Mailman 3 March 2007 - SciPy-Dev

A typo in the sparse.csc_matrix docstring
by Constantine Khroulev March 14, 2007

March 14, 2007

Hello all, I'm trying to build a CSC sparse matrix, and it seems like there is a typo in the following docstring: ---------- beginning of the docstring ---------- Compressed sparse column matrix This can be instantiated in several ways: - csc_matrix(d) with a dense matrix d - csc_matrix(s) with another sparse matrix s (sugar for .tocsc()) - csc_matrix((M, N), [nzmax, dtype]) to construct a container, where (M, N) are dimensions and nzmax, dtype are optional, defaulting to nzmax=sparse.NZMAX and dtype='d'. - csc_matrix((data, ij), [(M, N), nzmax]) where data, ij satisfy: a[ij[k, 0], ij[k, 1]] = data[k] - csc_matrix((data, row, ptr), [(M, N)]) standard CSC representation ------------ end of the docstring -------------- According to the sparse.py itself, the line "a[ij[k, 0], ij[k, 1]] = data[k]" should read "a[ij[0, k], ij[1, k]] = data[k]". (Which I kind of like, because it makes porting things from MATLAB a little easier -- no need to call zip()). :) Thank you. -- Constantine

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network outage
by Jeff Strunk March 14, 2007

March 14, 2007

Good evening, Earlier this evening we had a network outage due to a network equipment malfunction. This outage prevented access to the Enthought and SciPy servers from about 8:45-10pm CDT. I have fixed the problem and everything should be back to normal. I apologize for the inconvenience. Jeff Strunk IT Administrator Enthought, Inc.

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network outage
by Jeff Strunk March 14, 2007

March 14, 2007

Good evening, Earlier this evening we had a network outage due to a network equipment malfunction. This outage prevented access to the Enthought and SciPy servers from about 8:45-10pm CDT. I have fixed the problem and everything should be back to normal. I apologize for the inconvenience. Jeff Strunk IT Administrator Enthought, Inc.

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network outage
by Jeff Strunk March 14, 2007

March 14, 2007

Good evening, Earlier this evening we had a network outage due to a network equipment malfunction. This outage prevented access to the Enthought and SciPy servers from about 8:45-10pm CDT. I have fixed the problem and everything should be back to normal. I apologize for the inconvenience. Jeff Strunk IT Administrator Enthought, Inc.

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problem compiling arpack library from the sandbox
by Adam Malinowski March 13, 2007

March 13, 2007

Hi all, I have compiled numpy and scipy from the latest svn with no problem, but on attempting to install the arpack library I get the following result: --- running install running build running config_fc running build_src building library "arpack" sources building extension "arpack._arpack" sources f2py options: [] adding 'build\src.win32-2.5\fortranobject.c' to sources. adding 'build\src.win32-2.5' to include_dirs. adding 'build\src.win32-2.5\build\src.win32-2.5\_arpack-f2pywrappers.f' to sou rces. building data_files sources running build_py running build_clib No module named msvccompiler in numpy.distutils, trying from distutils.. customize MSVCCompiler customize MSVCCompiler using build_clib customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_clib building 'arpack' library compiling Fortran sources Fortran f77 compiler: C:\cygwin\bin\g77.exe -g -Wall -fno-second-underscore -mno -cygwin -O3 -funroll-loops -march=pentium4 -mmmx -msse2 -msse -fomit-frame-point er -malign-double compile options: '-c' g77.exe:f77: .\ARPACK\SRC\cgetv0.f .\ARPACK\SRC\cgetv0.f: In subroutine `cgetv0': .\ARPACK\SRC\cgetv0.f:123: include 'debug.h' ^ Unable to open INCLUDE file `debug.h' at (^) .\ARPACK\SRC\cgetv0.f:124: include 'stat.h' ^ Unable to open INCLUDE file `stat.h' at (^) error: Command "C:\cygwin\bin\g77.exe -g -Wall -fno-second-underscore -mno-cygwi n -O3 -funroll-loops -march=pentium4 -mmmx -msse2 -msse -fomit-frame-pointer -ma lign-double -c -c .\ARPACK\SRC\cgetv0.f -o build\temp.win32-2.5\ARPACK\SRC\cgetv 0.o" failed with exit status 1 --- I'm running windows 2000 and compiling with cygwin. Please ask if any more information is required. Any help would be very much appreciated. Thanks, Adam

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Combining Numpy/C/fortran ?
by Pierre GM March 12, 2007

March 12, 2007

Folks, I'm trying to write an interface to numpy for a piece of mixed C/fortran code, and I'm getting nowhere fast. Roughly, the code is organized as such: a first C file defines some base structures (involving long and double arrays) and initializes their members by calling Fortran routines, either directly or through a set of C functions defined in a second file. I need to get access to the initialized structures. I first started to get rid of the C structures by redefining them in Python, so that I would only have to call functions with array arguments (and not structures) and use f2py for the interface. However, this is not exactly a bug-safe approach. The best would be to get an interface Python/C structure, so that I could send ndarrays as inputs and get ndarrays as outputs. What is the easiest way to write such an interface ? Thanks a lot for any idea...

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crash with 'import scipy.linalg' and 'import scipy.io'
by John Pye March 9, 2007

March 9, 2007

Hi all, I am getting a crash when I call "from scipy import io". Normally this works fine, but when I make the call from an *embedded* python script, it goes haywire. See below for some GDB output. You can see the C code has done some stuff, then the embedded python frame starts up. But there is a crash when it gets to "import scipy.linalg", although "import scipy" works fine. "import scipy.io" also gives a crash. Note that this is with standard Ubuntu packages for numpy and scipy, but with a locally build newer package of matplotlib. john@roadwork:~/ascend$ dpkg -l matplotlib python-scipy python-numpy Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad) ||/ Name Version Description +++-==========================-==========================-==================================================================== ii matplotlib 0.90.0-2 Matlab(TM) style python plotting package ii python-numpy 1.0rc1-0ubuntu1 Numerical Python adds a fast array facility to the Python language ii python-scipy 0.5.1-3ubuntu2 scientific tools for Python john@roadwork:~/ascend$ Has anyone else seen this behaviour? Is there anything I can do to work around this problem? Cheers JP base/generic/integrator/ida.c:1707 (integrator_ida_write_matrix): Calculating dg/dx... base/generic/system/jacobian.c:78 (system_jacobian): nr = 0 base/generic/system/jacobian.c:79 (system_jacobian): nv = 2 base/generic/linear/mtx_basic.c:3234 (mtx_write_region_mmio): Wrote matrix range (0 x 2) to file WROTE MATRICES TO FILE. NOW PROCESSING... IMPORTING scipy... IMPORTING scipy.linang... Program received signal SIGSEGV, Segmentation fault. [Switching to Thread -1209911104 (LWP 22996)] 0xb5a60b41 in PyArray_API () from /usr/lib/python2.4/site-packages/numpy/core/multiarray.so (gdb) where #0 0xb5a60b41 in PyArray_API () from /usr/lib/python2.4/site-packages/numpy/core/multiarray.so #1 0xb3987fc7 in init_flinalg () at /usr/lib/python2.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:952 #2 0x080d6844 in _PyImport_LoadDynamicModule (name=0xbf8577d7 "scipy.linalg._flinalg", pathname=0xbf856767 "/usr/lib/python2.4/site-packages/scipy/linalg/_flinalg.so", fp=0x869f8a8) at ../Python/importdl.c:53 #3 0x080d47d5 in load_module (name=0xbf8577d7 "scipy.linalg._flinalg", fp=0xb5a60b40, buf=0xbf856767 "/usr/lib/python2.4/site-packages/scipy/linalg/_flinalg.so", type=3, loader=0x8) at ../Python/import.c:1689 #4 0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf8577e4 "_flinalg", fullname=0xbf8577d7 "scipy.linalg._flinalg") at ../Python/import.c:2276 #5 0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58, p_name=<value optimized out>, buf=0xbf8577d7 "scipy.linalg._flinalg", p_buflen=0xbf8577cc) at ../Python/import.c:2096 #6 0x080d563e in PyImport_ImportModuleEx (name=0xb39b5f54 "_flinalg", globals=0xb39a11c4, locals=0xb39a11c4, fromlist=0x8124c58) at ../Python/import.c:1931 #7 0x080af9e0 in builtin___import__ (self=0x0, args=0xb39b81bc) at ../Python/bltinmodule.c:45 #8 0x08058c27 in PyObject_Call (func=0x8, arg=0xb39b81bc, kw=0x0) at ../Objects/abstract.c:1795 #9 0x080b395c in PyEval_CallObjectWithKeywords (func=0xb7debd6c, arg=0xb39b81bc, kw=0x0) at ../Python/ceval.c:3435 #10 0x080b77b3 in PyEval_EvalFrame (f=0x8424b1c) at ../Python/ceval.c:2020 #11 0x080ba4b9 in PyEval_EvalCodeEx (co=0xb39b6aa0, globals=0xb39a11c4, locals=0xb39a11c4, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2741 #12 0x080ba527 in PyEval_EvalCode (co=0xb39b6aa0, globals=0xb39a11c4, locals=0xb39a11c4) at ../Python/ceval.c:484 #13 0x080d3d8c in PyImport_ExecCodeModuleEx (name=0xbf85abb7 "scipy.linalg.flinalg", co=0xb39b6aa0, pathname=0xbf858b07 "/usr/lib/python2.4/site-packages/scipy/linalg/flinalg.pyc") at ../Python/import.c:636 #14 0x080d4406 in load_source_module (name=0xbf85abb7 "scipy.linalg.flinalg", pathname=0xbf858b07 "/usr/lib/python2.4/site-packages/scipy/linalg/flinalg.pyc", fp=<value optimized out>) at ../Python/import.c:915 #15 0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf85abc4 "flinalg", fullname=0xbf85abb7 "scipy.linalg.flinalg") at ../Python/import.c:2276 #16 0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58, p_name=<value optimized out>, buf=0xbf85abb7 "scipy.linalg.flinalg", p_buflen=0xbf85abac) at ../Python/import.c:2096 #17 0x080d563e in PyImport_ImportModuleEx (name=0xb39b5e54 "flinalg", globals=0xb481ef0c, locals=0xb481ef0c, fromlist=0xb48215cc) at ../Python/import.c:1931 #18 0x080af9e0 in builtin___import__ (self=0x0, args=0xb39b80f4) at ../Python/bltinmodule.c:45 #19 0x08058c27 in PyObject_Call (func=0x8, arg=0xb39b80f4, kw=0x0) at ../Objects/abstract.c:1795 #20 0x080b395c in PyEval_CallObjectWithKeywords (func=0xb7debd6c, arg=0xb39b80f4, kw=0x0) at ../Python/ceval.c:3435 #21 0x080b77b3 in PyEval_EvalFrame (f=0x81a7374) at ../Python/ceval.c:2020 #22 0x080ba4b9 in PyEval_EvalCodeEx (co=0xb39b6960, globals=0xb481ef0c, locals=0xb481ef0c, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2741 #23 0x080ba527 in PyEval_EvalCode (co=0xb39b6960, globals=0xb481ef0c, locals=0xb481ef0c) at ../Python/ceval.c:484 #24 0x080d3d8c in PyImport_ExecCodeModuleEx (name=0xbf85df97 "scipy.linalg.basic", co=0xb39b6960, pathname=0xbf85bee7 "/usr/lib/python2.4/site-packages/scipy/linalg/basic.pyc") at ../Python/import.c:636 #25 0x080d4406 in load_source_module (name=0xbf85df97 "scipy.linalg.basic", pathname=0xbf85bee7 "/usr/lib/python2.4/site-packages/scipy/linalg/basic.pyc", fp=<value optimized out>) at ../Python/import.c:915 #26 0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf85dfa4 "basic", fullname=0xbf85df97 "scipy.linalg.basic") at ../Python/import.c:2276 #27 0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58, p_name=<value optimized out>, buf=0xbf85df97 "scipy.linalg.basic", p_buflen=0xbf85df8c) at ../Python/import.c:2096 ---Type <return> to continue, or q <return> to quit---

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bug in scipy.stats.norm.cdf ?
by John Hunter March 8, 2007

March 8, 2007

I was surprised by the nans in the cdf output below; ditto for the survival function which is probably using the same code (svn scipy compiled for OS X panther python2.3) In [1]: import scipy In [2]: import scipy.stats In [3]: scipy.__version__ Out[3]: '0.5.3.dev2818' In [4]: distribution = scipy.stats.norm(loc=0, scale=1) In [5]: x = scipy.arange(-3,3,0.1) In [6]: distribution.cdf(x) Out[6]: array([ 0.0013499 , 0.00186581, 0.00255513, 0.00346697, 0.00466119, nan, 0.00819754, 0.01072411, 0.01390345, 0.01786442, nan, 0.02871656, 0.03593032, 0.04456546, 0.05479929, nan, 0.08075666, 0.09680048, 0.11506967, 0.13566606, nan, 0.18406013, 0.2118554 , 0.24196365, 0.27425312, nan, 0.34457826, 0.38208858, 0.42074029, 0.46017216, 0.5 , 0.53982784, 0.57925971, 0.61791142, 0.65542174, 0.69146246, 0.72574688, 0.75803635, 0.7881446 , 0.81593987, 0.84134475, 0.86433394, 0.88493033, 0.90319952, 0.91924334, 0.9331928 , 0.94520071, 0.95543454, 0.96406968, 0.97128344, 0.97724987, 0.98213558, 0.98609655, 0.98927589, 0.99180246, 0.99379033, 0.99533881, 0.99653303, 0.99744487, 0.99813419]) John-Hunters-Computer:~> uname -a Darwin John-Hunters-Computer.local 7.9.0 Darwin Kernel Version 7.9.0: Wed Mar 30 20:11:17 PST 2005; root:xnu/xnu-517.12.7.obj~1/RELEASE_PPC Power Macintosh powerpc

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[ANN] alpha release of the timeseries module
by Matt Knox March 7, 2007

March 7, 2007

Hi everyone, As you may or may not be aware, over the past several months we (Matt and Pierre) have been busy developing a timeseries module for scipy. The module has been completely overhauled from its original form when it was added to the scipy sandbox at the end of last year. In particular, masked arrays are now fully supported, and the dependence on the external package mxDateTime has been removed. The purpose of this package is to manipulate data indexed by dates (and time). The package defines three main classes: Date (as a single element), DateArray (as a ndarray of Date objects), and TimeSeries (as the combination of a DateArray and a masked array). Each of these main classes support a wide variety of frequencies: annual, quarterly, monthly, weekly, daily, business day, hourly, minutely, secondly, and more. Additional frequencies can be added fairly easily. Note that by frequency, we really mean time units. Time series usually do NOT have to be regularly spaced : the smallest time increment between two consecutive data is just expressed in one particular set of units. Dates (and hence DateArrays and TimeSeries) can be easily converted to other frequencies (the conversion algorithms implemented in C). TimeSeries can be indexed (and sliced!) by Date objects/strings, or indexed in the convential numpy way . The TimeSeries class is a subclass of the new MaskedArray class (the version in the scipy sandbox, which is itself a subclass of ndarray). Therefore, missing data are naturally supported, and the series are recognized as ndarrays by asarray/asanyarray. In addition to these three classes, we developed a series of addons: * a plotting add-on, that allows TimeSeries objects to be easily plotted using matplotlib with dynamic, intelligent axis labels (a tad slow at the moment, but very pretty...).* A report class for generating TimeSeries reports, to export the results to a spreadsheet program via csv, generate html tables, or inspect data from the console, etc.* The 'interpolate' sub-module, that permits to interpolate masked values in a MaskedArray (and hence, TimeSeries also) * A 'filters' sub-module provides some functions for 'running window' based filtering (this is rather incomplete at this point) * An io.fame sub-module allows reading/writing to/from FAME databases (still highly experimental) Our future plans include:* Porting the Date class entirely to C. This is partly underway, so you may notice some unusual redundancy between the python and C code with regards to Date handling. * Adding some more frequencies (quarterly with different year ends, groups of months, possibly higher frequencies than secondly, possibly user defined custom frequencies) * Improving the frequency support of the plotting module (it currently supports only Annual, Quarterly, Monthly, Daily, and Business Day. and weekly, vaguely). * Add additional library functions: percent change, ARMA models, moving standard deviation... If you are interested in the module, we would very much appreciate your feedback. The module is still under-going active development, so API changes are quite possible at this point (even if most of the core is failry stabilized). Please see the wiki at http://www.scipy.org/TimeSeriesPackage for some documentation. There should be enough there to get you started, although we don't claim it is completely comprehensive at this point. You can download the maskedarray and timeseries modules from the scipy sandbox in SVN. Please feel free to contact us on or off the mailing list with any questions/comments/suggestions you have about the module. - Matt Knox & Pierre Gerard-Marchant

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sandbox packages maskedarray and timeseries
by Nils Wagner March 2, 2007

March 2, 2007

Hi all, I have enabled the sandbox packages maskedarray and timeseries. The file enabled_packages.txt in /scipy/Lib/sandbox contains delaunay pyem numexpr arpack spline rbf maskedarray timeseries If I try to import maskedarray and timeseries I get Python 2.4 (#1, Oct 13 2006, 16:43:49) [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy.sandbox import maskedarray >>> from scipy.sandbox import timeseries Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib64/python2.4/site-packages/scipy/sandbox/timeseries/__init__.py", line 16, in ? import tcore File "/usr/lib64/python2.4/site-packages/scipy/sandbox/timeseries/tcore.py", line 18, in ? import maskedarray as MA ImportError: No module named maskedarray >>> import scipy >>> scipy.__version__ '0.5.3.dev2806' How can I fix this problem ? Nils

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