Mailman 3 February 2006 - SciPy-User

savespace equivalent in numpy?
by iCy-fLaME Feb. 10, 2006

Feb. 10, 2006

I am in the process of moving my Numeric based code to the new numpy, i came across several places where i deliberately tried to restrict the auto up casting function. While it may not be the end of the world to live without the "savespace" option, i am wondering if there is an equivalent option with numpy, so i can have a smoother transition to numpy. -- iCy-fLaME The body maybe wounded, but it is the mind that hurts.

3 2

'obj2dtype' not found in 'mio.py'
by Michael Sorich Feb. 10, 2006

Feb. 10, 2006

Hi, In the course of trying to use scipy.io.loadmat to load a v4 matlab file, I have run across this error. Does anyone know where obj2dtype is defined? (Using an old version of scipy version (3.x) this matlab file could be loaded.) >> import scipy.io >>> scipy.io.loadmat('D:\\test.mat') Traceback (most recent call last): File "<interactive input>", line 1, in ? File "D:\Python24\Lib\site-packages\scipy\io\mio.py", line 803, in loadmat varname = fid.fread(header[-1],'char')[:-1] File "D:\Python24\Lib\site-packages\scipy\io\mio.py", line 249, in read howmany,stype = getsize_type(stype) File "D:\Python24\Lib\site-packages\scipy\io\mio.py", line 48, in getsize_type mtype = obj2dtype(mtype) NameError: global name 'obj2dtype' is not defined >>> scipy.__version__ '0.4.4' >>> import numpy >>> numpy.__version__ '0.9.4' >>> numpy-0.9.4.win32-py2.4.exe and scipy-0.4.4.win32-py2.4-P4SSE2.exe were used to install the code on windows XP with Python 2.4.2. On a less important note it seems that scipy.io.loadmat does not accept file names separated with '/' on windows >>> scipy.io.loadmat('D:/test.mat') Traceback (most recent call last): File "<interactive input>", line 1, in ? File "D:\Python24\Lib\site-packages\scipy\io\mio.py", line 740, in loadmat raise IOError, "%s not found on the path." % name IOError: test not found on the path. >>> The line 'if os.sep in name:' is evaluated as false as os.sep is ''\\' on windows and thus the code assumes that the file name is not a full path name. However, the os.path module recognises '/' as a path separator. Eg >>> import os.path >>> os.path.isabs('D:/test.mat') True >>> os.path.split('D:/test.mat') ('D:/', 'test.mat') >>> If it considered OK to use '\' as a path separator on windows perhaps this line can be changed to 'if os.path.isabs(name):' or maybe 'if os.path.split('D/test.mat')[0] != "":' Michael

3 2

Concatenating 1D arrays
by Rudolph van der Merwe Feb. 10, 2006

Feb. 10, 2006

What is the Numpy prefered way of recursively concatenating 1D arrays (vectors) into a 2D array (matrix)? I'm trying to convert the following Matlab code to Python: x=[]; y=[]; for k=1:N, c = get_column_vector_from_somewhere() r = get_row_vector_from_somewhere() x = [x c] y = [y; r] end In other words, x and y get initialized to empty arrays and then grown in-place. x is grown (appended) column wise with vectors c and y is appended (row wise) with vectors r. In Numpy (numpy), how do I initialize an empty array with the correct dimensions which can then be used with functions like: column_stack(), concatenate(), etc. ? -- Rudolph van der Merwe

5 11

SciPy tutorial update
by Dave Kuhlman Feb. 10, 2006

Feb. 10, 2006

I've updated my SciPy tutorial/course outline. I'd like to add a link to it on the SciPy Wiki Documentation page under tutorials. But, before I do, I'd like an opinion on whether it fits there and whether it would be helpful. Would someone be willing to take a quick look? You can find it here: http://www.rexx.com/~dkuhlman/scipy_course_01.html Dave -- Dave Kuhlman http://www.rexx.com/~dkuhlman

1 0

parameter bounds using leastsq
by mike cantor Feb. 9, 2006

Feb. 9, 2006

Is there any way to enforce upper and/or lower bounds on parameters (x0) optimized by leastsq? If not can anyone tell me where I might look to hack this? Thanks, -mike

7 8

Can't even begin to build/install scipy 0.4.4
by skip＠pobox.com Feb. 9, 2006

Feb. 9, 2006

We'd been running an old version of scipy (0.3) in our Solaris 8/9/10 environment. In preparation for migrating to a new GCC (3.4 from 3.3.2), Python (2.4.2 from 2.3.4) and Gtk (2.6 from 2.4), we have been busy rebuilding all our libraries and applications. One application (the one I happen to work on) uses a tiny bit of scipy. The guy doing the building tried to build scipy 0.3.2. That failed. He got to a certain point but found that scipy's distutils apparently fails to honor the --rpath flag. I told him I'd take a look at it and decided to try scipy 0.4.4 instead (no sense fiddling with an old version that won't build - might as well see if the new version is any better). I downloaded numpy 0.9.4, but can't even get help. For some reason, distutils believes it needs to compile something just to give me help: $ python setup.py --help Running from numpy source directory. Assuming default configuration (numpy/distutils/command/{setup_command,setup}.py was not found) Appending numpy.distutils.command configuration to numpy.distutils Assuming default configuration (numpy/distutils/fcompiler/{setup_fcompiler,setup}.py was not found) Appending numpy.distutils.fcompiler configuration to numpy.distutils Appending numpy.distutils configuration to numpy Appending numpy.testing configuration to numpy F2PY Version 2_1975 Appending numpy.f2py configuration to numpy blas_opt_info: blas_mkl_info: NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/opt/lib'] language = c include_dirs = ['/opt/include'] running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x4568501b.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'atlas_version' extension compiling C sources gcc options: '-fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' compile options: '-I/opt/include -Inumpy/core/include -I/opt/app/g++lib6/python-2.4/include/python2.4 -c' /opt/lang/gcc-3.4/bin/gcc -shared build/temp.solaris-2.8-i86pc-2.4/build/src/atlas_version_0x4568501b.o -L/opt/lib -lptf77blas -lptcblas -latlas -o build/temp.solaris-2.8-i86pc-2.4/atlas_version.so Text relocation remains referenced against symbol offset in file <unknown> 0x7 /opt/lib/libatlas.a(ATL_buildinfo.o) <unknown> 0xc /opt/lib/libatlas.a(ATL_buildinfo.o) <unknown> 0x11 ... blah blah blah ... ##### msg: error: Command "/opt/lang/gcc-3.4/bin/gcc -shared ##### build/temp.solaris-2.8-i86pc-2.4/build/src/atlas_version_0x4568501b.o ##### -L/opt/lib -lptf77blas -lptcblas -latlas -o ##### build/temp.solaris-2.8-i86pc-2.4/atlas_version.so" failed with exit ##### status 1 error: Command "/opt/lang/gcc-3.4/bin/gcc -shared build/temp.solaris-2.8-i86pc-2.4/build/src/atlas_version_0x4568501b.o -L/opt/lib -lptf77blas -lptcblas -latlas -o build/temp.solaris-2.8-i86pc-2.4/atlas_version.so" failed with exit status 1 FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/opt/lib'] language = c define_macros = [('NO_ATLAS_INFO', 2)] include_dirs = ['/opt/include'] distutils distribution has been initialized, it may be too late to add an extension _dotblas Traceback (most recent call last): File "setup.py", line 73, in ? setup_package() File "setup.py", line 58, in setup_package config.add_subpackage('numpy') File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 409, in add_subpackage config = self.get_subpackage(subpackage_name,subpackage_path) File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 399, in get_subpackage config = setup_module.configuration(*args) File "/home/ink/skipm/src/numpy-0.9.4/numpy/setup.py", line 10, in configuration config.add_subpackage('core') File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 409, in add_subpackage config = self.get_subpackage(subpackage_name,subpackage_path) File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 399, in get_subpackage config = setup_module.configuration(*args) File "numpy/core/setup.py", line 201, in configuration config.add_data_dir('tests') File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 453, in add_data_dir self.add_data_files((ds,filenames)) File "/home/ink/skipm/src/numpy-0.9.4/numpy/distutils/misc_util.py", line 508, in add_data_files dist.data_files.extend(data_dict.items()) AttributeError: 'NoneType' object has no attribute 'extend' What's up with that? Thx, -- Skip Montanaro http://www.musi-cal.com/ skip(a)pobox.com

2 3

What shape should arg 2 of integrate.trapz be?
by Gregory Novak Feb. 9, 2006

Feb. 9, 2006

If I do this: (Note: nrange is like arange, except you specify the number of samples instead of dx). In [474]: x = nrange(-1,1,4) In [475]: y = nrange(-1,1,5) In [476]: z = reshape(arange(20.), (4,5)) In [479]: shape(integrate.trapz(z,axis=0)) Out[479]: (5,) the output is as I expect: I integrate away the (length 4) x dimension and am left with an answer for each y value. However, if I try to specify the x axis, I get the following traceback: In [480]: shape(integrate.trapz(z,x,axis=0)) --------------------------------------------------------------------------- /sw/lib/python2.3/site-packages/scipy/integrate/quadrature.py in trapz(y, x, dx, axis) 96 slice1[axis] = slice(1,None) 97 slice2[axis] = slice(None,-1) ---> 98 return add.reduce(d * (y[slice1]+y[slice2])/2.0,axis) 99 100 def cumtrapz(y, x=None, dx=1.0, axis=-1): ValueError: frames are not aligned I can make this work again by explicitly making the x array be 2dim instead of 1dim: In [481]: shape(integrate.trapz(z,x[:,NewAxis],axis=0)) Out[481]: (5,) The question is: Is this the desired behavior? It seems to me that In[479] is well-specified and should give the correct result. Is there some reason that one would want to pass in a multi-d array as the grid for the independent variable? Thanks, Greg

1 0

installation problem
by Ryan Krauss Feb. 9, 2006

Feb. 9, 2006

I am trying to install scipy/numpy from SVN on a computer on campus. I have what I thought was an identical Ubuntu installation to the one I have at home where everything is working beautifully. I am getting the following while trying to install numpy: I am getting a message about lapack not being in atlas, which I don't understand since I have the ubuntu packages for both installed (which I think is just like on my home computer). Thanks for your help, Ryan ryan@Lagrange:~/svn/numpy$ sudo python setup.py install Running from numpy source directory. Warning: not existing data path in numpy/distutils: site.cfg No module named __svn_version__ F2PY Version 2_2059 blas_opt_info: blas_mkl_info: NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE atlas_blas_info: FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c include_dirs = ['/usr/include'] running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_-0xf63e660.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/include'] lapack_opt_info: lapack_mkl_info: mkl_info: NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: numpy.distutils.system_info.atlas_info /home/ryan/svn/numpy/numpy/distutils/system_info.py:811: UserWarning: ********************************************************************* Could not find lapack library within the ATLAS installation. ********************************************************************* warnings.warn(message) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c define_macros = [('ATLAS_WITHOUT_LAPACK', None)] include_dirs = ['/usr/include'] running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x39f8be52.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['f77blas', 'cblas', 'atlas', 'lapack'] library_dirs = ['/usr/lib/sse2', '/usr/lib'] define_macros = [('ATLAS_WITHOUT_LAPACK', None), ('ATLAS_INFO', '"\\"3.6.0\\""')] language = f77 include_dirs = ['/usr/include'] running install running build running config_fc running build_src building py_modules sources building extension "numpy.core.multiarray" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__multiarray_api.h' to sources. adding 'build/src/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src/numpy/core/src/scalartypes.inc', 'build/src/numpy/core/src/arraytypes.inc', 'build/src/numpy/core/config.h', 'build/src/numpy/core/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__ufunc_api.h' to sources. adding 'build/src/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src/numpy/core/src/scalartypes.inc', 'build/src/numpy/core/src/arraytypes.inc', 'build/src/numpy/core/config.h', 'build/src/numpy/core/__ufunc_api.h'] building extension "numpy.core._sort" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__multiarray_api.h' to sources. numpy.core - nothing done with h_files= ['build/src/numpy/core/config.h', 'build/src/numpy/core/__multiarray_api.h'] building extension "numpy.core._dotblas" sources adding 'numpy/core/blasdot/_dotblas.c' to sources. building extension "numpy.lib._compiled_base" sources building extension "numpy.dft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources adding 'numpy/linalg/lapack_litemodule.c' to sources. building extension "numpy.random.mtrand" sources building data_files sources running build_py copying build/src/numpy/__config__.py -> build/lib.linux-i686-2.4/numpy copying build/src/numpy/distutils/__config__.py -> build/lib.linux-i686-2.4/numpy/distutils copying numpy/f2py/__svn_version__.py -> build/lib.linux-i686-2.4/numpy/f2py copying numpy/core/__svn_version__.py -> build/lib.linux-i686-2.4/numpy/core running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'numpy.core.multiarray' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' compile options: '-Ibuild/src/numpy/core/src -Inumpy/core/include -Ibuild/src/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c' gcc: numpy/core/src/multiarraymodule.c In file included from numpy/core/src/multiarraymodule.c:65: numpy/core/src/arrayobject.c:3527: error: conflicting types for 'PyArray_CheckStrides' build/src/numpy/core/__multiarray_api.h:157: error: previous declaration of 'PyArray_CheckStrides' was here In file included from numpy/core/src/multiarraymodule.c:65: numpy/core/src/arrayobject.c:3527: error: conflicting types for 'PyArray_CheckStrides' build/src/numpy/core/__multiarray_api.h:157: error: previous declaration of 'PyArray_CheckStrides' was here error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -Ibuild/src/numpy/core/src -Inumpy/core/include -Ibuild/src/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c numpy/core/src/multiarraymodule.c -o build/temp.linux-i686-2.4/numpy/core/src/multiarraymodule.o" failed with exit status 1

2 2

Replacing Numeric With NumPy
by Rich Shepard Feb. 9, 2006

Feb. 9, 2006

Last evening I downloaded numpy-0.9.4 and scipy-0.4.4. I have an earlier version of Numeric in /usr/lib/python2.4/site-packages/Numeric/. Should I remove all references to Numeric before installing NumPy? Rich -- Richard B. Shepard, Ph.D. | Author of "Quantifying Environmental Applied Ecosystem Services, Inc. (TM) | Impact Assessments Using Fuzzy Logic" <http://www.appl-ecosys.com> Voice: 503-667-4517 Fax: 503-667-8863

6 7

other strange behavior
by Ryan Krauss Feb. 9, 2006

Feb. 9, 2006

I am seeing other strange instances (completely unrelated to my other post) of code executing correctly when I step through it with the debugger, but not executing correctly if I just run it as a script. Has anyone else see this before? Ryan

2 1