Mailman 3 June 2006 - NumPy-Discussion

addressing a submatrix
by Martin Wiechert June 14, 2006

June 14, 2006

Hi list, is there a concise way to address a subrectangle of a 2d array? So far I'm using A [I] [:, J] which is not pretty and more importantly only works for reading the subrectangle. Writing does *not* work. (Cf. session below.) Any help would be appreciated. Thanks, Martin In [1]:a = zeros ((4,4)) In [2]:b = ones ((2,2)) In [3]:c = array ((1,2)) In [4]:a [c] [:, c] = b In [5]:a Out[5]: array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]) In [6]:a [:, c] [c] = b In [7]:a Out[7]: array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]) In [8]:a [c, c] = b In [9]:a Out[9]: array([[0, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 0]]) In [10]:a [c] [:, c] Out[10]: array([[1, 0], [0, 1]]) In [11]:

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dealing with large arrays
by Mathew Yeates June 14, 2006

June 14, 2006

Hi I typically deal with very large arrays that don't fit in memory. How does Numpy handle this? In Matlab I can use memory mapping but I would prefer caching as is done in The Gimp. Any pointers appreciated. Mathew

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Atlas missing dgeev
by Mathew Yeates June 14, 2006

June 14, 2006

I finally got things linked with libg2c but now I get import linalg -> failed: ld.so.1: python: fatal: relocation error: file /u/fuego0/myeates/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so: symbol dgeev_: referenced symbol not found I looked all through my ATLAS source and I see no dgeenv anywhere.No file of that name and no refernces to that function. Anybody know what up with this? Mathew

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Array Interface updated
by Travis Oliphant June 14, 2006

June 14, 2006

I've updated the description of the array interface (array protocol). The web-page is http://numeric.scipy.org/array_interface.html Basically, the Python-side interface has been compressed to the single attribute __array_interface__. There is still the __array_struct__ attribute which now has a descr member to the structure returned (but the ARR_HAS_DESCR flag must be set or it must be ignored). NumPy has been updated so that the old Python-side attributes are now spelled: __array_<somename>__ --> __array_interface__['<somename>'] -Travis

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build problems on Solaris
by Mathew Yeates June 14, 2006

June 14, 2006

Heres the problem.... The function get_flags_linker_so in numpy/distutils/fcompiler/gnu.py is not called anywhere. Because of this, g2c is not added as a library and -mimpure-text is not set. This causes the "s_wsfe unresolved" problem. Anybody know how to fix this? Mathew

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super secret
by Desperate June 13, 2006

June 13, 2006

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eighteen bourbon
by Nolly Sosa June 13, 2006

June 13, 2006

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S,T,O,C,K moving crazy!
by Simpson Greta June 13, 2006

June 13, 2006

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finding connected areas?
by stephen emslie June 13, 2006

June 13, 2006

I have used adaptive thresholding to turn an image into a binary image so that I can locate a particularly large bright spot. However, now that I have the binary image I need to be able to group connected cell's together and determine their relative sizes. Matlab has a function called bwlabel (http://tinyurl.com/fcnvd) that labels connected objects in a matrix. That seems like a good way to start, and I'm sure there is a way for me to do something similar in numpy, but how? Thanks Stephen Emslie

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svn build fails
by Steve Schmerler June 13, 2006

June 13, 2006

The latest svn build fails. ==================================================================================== elcorto@ramrod:~/install/python/scipy/svn$ make build cd numpy; python setup.py build Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' No module named __svn_version__ F2PY Version 2_2607 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not find in /usr/local/lib libraries mkl,vml,guide not find in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not find in /usr/local/lib libraries ptf77blas,ptcblas,atlas not find in /usr/lib/atlas libraries ptf77blas,ptcblas,atlas not find in /usr/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not find in /usr/local/lib libraries f77blas,cblas,atlas not find in /usr/lib/atlas FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c Could not locate executable gfortran Could not locate executable f95 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc -pthread _configtest.o -L/usr/lib -lf77blas -lcblas -latlas -o _configtest _configtest.o: In function `main': /home/elcorto/install/python/scipy/svn/numpy/_configtest.c:5: undefined reference to `ATL_buildinfo' collect2: ld returned 1 exit status _configtest.o: In function `main': /home/elcorto/install/python/scipy/svn/numpy/_configtest.c:5: undefined reference to `ATL_buildinfo' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "setup.py", line 84, in ? setup_package() File "setup.py", line 77, in setup_package configuration=configuration ) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/core.py", line 140, in setup config = configuration() File "setup.py", line 43, in configuration config.add_subpackage('numpy') File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 740, in add_subpackage caller_level = 2) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 723, in get_subpackage caller_level = caller_level + 1) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 670, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./numpy/setup.py", line 9, in configuration config.add_subpackage('core') File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 740, in add_subpackage caller_level = 2) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 723, in get_subpackage caller_level = caller_level + 1) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/misc_util.py", line 670, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "numpy/core/setup.py", line 207, in configuration blas_info = get_info('blas_opt',0) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/system_info.py", line 256, in get_info return cl().get_info(notfound_action) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/system_info.py", line 397, in get_info self.calc_info() File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/system_info.py", line 1224, in calc_info atlas_version = get_atlas_version(**version_info) File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/system_info.py", line 1085, in get_atlas_version library_dirs=config.get('library_dirs', []), File "/home/elcorto/install/python/scipy/svn/numpy/numpy/distutils/command/config.py", line 121, in get_output return exitcode, output UnboundLocalError: local variable 'exitcode' referenced before assignment ==================================================================================== I removed the old /build dir and even did a complete fresh checkout but it still fails to build. cheers, steve -- Random number generation is the art of producing pure gibberish as quickly as possible.

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