Mailman 3 April 2006 - SciPy-User

import/include in f2py
by Ryan Krauss 22 Apr '06

22 Apr '06

If I have a user-defined function in a seperate .f or .so file, how do I include that function in another fortran file for use with f2py? i.e. if I define: double complex function zcosh(z) double complex z zcosh = 0.5*(exp(z)+exp(-z)) RETURN END in mylib.f and then I want to use it like this: double complex function bode(s) double complex s double complex zsinh, zcosh in bode(s) in otherfile.f, what line(s) do I need in otherfile.f to make it find zcosh(z)? I guess I am asking what is the fortran equivalent of include from c or import in python? I have looked in numerous fortran books and poked around in google, but I am missing something here. Thanks, Ryan

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[OT] - what happens to the cmd module in python 2.3.5 on windows?
by massimo sandal 22 Apr '06

22 Apr '06

Hi, Sorry for the off-topic request, but I can't find anything by googling and I'm sure to talk to a crowd of expert Pythoneers, so... I'm building a CLI+GUI app for data analysis using wxpython and matplotlib for the GUI, and the Cmd standard Python module for the command line. The cli and the gui run in two separate threads. On Debian GNU/Linux the application works perfectly. I'm trying to get it working on Windows too. I'd like it to be able to work with the Enthought python distribution on Windows, that already includes 90% of the external libraries (scipy, numarray, wxpython etc.) I need, so people don't have to install a bazillion dependencies one by one to get it working -just a few must be downloaded in addition. This distribution ships Python 2.3.5. Now, on windows the GUI thread starts apparently correctly, but the CLI doesn't work and stops with the following error: Exception in thread Thread-1:Traceback (most recent call last): File "C:\Python23\lib\threading.py", line 442, in __bootstrap self.run() File "hooke.py", line 57, in run cli.cmdloop() File "C:\Python23\lib\cmd.py", line 109, in cmdloop self.preloop() File "C:\Python23\lib\cmd.py", line 152, in preloop import readline File "C:\Python23\lib\site-packages\readline\__init__.py", line 1, in ? from PyReadline import * File "C:\Python23\lib\site-packages\readline\PyReadline.py", line 1091, in ? rl = Readline() File "C:\Python23\lib\site-packages\readline\PyReadline.py", line 46, in __ini t__ self.emacs_editing_mode(None) File "C:\Python23\lib\site-packages\readline\PyReadline.py", line 1008, in ema cs_editing_mode self._bind_key('"%s"' % chr(c), self.self_insert) File "C:\Python23\lib\site-packages\readline\PyReadline.py", line 1000, in _bi nd_key keyinfo = key_text_to_keyinfo(key) File "C:\Python23\lib\site-packages\readline\keysyms.py", line 101, in key_tex t_to_keyinfo return keyseq_to_keyinfo(keytext[1:-1]) File "C:\Python23\lib\site-packages\readline\keysyms.py", line 163, in keyseq_ to_keyinfo res.append(char_to_keyinfo(keyseq[0], control, meta, shift)) File "C:\Python23\lib\site-packages\readline\keysyms.py", line 111, in char_to _keyinfo raise ValueError, 'bad key' ValueError: bad key I really can't understand how to patch the thing here. Any suggestion? Thanks again for your patience, m. -- Massimo Sandal University of Bologna Department of Biochemistry "G.Moruzzi" snail mail: Via Irnerio 48, 40126 Bologna, Italy email: massimo.sandal(a)unibo.it tel: +39-051-2094388 fax: +39-051-2094387

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array vs matrix, converting code from matlab
by David Cournapeau 21 Apr '06

21 Apr '06

Dear numpy users, I am converting some code from matlab to numpy/scipy, but still a bit confused by numpy, mostly the array vs matrix issue. Looking at the scipy website, the matrix type looks the closest to matlab syntax, but I still have some issues: - under matlab, everything, including scalar, are matrices in matlab sense. In python, they are not. So, of I want to handle scalar case in a function which takes arrays, what should I do ? Having special case for scalar sounds like a pain, so is asarray/asmatrix the best way to handle those cases so my function only deal with array types ? - what is the difference between matrix and array, except syntax ? If I want to handle both in one function, what is the "best" method ? Using one type only (for example matrix), and using asmatrix on all arguments accordingly ? To convert my matlab code, I was thinking about using asmatrix for arguments in all my functions, but I am not sure this is really the "right" way. I was hoping some other people would have some experience with the same issues, and could give me some general advices thank you, David P.S: it would be great to have this kind of information on scipy website; right now, the scipy for matlab users part is a bit sparse... I am willing to change this once I understand the problem myself, of course:)

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(no subject)
by Chuckles McGregor 21 Apr '06

21 Apr '06

good day, I've been trying to get weave working, I'm on a win2k box running python 2.4.3, with mingw g++ ver 3.4.2, scipy 0.4.8, numpy 0.9.6 and I can't get this example (and some of the others) from the doc to work. the error is: `Py' has not been declared what did I miss in installing/configuring this? I got hello world to work ok. chuckles >>> a=1 >>> a = weave.inline("return_val = Py::new_reference_to(Py::Int(a+1));",['a']) <weave: compiling> No module named msvccompiler in numpy.distutils, trying from distutils.. cc1plus.exe: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:1: warning: ignoring #pragma warning c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:2: warning: ignoring #pragma warning c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp: In function `PyObject* file_to_py(FILE*, char*, char*)': c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:399: warning: unused variable 'py_obj' c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp: In function `PyObject* compiled_func(PyObject*, PyObject*)': c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:658: error: `Py' has not been declared c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:658: error: `Py' has not been declared c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:658: error: `Int' undeclared (first use this function) c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:658: error: (Each undeclared identifier is reported only once for each function it appears in.) c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp:658: error: `new_reference_to' undeclared (first use this function) Traceback (most recent call last): File "<pyshell#5>", line 1, in -toplevel- a = weave.inline("return_val = Py::new_reference_to(Py::Int(a+1));",['a']) File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 334, in inline auto_downcast = auto_downcast, File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 442, in compile_function verbose=verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", line 353, in compile verbose = verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", line 274, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "C:\Python24\Lib\site-packages\numpy\distutils\core.py", line 85, in setup return old_setup(**new_attr) File "C:\Python24\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) CompileError: error: Command "g++ -O2 -Wall -Wstrict-prototypes -IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.cpp -o c:\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_intermediate\compiler_d41d8cd98f00b204e9800998ecf8427e\Release\docume~1\mcgreg~1\locals~1\temp\mcgregor1\python24_compiled\sc_5b09eaf68ff529a1fbaedc892ca5a4530.o" failed with exit status 1 >>>

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stupid python question : for in in range(nlines) :
by Eric Emsellem 20 Apr '06

20 Apr '06

Hi, I have a very dum python question here, hopefully someone can answer this in no time: I have a script including lines such as (reading a file with "nlines" lines): ############################## for i in range(nlines) : ... ... while i < nlines : .... i += 1 if ... : break ############################# But of course the "while" loop changes the increment "i", but then, when the break condition is valid, it returns to the "for" loop and starts again with the set of lines WITHOUT taking into account the fact that "i" was incremented (so that it should not read these lines AGAIN). Hope this is clear. Let me know if you have a simple solution (my scripting habits are coming from C, hence the way I stupily wrote things here...) Thanks in advance for any help there Eric

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F2PY, F90 ALLOCATED arrays and AMD64
by Neilen Marais 20 Apr '06

20 Apr '06

Hi. There seems to be a problem with recent version of F2PY on 64bit (or at least my 64bit) platforms. I'm using the Intel EM64T version of Intel Fortran 9.0. By default, this compiler doesn't work, since distutils don't recognise the EM64T versions of the compiler. After patching numpy/distutils/fcompilers/intel.py as explained in the thread "F2PY stopped working with new scipy", I was able to compile the wrappers, but they don't quite work right.I think the easiest way to explain it is by example. The following code in the file test_data.f90 is being wrapped : MODULE DATA IMPLICIT NONE REAL, DIMENSION(:), ALLOCATABLE :: test_arr CONTAINS SUBROUTINE init() ALLOCATE(test_arr(10)) test_arr=55 END SUBROUTINE init END MODULE DATA using this command: $ f2py --fcompiler=intel -m testmod -c test_data.f90 Using this version of f2py: $ f2py -v 2.46.243_2020 I get the expected output: $ python Python 2.4.2 (#2, Sep 30 2005, 22:19:27) [GCC 4.0.2 20050808 (prerelease) (Ubuntu 4.0.1-4ubuntu8)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import testmod >>> testmod.data.init() >>> testmod.data.test_arr array([ 55., 55., 55., 55., 55., 55., 55., 55., 55., 55.],'f') >>> If, instead, I use this version of f2py: $ f2py -v 2_2383 I get: $ python Python 2.4.2 (#2, Sep 30 2005, 22:19:27) [GCC 4.0.2 20050808 (prerelease) (Ubuntu 4.0.1-4ubuntu8)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import testmod >>> testmod.data.init() >>> testmod.data.test_arr Traceback (most recent call last): File "<stdin>", line 1, in ? ValueError: negative dimensions are not allowed I also checked on a very similarly setup 32-bit machine. I first ran into a problem compiling: $ f2py --fcompiler=intel -m testmod -c test_data.f90 ....... ifort:f90: test_data.f90 ifort: Command line warning: extension 'M' not supported ignored in option '-x' ifort: Command line error: Unrecognized keyword 'SSE' for option '-arch' ifort: Command line warning: extension 'M' not supported ignored in option '-x' ifort: Command line error: Unrecognized keyword 'SSE' for option '-arch' error: Command "/usr/local/bin/ifort -FR -KPIC -cm -O3 -unroll -tpp6 -xM -arch SSE -I/tmp/tmp1fRBC7/src -I/usr/lib/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c -c test_data.f90 -o /tmp/tmp1fRBC7/test_data.o -module /tmp/tmp1fRBC7/ -I/tmp/tmp1fRBC7/" failed with exit status 1 I fixed this by commenting out the offending compiler options in intel.py. After this, the wrapped code works both with the old and new f2py. I must add that the 32-bit system is running python 2.4.3 instead of 2.4.2. Don't know if this would make any difference. Thanks Neilen -- you know its kind of tragic we live in the new world but we've lost the magic -- Battery 9 (www.battery9.co.za)

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F2PY stopped working with new scipy
by Neilen Marais 20 Apr '06

20 Apr '06

Hi I'm using F2PY with the intel fortran compiler under Ubunty Breezy (05.10) AMD64 to wrap some F90 code. If I use the old scipy (package version 0.3.2-2ubuntu1) with: F2PY Version:2.46.243_2020 scipy.distutils Version: 0.3.2 the following test command works as expected: $ f2py --fcompiler=intel -m testmod -c test_data.f90 test_prog.f90 Before I install new scipy, I removed all the f2py files , since it is now included with scipy. I also removed the ubuntu scipy package. After installing numpy-0.9.6 and scipy-0.4.8, trying to generate the wrappers results in the following output: $ f2py --fcompiler=intel -m testmod -c test_data.f90 test_prog.f90 running build running config_fc running build_src building extension "testmod" sources f2py options: [] f2py:> /tmp/tmp_cZX2X/src/testmodmodule.c creating /tmp/tmp_cZX2X creating /tmp/tmp_cZX2X/src Reading fortran codes... Reading file 'test_data.f90' (format:free) Reading file 'test_prog.f90' (format:free) Post-processing... Block: testmod Block: data Block: prog Block: init_data Block: process_data Post-processing (stage 2)... Block: testmod Block: unknown_interface Block: data Block: prog Block: init_data Block: process_data Building modules... Building module "testmod"... Constructing F90 module support for "data"... Variables: test_arr Constructing F90 module support for "prog"... Constructing wrapper function "prog.init_data"... init_data() Constructing wrapper function "prog.process_data"... process_data(factors,[n]) Wrote C/API module "testmod" to file "/tmp/tmp_cZX2X/src/testmodmodule.c" Fortran 90 wrappers are saved to "/tmp/tmp_cZX2X/src/testmod-f2pywrappers2.f90" adding '/tmp/tmp_cZX2X/src/fortranobject.c' to sources. adding '/tmp/tmp_cZX2X/src' to include_dirs. copying /usr/lib/python2.4/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmp_cZX2X/src copying /usr/lib/python2.4/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmp_cZX2X/src adding '/tmp/tmp_cZX2X/src/testmod-f2pywrappers2.f90' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext Could not locate executable efort Could not locate executable efc warning: build_ext: fcompiler=intel is not available. building 'testmod' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' creating /tmp/tmp_cZX2X/tmp creating /tmp/tmp_cZX2X/tmp/tmp_cZX2X creating /tmp/tmp_cZX2X/tmp/tmp_cZX2X/src compile options: '-I/tmp/tmp_cZX2X/src -I/usr/lib/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c' gcc: /tmp/tmp_cZX2X/src/fortranobject.c gcc: /tmp/tmp_cZX2X/src/testmodmodule.c Traceback (most recent call last): File "/usr/bin/f2py", line 6, in ? f2py.main() File "/usr/lib/python2.4/site-packages/numpy/f2py/f2py2e.py", line 546, in main run_compile() File "/usr/lib/python2.4/site-packages/numpy/f2py/f2py2e.py", line 533, in run_compile setup(ext_modules = [ext]) File "/usr/lib/python2.4/site-packages/numpy/distutils/core.py", line 85, in setup return old_setup(**new_attr) File "/usr/lib/python2.4/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib/python2.4/distutils/dist.py", line 946, in run_commands self.run_command(cmd) File "/usr/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/usr/lib/python2.4/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/usr/lib/python2.4/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/usr/lib/python2.4/site-packages/numpy/distutils/command/build_ext.py", line 109, in run self.build_extensions() File "/usr/lib/python2.4/distutils/command/build_ext.py", line 405, in build_extensions self.build_extension(ext) File "/usr/lib/python2.4/site-packages/numpy/distutils/command/build_ext.py", line 220, in build_extension if self.fcompiler.module_dir_switch is None: AttributeError: 'NoneType' object has no attribute 'module_dir_switch' Is there something wrong with my setup, or what is causing this behaviour? Thanks Neilen -- you know its kind of tragic we live in the new world but we've lost the magic -- Battery 9 (www.battery9.co.za)

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Re: [SciPy-user] wofz and optimized Humlicek algorithm.
by morovia 20 Apr '06

20 Apr '06

Thanks for the responses. > I've written a C version of a fast Humlicek algorithm, which I use for > spectral fitting. I'm willing to part with it if someone would like to > include it in SciPy. Paul : I dont know how to write wrappers around c programmes. > I have wrapped the humdev subroutine found here > http://www-atm.physics.ox.ac.uk/user/wells/voigt.html > some time ago with f2py but switched to wofz since I didn't need high > speed. I can look for the .pyf file if you're interested. Christian : I will try this option, if you can send it. Thanks, Morovia.

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interp2d raises AttributeError: interp2d instance has no attribute 'tck', scipy 0.4.8, numpy 0.9.6
by Albert Huang 20 Apr '06

20 Apr '06

Hi, The following program raises an AttributeError file: testinterp2d.py ==== from scipy.interpolate.interpolate import interp2d from numpy import * X, Y = mgrid[0:3, 0:3] Z = X * Y ip = interp2d( X, Y, Z ) ip( 0.5, 0.5 ) ==== # python testinterp2d.py Traceback (most recent call last): File "testinterp2d.py", line 9, in ? ip( 0.5, 0.5 ) File "/home/albert/local/lib/python2.4/site-packages/scipy/interpolate/interpolate.py", line 64, in __call__ z,ier=fitpack._fitpack._bispev(*(self.tck+[x,y,dx,dy])) AttributeError: interp2d instance has no attribute 'tck' ==== This is on scipy 0.4.8, numpy 0.9.6, Ubuntu 5.10, python 2.4 Am I not using interp2d correctly? Thanks, -albert

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wofz and optimized Humlicek algorithm.
by morovia 19 Apr '06

19 Apr '06

Hi, I would like to know if anyone had tried on wofz and the optimized Humlicek algorithm for the voigt algorithm developed by F. Schreier (Courtesy : http://www.op.dlr.de/ne-oe/ir/voigt.html). I dont know about the license issue of this code but nice to use the optimized one to save computation time. I tried to f2py the above code but since I am using enthought edition of scipy it demands visual studio. Thanks for your comments and info in advance, Best regards, Morovia.

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