import * import IPython a = rand(4,4) who() speye=sparse.csc_matrix(identity(4)) print speye who() Name Shape Bytes Type =========================================================== a 4 x 4 128 double Upper bound on total bytes = 128 (0, 0) 1.0 (1, 1) 1.0 (2, 2) 1.0 (3, 3) 1.0 Name Shape Bytes Type =========================================================== a 4 x 4 128 double Upper bound on total bytes = 128 speye is not displayed by who(). For what reason ? Nils

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feature request: expressions in mat strings
by Alan G Isaac Dec. 1, 2004

Dec. 1, 2004

>>> print mat('1/2') Matrix([ [12]) i. This is both unexpected and as far as I can tell undocumented. Unexpected is always a problem... ii. Parsing lines on spaces or commas and evaluating the resulting tokens seems more reasonable and makes 'mat' more useful. Please consider this. Thank you, Alan Isaac

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