Mailman 3 September 2006 - SciPy-User

PYFITS 1.1 "beta 3" RELEASE
by Christopher Hanley 19 Sep '06

19 Sep '06

------------------ | PYFITS Release | ------------------ Space Telescope Science Institute is pleased to announce the "beta 3" release of PyFITS 1.1. This release includes support for both the NUMPY and NUMARRAY array packages. This software can be downloaded at: http://www.stsci.edu/resources/software_hardware/pyfits/Download The NUMPY support in PyFITS is not nearly as well tested as the NUMARRAY support. We expect that you will encounter bugs. Please send bug reports to "help(a)stsci.edu". We intend to support NUMARRAY and NUMPY simultaneously for a transition period of no less than 1 year. Eventually, however, support for NUMARRAY will disappear. During this period, it is likely that new features will appear only for NUMPY. The support for NUMARRAY will primarily be to fix serious bugs and handle platform updates. ----------- | Version | ----------- Version 1.1b3; September 19, 2006 ------------------------------- | Major Changes since v1.1b2 | ------------------------------- * Pyfits will now read fits files that have been compressed using either gzip or zip. Fits files compressed with gzip are expected to have the extension .gz. Files compressed using zip are expected to have the extension .zip. * A user can now provide a url (either http or ftp) instead of a file specification as the file name argument to fitsopen, or any other pyfits function that opens a fits file (getdata(), getheader(),info()). * Modified the numpy version of pyfits to recognize the numpy data types. This allows the int32scalar object to be treated like a python int. The same goes for the numpy floating and complex types. * Removed dependencies on deprecated data type names from the numpy version of pyfits. * Replaced ".dtype.fields[-1]" with ".dtype.names" to reflect numpy interface change. * Created a fix for bug in creating new tables with no rows and no input data. * Added the _gap attribute to the FITS_rec class. This missing attribute was causing problems when trying to write tables. * Create a fix for bug that prevented the use of index arrays with FITS_rec objects. * Added the __setitem__() method to the FITS_rec and FITS_record classes to facilitate assignment between tables. * Added a ".names" attribute to the numarray version of the FITS_rec class. ------------------------- | Software Requirements | ------------------------- PyFITS Version 1.1b3 REQUIRES: * Python 2.3 or later * NUMPY 1.0b5(or later) or NUMARRAY --------------------- | Installing PyFITS | --------------------- PyFITS 1.1b is distributed as a Python distutils module. Installation simply involves unpacking the package and executing % python setup.py install to install it in Python's site-packages directory. Alternatively the command %python setup.py install --local="/destination/directory/" will install PyFITS in an arbitrary directory which should be placed on PYTHONPATH. Once numarray or numpy has been installed, then PyFITS should be available for use under Python. ----------------- | Download Site | ----------------- http://www.stsci.edu/resources/software_hardware/pyfits/Download ---------- | Usage | ---------- Users will issue an "import pyfits" command as in the past. However, the use of the NUMPY or NUMARRAY version of PyFITS will be controlled by an environment variable called NUMERIX. Set NUMERIX to 'numarray' for the NUMARRAY version of PyFITS. Set NUMERIX to 'numpy' for the NUMPY version of pyfits. If only one array package is installed, that package's version of PyFITS will be imported. If both packages are installed the NUMERIX value is used to decide which version to import. If no NUMERIX value is set then the NUMARRAY version of PyFITS will be imported. Anything else will raise an exception upon import. --------------- | Bug Reports | --------------- Please send all PyFITS bug reports to help(a)stsci.edu ------------------ | Advanced Users | ------------------ Users who would like the "bleeding" edge of PyFITS can retrieve the software from our SUBVERSION repository hosted at: http://astropy.scipy.org/svn/pyfits/trunk We also provide a Trac site at: http://projects.scipy.org/astropy/pyfits/wiki -- Christopher Hanley Systems Software Engineer Space Telescope Science Institute 3700 San Martin Drive Baltimore MD, 21218 (410) 338-4338

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3d interpolation
by Fabian Braennstroem 19 Sep '06

19 Sep '06

Hi, I would like to do some 3d interpolations. Is it possible with scipy or should I use something different? Greetings! Fabian

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sparsetools intel mac install problem and 2 failed tests
by Aaron Hoover 19 Sep '06

19 Sep '06

Hi All, I just finished building 0.5.1 on my MacBook Pro with NumPy 1.0b5. I followed the instructions on the "Installing SciPy/Mac OS X" page on the wiki and everything seemed to come off without a hitch. That is, the build and installation completed without errors. However, a couple of things aren't working quite right. First off, whenever I do 'from scipy import *' I get the following error that comes from trying to import sparse: ImportError: Failure linking new module: /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ sparse/sparsetools.so: Symbol not found: ___dso_handle Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ lib/python2.4/site-packages/scipy/sparse/sparsetools.so Expected in: dynamic lookup For the time being, I can do without the sparse module by just commenting out its inclusion in the setup.py file, but I just thought I'd see if anyone else has figured out how to fix this issue. I saw earlier posts, but no definitive solution. Also, when I run scipy.test(10), I get the following 2 errors: ====================================================================== ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/io/tests/test_array_import.py", line 55, in check_integer from scipy import stats File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/stats/__init__.py", line 7, in ? from stats import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/stats/stats.py", line 191, in ? import scipy.special as special File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/special/__init__.py", line 8, in ? from basic import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/special/basic.py", line 8, in ? from _cephes import * ImportError: Failure linking new module: /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ special/_cephes.so: Symbol not found: ___dso_handle Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ lib/python2.4/site-packages/scipy/special/_cephes.so Expected in: dynamic lookup ====================================================================== ERROR: check_simple_todense (scipy.io.tests.test_mmio.test_mmio_coordinate) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/io/tests/test_mmio.py", line 151, in check_simple_todense b = mmread(fn).todense() AttributeError: 'numpy.ndarray' object has no attribute 'todense' ---------------------------------------------------------------------- Ran 413 tests in 1.450s FAILED (errors=2) However, none of the functionality I use regularly seems to be affected, so it's not really an urgent issue for me. Lastly, I just want to say thanks to everyone who has contributed to SciPy. It's really exciting for me to see a truly viable open source, free alternative to Matlab. Cheers, Aaron

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Ubuntu installation requirements, and wetting my feet.
by Stephen Kelly 18 Sep '06

18 Sep '06

Hi. I emailed this list a while ago about possible subject matter for a final year project in engineering ( http://news.gmane.org/find-root.php?group=gmane.comp.python.scientific.user…). There was no project resulting directly from the mailing list, but I have now started a project concerning the correction of xray diffraction data using python. It will mainly be concerned with designing a good user interface, but could also involve interpolation and plotting, so I want to see what I can do with scipy in a reasonable time to do this. The installation instructions on the wiki are a bit confusing. I'm inclined to get the optimised packages, so: > To build SciPy <http://scipy.org/SciPy> using optimized lapack and blas on the ubuntu system you should install atlas-3dnow-dev or atlas-sse2-dev or atlas-sse3-dev depending on your system. But those packages are not available in the repos available to me. There are others with similar names, but I'm not certain which to choose. What characteristics of my system will affect this? > atlas2 atlas2-sse-dev atlas3-headers atlas-dev > atlas2-3dnow-dev atlas3-3dnow atlas3-sse atlas-doc > atlas2-base-dev atlas3-3dnow-dev atlas3-sse2 atlas-test > atlas2-dev atlas3-base atlas3-sse2-dev > atlas2-headers atlas3-base-dev atlas3-sse-dev > atlas2-sse2-dev atlas3-doc atlas3-test On an unrelated matter, I'm already using the numpy deb package provided at astraw.com, and as a learning excercise started making a mechanics of materials module for tensor calculations. I'm not sure if numpy/scipy already provides such functions, so I don't know if this is reinventing the wheel. To calculate the sencond scalar invariant, I thought an easy way would be to calculate the trace of the adjoint of the stress tensor I define. When I went to do it though, I couldn't find any functions in numpy to get an adjoint of a matrix, or get cofactors. Are these functions available in numpy or scipy? I've got it working now by multiplying the inverse of the matrix by the determinant, but if there's a better way I'd like to know. Also, I'd like to assess the validity of such a stress matrix by checking if it's symmetric, but I haven't seen any way to do that either. I thought there might be a foo.isSymmetric() bool, but there doesn't seem to be, so I tried doing a comparison, if foo == foo.T: etc., but comparison of matrices doesn't seem to work either. Is the only way to compare them to loop over them using regular python methods? Thanks for help on this. I may be seen a bit more on this mailing list once I get into the computation parts of this project. Is there any interest in using #scipy on freenode? Thanks, Steve

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Re: [SciPy-user] Installation problems Mac OS X 10.4.7
by Brendan Simons 17 Sep '06

17 Sep '06

David, Helmut I also had problems with the Matplotlib included in the superpack. The solution was to download a new matplotlib binary (one compatible with numpy 1.0b5) from here: http://euclid.uits.iupui.edu/mplfiles/ Hopefully these kind of compatibility issues will subside once numpy reaches a stable 1.0. Brendan > ------------------------------ > > Message: 6 > Date: Sun, 17 Sep 2006 11:01:26 +0200 > From: "David Andrews" <irbdavid(a)gmail.com> > Subject: Re: [SciPy-user] Installation problems Mac OS X 10.4.7 > To: "SciPy Users List" <scipy-user(a)scipy.org> > Message-ID: > <8edec5ec0609170201p3ecb5021y4eda8506f71b9607(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Helmut, > > I've been having precisely the same problem. As far as I can tell > there is no way to get the stuff in the superpack working together > properly. Numpy and Scipy install fine from it, but the matplotlib > mpkg in it is broken. I had no real progress using the 'official' > matplotlib packages from their site, as they expect a different > version of numpy, despite the fact that its supposed to be fine with > all 1.0+ versions of numpy. > > I'm not sure how to resolve this problem, It has been suggested that > its best to install packages from > http://pythonmac.org/packages/py24-fat/index.html though scipy is > currently not available there. > > Let me know if you make any progress :) > > Cheers, > > Dave

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Re: [SciPy-user] SciPy-user Digest, Vol 37, Issue 18
by Volker Lorrmann 16 Sep '06

16 Sep '06

> Hello scipy users, > for a short time now, I am using python, numpy and scipy as a > replacement for matlab. My setup at the moment is the "scite"-editor and > the "ipython"-shell. I am happy using the "run -i" command to access the > current workspace with my scripts written with scite. > There is one feature that I know from matlab that I miss a little. Maybe > its not crucial but it would be nice to have: > When I made a change to my script in scite, I have to > *save it > *change scope to ipython > *recall the "run -i myScript.py" command > *press <enter> > In matlab it is possible to hit <F5> to get the same effect. How can I > achieve this with scite/ipython? I think, I need a way to tell ipython > "from extern" to execute the "run"-command. I would put this to my > scite-config-file to connect it with, say, the <F5> button and would be > fine. Is this possible? > Thanks for every comment > Lars Hi Lars, i´m using pida (http://pida.berlios.de/) kate or scite. All can do what you want. Volker

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scipy.optimize.leastsq with float32
by Sebastian Haase 15 Sep '06

15 Sep '06

Hi, I have data in float32 dtype. leastsq() just returns the same parameter values that I give as initial guess. Same happens for int16. (float64 and int32 work) Is this a fundamental limitation of the underlying fortran lib !? Thanks, Sebastian Haase

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scipy.test errors (generic ld filter, loadmat case callnest)
by Michael Williams 15 Sep '06

15 Sep '06

Hi, I'm running scipy 0.8.5 and numpy 1.0b5 built from source using Debian's stable environment (gcc 3.3, Python 2.3.5) on an AMD64 machine. numpy.test() runs fine, but scipy.test does not. Here are the errors: ====================================================================== ERROR: generic 1d filter 1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/williams/usr/lib/python2.3/site-packages/scipy/ndimage/tests/test_ndimage.py", line 1141, in test_generic_filter1d01 extra_keywords = {'total': weights.sum()}) File "/home/williams/usr//lib/python2.3/site-packages/scipy/ndimage/filters.py", line 632, in generic_filter1d mode, cval, origin, extra_arguments, extra_keywords) MemoryError ====================================================================== ERROR: check loadmat case cellnest ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/williams/usr/lib/python2.3/site-packages/scipy/io/tests/test_mio.py", line 80, in cc self._check_case(name, expected) File "/home/williams/usr/lib/python2.3/site-packages/scipy/io/tests/test_mio.py", line 75, in _check_case self._check_level(k_label, expected, matdict[k]) File "/home/williams/usr/lib/python2.3/site-packages/scipy/io/tests/test_mio.py", line 33, in _check_level self._check_level(level_label, ev, actual[i]) File "/home/williams/usr/lib/python2.3/site-packages/scipy/io/tests/test_mio.py", line 30, in _check_level assert len(expected) == len(actual), "Different list lengths at %s" % label TypeError: len() of unsized object ---------------------------------------------------------------------- Ran 1569 tests in 2.105s FAILED (errors=2) I would be very grateful for any suggestions? Indeed, should I even worry about this? Thanks, -- Michael Williams Theoretical Physics, University of Oxford

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signal.lti
by Ryan Krauss 15 Sep '06

15 Sep '06

I am having a rough time trying to use the lti portion of scipy.signal. For starters, I just wanted to generate a step response for an integrator (1/s). I tried creating this system two ways, and neither seems to work correctly. I think this system has a numerator of 1 and a denominator of [1,0]. If I create the system based on the num, den I get: In [51]: mysys=scipy.signal.lti(1,[1,0]) In [52]: mysys.A Out[52]: NumPy array, format: long [[-0.]] In [53]: mysys.B Out[53]: NumPy array, format: long [[1]] In [54]: mysys.C Out[54]: NumPy array, format: long [[ 1.]] In [55]: mysys.D Out[55]: NumPy array, format: long [ 0.] I get an error when I try to find the step response of this system. I think part of the problem is that the matrices aren't right. I think they should be In [46]: A=array([[0,1],[0,0]]) In [47]: B=array([[0],[1]]) In [48]: C=array([[1,0]]) In [49]: D=array([[0]]) but for some reason I can't create a system with these matrices: In [50]: mysys=scipy.signal.lti(A,B,C,D) --------------------------------------------------------------------------- exceptions.TypeError Traceback (most recent call last) /home/ryan/siue/mechatronics/system_modeling/<ipython console> /usr/lib/python2.4/site-packages/scipy/signal/ltisys.py in __init__(self, *args, **kwords) 223 self.__dict__['C'], \ 224 self.__dict__['D'] = abcd_normalize(*args)--> 225 self.__dict__['zeros'], self.__dict__['poles'], \ 226 self.__dict__['gain'] = ss2zpk(*args) 227 self.__dict__['num'], self.__dict__['den'] = ss2tf(*args) /usr/lib/python2.4/site-packages/scipy/signal/ltisys.py in ss2zpk(A, B, C, D, input) 183 z, p, k -- zeros and poles in sequences and gain constant. 184 """ --> 185 return tf2zpk(*ss2tf(A,B,C,D,input=input)) 186 187 class lti: /usr/lib/python2.4/site-packages/scipy/signal/ltisys.py in ss2tf(A, B, C, D, input) 154 for k in range(nout): 155 Ck = atleast_2d(C[k,:]) --> 156 num[k] = poly(A - dot(B,Ck)) + (D[k]-1)*den 157 158 return num, den TypeError: array cannot be safely cast to required type What am I doing wrong? Thanks, Ryan

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Can´t build numpy from svn
by Volker Lorrmann 15 Sep '06

15 Sep '06

Hi guys and girls, i´m trying to compile numpy from svn. So i check out the current svn and typed "python setup.py install" Than this error appears. : Running from numpy source directory. No module named __svn_version__ Traceback (most recent call last): File "setup.py", line 89, in ? setup_package() File "setup.py", line 82, in setup_package configuration=configuration ) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/core.py", line 144, in setup config = configuration() File "setup.py", line 48, in configuration config.add_subpackage('numpy') File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 753, in add_subpackage caller_level = 2) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 736, in get_subpackage caller_level = caller_level + 1) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 683, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./numpy/setup.py", line 8, in configuration config.add_subpackage('f2py') File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 753, in add_subpackage caller_level = 2) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 736, in get_subpackage caller_level = caller_level + 1) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 683, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "numpy/f2py/setup.py", line 39, in configuration config.make_svn_version_py() File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 1298, in make_svn_version_py self.add_data_files(('', generate_svn_version_py())) File "/var/abs/local/python-numpy-svn/src/numpy/numpy/distutils/misc_util.py", line 1281, in generate_svn_version_py assert revision is not None,'hmm, why I am not inside SVN tree???' AssertionError: hmm, why I am not inside SVN tree??? hope you can help me. Thanks so far. Volker -- ----------------------- Volker Lorrmann Universität Würzburg Experimentelle Physik 6 Am Hubland 97074 Wuerzburg Germany Tel: +49 931 888 5770 volker.lorrmann(a)physik.uni-wuerzburg.de

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