Mailman 3 September 2007 - SciPy-Dev

Question about Kaiser Implementation in firwin
by Buehler, Eric (AGRE) 04 Oct '08

04 Oct '08

Hello, I have been using the signal.firwin FIR design tool and I have a question about the implementation. Scipy-0.4.8 Numpy-0.9.6 I am generating a kaiser window with the following parameters: N = 128 Cutoff = ~4e7 width = .3 All of the special kaiser generation parameters in the function follow Oppenheim and Schafer well. Even the sinc function for linear phase is follows exactly. However, the last line of the firwin function is causing me some heartburn. filter_design.py 1538 win = get_window(window,N,fftbins=1) 1539 alpha = N//2 1540 m = numpy.arange(0,N) 1541 h = win*special.sinc(cutoff*(m-alpha)) 1542 return h / sum(h) Line 1542 of filter_design.py, "return h / sum(h)", normalizes the function where it doesn't seem necessary, at least in the kaiser window case. Without the normalization, the kaiser window already returns a value of 1 at the zero frequency point. This normalization scales all of the data, making the window difficult to use in the frequency domain. Can someone point me to the rationale for this line? Looking at the code, this seems to be a pretty recent change (within the last year/year and a half). Thanks, Eric Buehler eric <dot> buehler <at> smiths-aerospace <dot> com ****************************************** The information contained in, or attached to, this e-mail, may contain confidential information and is intended solely for the use of the individual or entity to whom they are addressed and may be subject to legal privilege. If you have received this e-mail in error you should notify the sender immediately by reply e-mail, delete the message from your system and notify your system manager. Please do not copy it for any purpose, or disclose its contents to any other person. The views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of the company. The recipient should check this e-mail and any attachments for the presence of viruses. The company accepts no liability for any damage caused, directly or indirectly, by any virus transmitted in this email. ******************************************

3 2

Status of sandbox.spline and my other code.
by John Travers 07 Apr '08

07 Apr '08

Hi all, This email is intended to clarify the status of various bits of code I've committed/not committed so I don't leave too much of a mess after me. I'm about to start writing my PhD thesis, so I'll be too busy to work on scipy until September. 1. sandbox.spline stuff The module here was supposed to be a tidy up of scipy.interpolate. All of the dierkx functionality has been moved to f2py wrappers, which I think makes maintenance easier. However, it does not add any new functionality, and in retrospect appears to have been a waste of my time. So I'll leave to you to decide if you want to integrate it into scipy.interpolate or not; though it was originaly planned to be a seperate module to clear up the ambiguity between interpolation and smoothing spline functionality. However I have added 20 unit tests to the code (most of which simply check the wrapper against the pure fortran output, but still useful I think) which could easily be moved over to the current scipy.interpolate module. 2. Radial basis function module in sandbox (rbf) This code has recently had attention from Robert Hetland and is quite improved. I'm not sure if I will ever go into scipy though?? If not, I will put it into a scikit at some point. Related to this, the wiki page has been updated, however, it is at http://www.scipy.org/RadialBasisFunctions but should probably be in the Cookbook. I don't know how to move it over, so some pointers would be helpful. In addition there are four unused attachments I uploaded that could be deleted. 3. Boundary value ODE solver (BVP_SOLVER) I have fairly functional code interfacing to some very good BVP solver code (http://cs.smu.ca/~muir/BVP_SOLVER_Webpage.shtml). The license is good for scipy (as confirmed by the authors), but the code if fortran 95 - therefore cannot apparently go into scipy. I'll make a scikit when I get time (probably September). 4. An interface to the pikaia genetic algorithm routine I have a python interface to pikaia fortran code for genetic algorithm optimisation of real valued functions (http://www.hao.ucar.edu/Public/models/pikaia/pikaia.html). The fortran code itself is robust and highly optimised for numerical work, though it is nowhere near as general as the sandbox.ga module. I think it is useful to go in scipy.optimization alongside the annealing module. If people disagree I'll make it into a scikit. I hope this clears a few things up. Best regards, John Travers

4 4

ZVODE, a Double Precision Complex ODE Solver
by Nils Wagner 20 Feb '08

20 Feb '08

This might be of interest. Nils From: Alan Hindmarsh <alanh(a)llnl.gov> Date: Wed, 6 Dec 2006 18:20:32 -0500 Subject: ZVODE, a Double Precision Complex ODE Solver Of the many solvers freely available for ODE initial value problems, there seem to be very few, if any, for the case of double precision complex dependent variables, even though there have been occasional user calls for this functionality. (Of course a complex system can be treated as a real system of twice the size, but direct treatment as a complex system is preferable.) I have provided such a solver: ZVODE. ZVODE is a straightforward modification of the Fortran ODE solver DVODE, for double precision real systems, making it part of a trio, SVODE/DVODE/ZVODE. ZVODE is available in two locations: (1) Netlib, in /ode (see file zvode.f), and (2) the LLNL CASC software site, www.llnl.gov/CASC/software.html (see VODE). The latter site also includes a demonstration program, zvdemo. Alan Hindmarsh Center for Applied Scientific Computing Lawrence Livermore National Laboratory

4 5

Illegal instruction in ndimage test
by Tom Loredo 23 Oct '07

23 Oct '07

Hi folks- My thanks to John Ollinger for the global context change to address SELinux issues. But it turns out that wasn't the cause of the "Illegal instruction" crash I was getting, as far as I can tell. The SELinux warning appears before scipy.test(1,1) crashes, and the crash continues to happen at the same place even after the context change (and even if I turn off text relocation protection in SELinux). Running scipy.test(1,10) helps pin down what's crashing: [snip] gaussian filter 6 ... ok gaussian gradient magnitude filter 1 ... ok gaussian gradient magnitude filter 2 ... ok gaussian laplace filter 1 ... ok gaussian laplace filter 2 ... ok generation of a binary structure 1 ... ok generation of a binary structure 2 ... ok generation of a binary structure 3 ... ok generation of a binary structure 4 ... ok generic filter 1Illegal instruction Hunting around, I found the offending test in ndimage/tests. If I rename this directory (so the tests are skipped), the tests proceed without crashing. I'd appreciate any advice on how to diagnose this problem (I don't use ndimage), or how to provide sufficient info on Trac to guide a bug fix if this is a bug. -Tom ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

8 17

ndimage problems
by Christopher Hanley 10 Oct '07

10 Oct '07

Hi, We have found two problems with ndimage. I have filed a ticket #455 on the scipy trac page. The first problem can be seen with this example: > import numpy as n > from scipy import ndimage as nd > a = n.ones((10,5),dtype=n.float32) * 12.3 > x = nd.rotate(a,90.0) > x Out[17]: array([[ 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 0. , 0. ], [ 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019], [ 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019], [ 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019], [ 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019, 12.30000019]], dtype=float32) }}} Notice that the last two entries of the first row are now 0. The second problem has to do with the reversing of byte order if you have big-endian data on a little endian machine. Please see the example below: >>> a = N.ones ((2,3), dtype=N.float32) * 12.3 >>> a = a.byteswap() >>> a.dtype = a.dtype.newbyteorder (">") >>> print a [[ 12.30000019 12.30000019 12.30000019] [ 12.30000019 12.30000019 12.30000019]] >>> print ndimage.rotate (a, 90.) [[ 0.00000000e+00 -4.28378144e+08] [ 0.00000000e+00 -4.28378144e+08] [ -4.28378144e+08 -4.28378144e+08]] I have taken a look at the ndimage python code and cannot find any explicit calls to byteswap. I'm guessing something is funny in one of the c-api calls. I haven't been able to track it down yet. Chris

2 3

Nifti support
by Matthieu Brucher 05 Oct '07

05 Oct '07

Hi, I saw that nifti file support was currently in the pipeline. If the license issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago. Matthieu

3 7

problems with numpy.setuptools("single_version_externally_managed")
by dmitrey 30 Sep '07

30 Sep '07

hi all, If I use in setup.py: import setuptools from numpy.distutils.system_info import system_info, NotFoundError, dict_append, so_ext I successfully install (OpenOpt) but Nils and I get the warning (with latest numpy) ******************************************************** WARNING!WARNING!WARNING!WARNING!WARNING!WARNING!WARNING! distutils has been imported before numpy.distutils and now numpy.distutils cannot apply all of its customizations to distutils effectively. To avoid this warning, make sure that numpy.distutils is imported *before* distutils. ******************************************************** (BTW note that distutils is not setuptools) If I use vise versa, as it is recommended: from numpy.distutils.system_info import system_info, NotFoundError, dict_append, so_ext import setuptools Then I get: $ sudo python setup.py install running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_py running install_lib Traceback (most recent call last): File "setup.py", line 93, in <module> 'Topic :: Scientific/Engineering'] File "/usr/lib/python2.5/site-packages/numpy/distutils/core.py", line 176, in setup return old_setup(**new_attr) File "distutils/core.py", line 151, in setup File "distutils/dist.py", line 974, in run_commands File "distutils/dist.py", line 994, in run_command File "/usr/lib/python2.5/site-packages/numpy/distutils/command/install.py", line 16, in run r = old_install.run(self) File "distutils/command/install.py", line 510, in run File "/usr/lib/python2.5/cmd.py", line 333, in run_command del help[cmd] File "distutils/dist.py", line 994, in run_command File "/usr/lib/python2.5/site-packages/setuptools/command/install_lib.py", line 21, in run outfiles = self.install() File "distutils/command/install_lib.py", line 116, in install File "/usr/lib/python2.5/site-packages/setuptools/command/install_lib.py", line 47, in copy_tree exclude = self.get_exclusions() File "/usr/lib/python2.5/site-packages/setuptools/command/install_lib.py", line 30, in get_exclusions if (nsp and self.get_finalized_command('install') File "/usr/lib/python2.5/cmd.py", line 112, in __getattr__ import readline AttributeError: single_version_externally_managed Do you know what does it means and how it could be fixed? Best regards, D.

9 25

multigrid
by Nils Wagner 29 Sep '07

29 Sep '07

Hi Nathan, Thank you very much for your prompt reply. test_coarsen.py works fine for me with latest svn python -i /usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/test_coarsen.py Found 7/7 tests for __main__ ....... ---------------------------------------------------------------------- Ran 7 tests in 8.015s OK >>> but python -i /usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/examples.py All Available Examples Are Listed Below torus.mtx.gz Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/examples.py", line 25, in <module> print repr(read_matrix(filename)) File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/examples.py", line 8, in read_matrix fid = gzip.open(filename) File "/usr/lib64/python2.5/gzip.py", line 49, in open return GzipFile(filename, mode, compresslevel) File "/usr/lib64/python2.5/gzip.py", line 95, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: 'sample_data/torus.mtx.gz' Best wishes Nils

1 0

Sandbox package multigrid
by Nils Wagner 29 Sep '07

29 Sep '07

Nathan, Please can you add the missing file "torus.mtx.gz". Thanks in advance. Cheers, Nils python -i /usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/test_coarsen.py Found 8/8 tests for __main__ ...E.... ====================================================================== ERROR: check_sample_data (__main__.test_sa_constant_interpolation) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/test_coarsen.py", line 153, in check_sample_data A = read_matrix(filename) File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/examples.py", line 8, in read_matrix fid = gzip.open(filename) File "/usr/lib64/python2.5/gzip.py", line 49, in open return GzipFile(filename, mode, compresslevel) File "/usr/lib64/python2.5/gzip.py", line 95, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: 'sample_data/torus.mtx.gz' ---------------------------------------------------------------------- Ran 8 tests in 8.699s FAILED (errors=1) status

2 1

Sandbox package Multigrid
by Nils Wagner 29 Sep '07

29 Sep '07

Nathan, Please can you add the missing file "torus.mtx.gz". Thanks in advance. Cheers, Nils python -i /usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/test_coarsen.py Found 8/8 tests for __main__ ...E.... ====================================================================== ERROR: check_sample_data (__main__.test_sa_constant_interpolation) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/test_coarsen.py", line 153, in check_sample_data A = read_matrix(filename) File "/usr/local/lib64/python2.5/site-packages/scipy/sandbox/multigrid/tests/examples.py", line 8, in read_matrix fid = gzip.open(filename) File "/usr/lib64/python2.5/gzip.py", line 49, in open return GzipFile(filename, mode, compresslevel) File "/usr/lib64/python2.5/gzip.py", line 95, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: 'sample_data/torus.mtx.gz' ---------------------------------------------------------------------- Ran 8 tests in 8.699s FAILED (errors=1)

1 0