Mailman 3 November 2008 - SciPy-User

Re: [SciPy-user] Questions about Line Integral Convolution tutorial
by Bridgman, William T. 24 Nov '08

24 Nov '08

Anne, As long as some notation of the issue is available in this forum, that should help a number of users wanting to work with it for now. Is there any protocol for others updating the Wiki entry? I've just joined Scipy but been a member of AstroPy since its inception - but I have yet to write or update a Wiki page. I'm still getting some type of 'shifting' of my dataset after running LIC, so I need to examine the Cabral reference more closely. I think I'm still missing something. Thanks, Tom > > 2008/11/24 Bridgman, William T. <William.T.Bridgman(a)nasa.gov>: > >> I had found the Cabral reference, as well as a few others that >> described either different algorithms or described them in radically >> different notation. > > I implemented my code based on the Cabral reference. Currently it does > not quite do everything they recommend. > >> Transposing the texture solved my crashing problem. That seems kind >> of counter-intuitive. Perhaps it could be noted in the docs >> somewhere >> or changed in the interface? > > Looks like a bug. Indeed I only tested my code with square arrays. It > wasn't really ready for release, but there was some interest, and I > have no time at all to work on it just now. > > Anne -- Dr. William T."Tom" Bridgman Scientific Visualization Studio Global Science & Technology, Inc. NASA/Goddard Space Flight Center Email: William.T.Bridgman(a)nasa.gov Code 610.3 Phone: 301-286-1346 Greenbelt, MD 20771 FAX: 301-286-1634 http://svs.gsfc.nasa.gov/

2 1

Log-error function
by Anand Patil 24 Nov '08

24 Nov '08

Hi all, I'm looking for a C or Fortran routine that computes log(erf(x)) without ever computing erf(x) directly, for use in PyMC. Does anyone have one laying around? It looks like GSL has such a thing, but it's GPL and we're using the MIT license. Thanks, Anand

1 1

Re: [SciPy-user] Questions about Line Integral Convolution tutorial
by Bridgman, William T. 24 Nov '08

24 Nov '08

David, I had found the Cabral reference, as well as a few others that described either different algorithms or described them in radically different notation. Transposing the texture solved my crashing problem. That seems kind of counter-intuitive. Perhaps it could be noted in the docs somewhere or changed in the interface? Thanks for the assistance, Tom > Hi William, > > I am not the author, but I may be able to answer some of your > questions. > > On Mon, Nov 24, 2008 at 11:46 AM, Bridgman, William T. < > William.T.Bridgman(a)nasa.gov> wrote: > > > Hello, > > > > I found the Line Integral Convolution (LIC) example very timely > for a > > project I'm working on. > > > > http://www.scipy.org/Cookbook/LineIntegralConvolution > > > > Once Cython & Pyrex were installed, the demo ran out of the box. > > Excellent. > > > > However, now I'm trying to apply this to a different dataset and > the C > > component is crashing with index errors. I suspect these are being > > caused by the fact that my dataset is not a square array. > > > > An examination in the .pyx file has a couple of locations where the > > array indices appear to be transposed between x,y vs i,j. I'm not > > sure if this is a bug or not. The high symmetry of the demo vector > > field would probably not reveal this if it were a bug. > > > > So my questions for the author of the code or the list are: > > > > 1) Is there a paper or other reference for the algorithm implemented > > here? My searches have revealed several types of LIC > > implementations. It would be nice if this were in code comments > or at > > least on the tutorial page. > > > > I am not sure which paper Anne has used, but I have found > > Cabral, Brian and Laeith Leedom. Imaging vector fields using line > integral > convolution. SIGGRAPH '93: Proceedings of the 20th annual conference > on > Computer graphics and interactive techniques, pages 263-270, 1993. > > a very useful reference. > > > > > 2) Is the algorithm, the demo code, or LIC in general, restricted to > > square arrays? > > > > Not that I know of. I have used it on rectangular arrays and it's > working, > although you may need to transpose the texture array to get it to > work. > > > > > > 3) Is there a pure-python or numpy-only (no Cython or Pyrex > > requirement) implementation? > > > Not that I know of. However, with Anne's consent, I have created a > scikit > named vectorplot using the code she posted in the cookbook. This can > be > installed with a simple > python setup.py install > It's still not pure python, but you won't need Cython to compile the > extension. I've added docstrings, a bit of documentation and utiliy > functions to generate kernels that I use to "animate" vector fields. > > You can check out the code with subversion at > http://svn.scipy.org/svn/scikits/trunk/vectorplot, but bear in mind > that the > user interface might change. > > HTH, > > David > -- Dr. William T."Tom" Bridgman Scientific Visualization Studio Global Science & Technology, Inc. NASA/Goddard Space Flight Center Email: William.T.Bridgman(a)nasa.gov Code 610.3 Phone: 301-286-1346 Greenbelt, MD 20771 FAX: 301-286-1634 http://svs.gsfc.nasa.gov/

3 2

Questions about Line Integral Convolution tutorial
by Bridgman, William T. 24 Nov '08

24 Nov '08

Hello, I found the Line Integral Convolution (LIC) example very timely for a project I'm working on. http://www.scipy.org/Cookbook/LineIntegralConvolution Once Cython & Pyrex were installed, the demo ran out of the box. Excellent. However, now I'm trying to apply this to a different dataset and the C component is crashing with index errors. I suspect these are being caused by the fact that my dataset is not a square array. An examination in the .pyx file has a couple of locations where the array indices appear to be transposed between x,y vs i,j. I'm not sure if this is a bug or not. The high symmetry of the demo vector field would probably not reveal this if it were a bug. So my questions for the author of the code or the list are: 1) Is there a paper or other reference for the algorithm implemented here? My searches have revealed several types of LIC implementations. It would be nice if this were in code comments or at least on the tutorial page. 2) Is the algorithm, the demo code, or LIC in general, restricted to square arrays? 3) Is there a pure-python or numpy-only (no Cython or Pyrex requirement) implementation? Thanks, Tom -- Dr. William T."Tom" Bridgman Scientific Visualization Studio Global Science & Technology, Inc. NASA/Goddard Space Flight Center Email: William.T.Bridgman(a)nasa.gov Code 610.3 Phone: 301-286-1346 Greenbelt, MD 20771 FAX: 301-286-1634 http://svs.gsfc.nasa.gov/

2 1

Problems with numpy and Python64 on Mac OS 1.5.5
by Roger Herikstad 24 Nov '08

24 Nov '08

Hi, After successfully installing a 4 bit universal of python (trunk:67176M) and building and installing numpy (1.3.0.dev5972), running the numpy.test() crashes my system. Has anyone else had the same problem? Here's the python output and the crash report: In [2]: numpy.test() Running unit tests for numpy NumPy version 1.3.0.dev5972 NumPy is installed in /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy Python version 2.7a0 (trunk:67176M, Nov 10 2008, 11:26:48) [GCC 4.0.1 (Apple Inc. build 5465)] nose version 0.10.4 ...............E....EE.....................Python64-64(1431) malloc: *** error for object 0x100e1e400: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x100e1e400: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug E......EEE......EE.............EPython64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Python64-64(1431) malloc: *** error for object 0x101c4c1e0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug F.F............................Segmentation fault Process: Python64-64 [1478] Path: /Library/Frameworks/Python64.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python64-64 Identifier: Python64-64 Version: ??? (???) Code Type: X86-64 (Native) Parent Process: bash [346] Date/Time: 2008-11-24 13:55:31.551 +0800 OS Version: Mac OS X 10.5.5 (9F33) Report Version: 6 Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000190 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x00007fff837604d7 tiny_malloc_from_free_list + 69 1 libSystem.B.dylib 0x00007fff837593ef szone_malloc + 203 2 libSystem.B.dylib 0x00007fff837592ef malloc_zone_malloc + 82 3 libSystem.B.dylib 0x00007fff83759280 malloc + 44 4 multiarray.so 0x00000001014b57ad array_alloc + 29 (arrayobject.c:6957) 5 multiarray.so 0x00000001014c1162 PyArray_NewFromDescr + 930 (arrayobject.c:5583) 6 multiarray.so 0x00000001014fbaff _strings_richcompare + 335 (arrayobject.c:4769) 7 multiarray.so 0x000000010150236c array_richcompare + 844 (arrayobject.c:5029) 8 Python64 0x00000001000575e9 PyObject_RichCompare + 201 9 Python64 0x00000001000be640 PyEval_EvalFrameEx + 16240 10 Python64 0x00000001000c0cec PyEval_EvalFrameEx + 26140 11 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 12 Python64 0x000000010003db0b function_call + 171 13 Python64 0x000000010000cd72 PyObject_Call + 98 14 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 15 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 16 Python64 0x000000010003db0b function_call + 171 17 Python64 0x000000010000cd72 PyObject_Call + 98 18 Python64 0x000000010001f9c1 instancemethod_call + 401 19 Python64 0x000000010000cd72 PyObject_Call + 98 20 Python64 0x000000010007486a slot_tp_call + 74 21 Python64 0x000000010000cd72 PyObject_Call + 98 22 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 23 Python64 0x00000001000c0cec PyEval_EvalFrameEx + 26140 24 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 25 Python64 0x000000010003db0b function_call + 171 26 Python64 0x000000010000cd72 PyObject_Call + 98 27 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 28 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 29 Python64 0x000000010003db0b function_call + 171 30 Python64 0x000000010000cd72 PyObject_Call + 98 31 Python64 0x000000010001f9c1 instancemethod_call + 401 32 Python64 0x000000010000cd72 PyObject_Call + 98 33 Python64 0x000000010007486a slot_tp_call + 74 34 Python64 0x000000010000cd72 PyObject_Call + 98 35 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 36 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 37 Python64 0x000000010003db0b function_call + 171 38 Python64 0x000000010000cd72 PyObject_Call + 98 39 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 40 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 41 Python64 0x000000010003db0b function_call + 171 42 Python64 0x000000010000cd72 PyObject_Call + 98 43 Python64 0x000000010001f9c1 instancemethod_call + 401 44 Python64 0x000000010000cd72 PyObject_Call + 98 45 Python64 0x000000010007486a slot_tp_call + 74 46 Python64 0x000000010000cd72 PyObject_Call + 98 47 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 48 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 49 Python64 0x000000010003db0b function_call + 171 50 Python64 0x000000010000cd72 PyObject_Call + 98 51 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 52 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 53 Python64 0x000000010003db0b function_call + 171 54 Python64 0x000000010000cd72 PyObject_Call + 98 55 Python64 0x000000010001f9c1 instancemethod_call + 401 56 Python64 0x000000010000cd72 PyObject_Call + 98 57 Python64 0x000000010007486a slot_tp_call + 74 58 Python64 0x000000010000cd72 PyObject_Call + 98 59 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 60 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 61 Python64 0x000000010003db0b function_call + 171 62 Python64 0x000000010000cd72 PyObject_Call + 98 63 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 64 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 65 Python64 0x000000010003db0b function_call + 171 66 Python64 0x000000010000cd72 PyObject_Call + 98 67 Python64 0x000000010001f9c1 instancemethod_call + 401 68 Python64 0x000000010000cd72 PyObject_Call + 98 69 Python64 0x000000010007486a slot_tp_call + 74 70 Python64 0x000000010000cd72 PyObject_Call + 98 71 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 72 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 73 Python64 0x000000010003db0b function_call + 171 74 Python64 0x000000010000cd72 PyObject_Call + 98 75 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 76 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 77 Python64 0x000000010003db0b function_call + 171 78 Python64 0x000000010000cd72 PyObject_Call + 98 79 Python64 0x000000010001f9c1 instancemethod_call + 401 80 Python64 0x000000010000cd72 PyObject_Call + 98 81 Python64 0x000000010007486a slot_tp_call + 74 82 Python64 0x000000010000cd72 PyObject_Call + 98 83 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 84 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 85 Python64 0x000000010003db0b function_call + 171 86 Python64 0x000000010000cd72 PyObject_Call + 98 87 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 88 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 89 Python64 0x000000010003db0b function_call + 171 90 Python64 0x000000010000cd72 PyObject_Call + 98 91 Python64 0x000000010001f9c1 instancemethod_call + 401 92 Python64 0x000000010000cd72 PyObject_Call + 98 93 Python64 0x000000010007486a slot_tp_call + 74 94 Python64 0x000000010000cd72 PyObject_Call + 98 95 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 96 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 97 Python64 0x000000010003db0b function_call + 171 98 Python64 0x000000010000cd72 PyObject_Call + 98 99 Python64 0x00000001000bcf59 PyEval_EvalFrameEx + 10377 100 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 101 Python64 0x000000010003db0b function_call + 171 102 Python64 0x000000010000cd72 PyObject_Call + 98 103 Python64 0x000000010001f9c1 instancemethod_call + 401 104 Python64 0x000000010000cd72 PyObject_Call + 98 105 Python64 0x000000010007486a slot_tp_call + 74 106 Python64 0x000000010000cd72 PyObject_Call + 98 107 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 108 Python64 0x00000001000c0cec PyEval_EvalFrameEx + 26140 109 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 110 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 111 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 112 Python64 0x000000010003db0b function_call + 171 113 Python64 0x000000010000cd72 PyObject_Call + 98 114 Python64 0x000000010001f9c1 instancemethod_call + 401 115 Python64 0x000000010000cd72 PyObject_Call + 98 116 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 117 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 118 Python64 0x000000010003db0b function_call + 171 119 Python64 0x000000010000cd72 PyObject_Call + 98 120 Python64 0x000000010001f9c1 instancemethod_call + 401 121 Python64 0x000000010000cd72 PyObject_Call + 98 122 Python64 0x0000000100074448 slot_tp_init + 88 123 Python64 0x0000000100072b5c type_call + 188 124 Python64 0x000000010000cd72 PyObject_Call + 98 125 Python64 0x00000001000be73d PyEval_EvalFrameEx + 16493 126 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 127 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 128 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 129 Python64 0x00000001000c086a PyEval_EvalFrameEx + 24986 130 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 131 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 132 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 133 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 134 Python64 0x00000001000c0cec PyEval_EvalFrameEx + 26140 135 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 136 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 137 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 138 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 139 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 140 Python64 0x00000001000bfecc PyEval_EvalFrameEx + 22524 141 Python64 0x00000001000c1cfb PyEval_EvalCodeEx + 1483 142 Python64 0x00000001000c20f6 PyEval_EvalCode + 54 143 Python64 0x00000001000e618e PyRun_FileExFlags + 174 144 Python64 0x00000001000e6f51 PyRun_SimpleFileExFlags + 801 145 Python64 0x00000001000f6d64 Py_Main + 2740 146 Python64-64 0x0000000100000f54 0x100000000 + 3924 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x000000000000006c rbx: 0x0000000101c3b8d0 rcx: 0x0000000000000004 rdx: 0x0000000000000190 rdi: 0x0000000100228000 rsi: 0x00000001002280d0 rbp: 0x00007fff5fbf52d0 rsp: 0x00007fff5fbf5290 r8: 0x000000007fffffff r9: 0x0000000000000000 r10: 0x0000000000000001 r11: 0x0000000100e28428 r12: 0x0000000100228000 r13: 0x0000000000000005 r14: 0x0000000000000005 r15: 0x0000000000000003 rip: 0x00007fff837604d7 rfl: 0x0000000000010206 cr2: 0x0000000000000190 Binary Images: 0x100000000 - 0x100000ff7 +Python64-64 ??? (???) <a28a225c50a284e301e54ddcd5a7a564> /Library/Frameworks/Python64.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python64-64 0x100003000 - 0x100156fe3 +Python64 ??? (???) <99b06332c391a0f5ae8bae5eb10589ef> /Library/Frameworks/Python64.framework/Versions/2.7/Python64 0x10026a000 - 0x10026bfff +cStringIO.so ??? (???) <a9b754bcb0c23a0039007d2ae48ac54f> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so 0x100270000 - 0x100273ff7 +strop.so ??? (???) <0081a0a8376397566c1f847049caadd1> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/strop.so 0x100278000 - 0x100279ff7 +time.so ??? (???) <ca5ea0b69961c4278944532d2649371d> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so 0x1002c4000 - 0x1002c5fff +termios.so ??? (???) <98c09d8a1e37817bd87d5ad6e71437db> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/termios.so 0x1002ca000 - 0x1002cbff7 +_hashlib.so ??? (???) <cb337cceda50e3a114023cdfa756f75d> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_hashlib.so 0x1002cf000 - 0x1002d1fff +_sha256.so ??? (???) <f875931d7eeae4938fe64a734f856e52> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_sha256.so 0x1002d4000 - 0x1002d7ff7 +_sha512.so ??? (???) <24033938710c3563bfb35d04ff17f039> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_sha512.so 0x1002da000 - 0x1002dcff7 +readline.so ??? (???) <55b90901600834f97c9fbc7a258a6452> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so 0x1002e5000 - 0x1002e6ff7 +resource.so ??? (???) <bfefc40e46afe692380ed67652b86c7f> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/resource.so 0x1002ee000 - 0x1002f2fff +operator.so ??? (???) <7a61eb0ffb187af484f88c9e87a84c49> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so 0x1002fa000 - 0x1002faff7 +_bisect.so ??? (???) <ff99dc355355a84570d3133f34404c74> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_bisect.so 0x100457000 - 0x100463fb1 +libgcc_s.1.dylib ??? (???) <bbb4eaffd7ec4b7a9aedc5bb3003bde0> /usr/local/lib/libgcc_s.1.dylib 0x1004ac000 - 0x1004b0fff +_collections.so ??? (???) <2124ddcb797ea8030d5d6b52d16b6c38> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_collections.so 0x1004b6000 - 0x1004b7ff7 +_heapq.so ??? (???) <401ecf6d5ee927d157bf9dcde04c5328> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_heapq.so 0x1004bb000 - 0x1004bcff7 +_functools.so ??? (???) <eb3617b5532bf213798447c195b73af7> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_functools.so 0x1004ff000 - 0x100505ff7 +itertools.so ??? (???) <b8e5b6b375166c2f831dcdf90e78a987> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/itertools.so 0x10050f000 - 0x100511fff +binascii.so ??? (???) <04a5c86232969859ff3a3ba578d75954> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so 0x100555000 - 0x100558fff +math.so ??? (???) <7c50fa952336956ba646addf6a57860c> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/math.so 0x10055e000 - 0x10055fff7 +_random.so ??? (???) <1cd450b07b79e6f7a432b4c305c846d2> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_random.so 0x100562000 - 0x100563fff +fcntl.so ??? (???) <e45892c0a0da75696157a8dd3b4f6773> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/fcntl.so 0x100566000 - 0x100568ff7 +_locale.so ??? (???) <898e4d0efd88f9803700dc4c70674638> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so 0x1005ec000 - 0x1005effff +select.so ??? (???) <a93618d24d2a30250dc1eeda5db910a5> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/select.so 0x1005f4000 - 0x1005f9ff7 +_struct.so ??? (???) <50aab31a15428f8c27361bb105b22486> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so 0x100600000 - 0x10060dfff +_curses.so ??? (???) <80a5f53a8ad93a01dc7c58741cb6f284> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_curses.so 0x100618000 - 0x10064efe7 libncurses.5.4.dylib ??? (???) <fce74e098f0f7c67cb0d73c9a8612cf9> /usr/lib/libncurses.5.4.dylib 0x10076d000 - 0x100798fef libssl.0.9.7.dylib ??? (???) <3543402bd8c92a4b9fa846c940ce4b6b> /usr/lib/libssl.0.9.7.dylib 0x1007a7000 - 0x1007d1fd9 +libreadline.5.2.dylib ??? (???) /usr/local/lib/libreadline.5.2.dylib 0x1007e5000 - 0x1007f1ff3 +libintl.8.dylib ??? (???) /usr/local/lib/libintl.8.dylib 0x101100000 - 0x101117ffb +_ctypes.so ??? (???) <2b250c749c6c3fb1fbacff96600f34f5> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so 0x101240000 - 0x101338fef libiconv.2.dylib ??? (???) <2b42104e7aa2da6e64f979e585af02e9> /usr/lib/libiconv.2.dylib 0x10133f000 - 0x10134fff7 +cPickle.so ??? (???) <3a54f1ff007030f6ac9042b9c7414d6d> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/cPickle.so 0x101357000 - 0x101359fff +_lsprof.so ??? (???) <850acf2138c2335c59e67a5d8a1cea3e> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_lsprof.so 0x10139d000 - 0x1013a4ff7 +_socket.so ??? (???) <f2276d7a9b3fd31c493e8dd5bb784e23> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_socket.so 0x1013ae000 - 0x1013b2fff +_ssl.so ??? (???) <83281f23577f1ef5505b275ecaf6885c> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_ssl.so 0x1013f7000 - 0x1013faff7 +_dotblas.so ??? (???) <573a6d3a70993971f6d6ba3b3041cf2b> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so 0x101451000 - 0x101453fff +_compiled_base.so ??? (???) <0edca42f1938d93de0d5a881a07cc045> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so 0x10149f000 - 0x101519fff +multiarray.so ??? (???) <21f57e288c348c05e94e60787d05e14f> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so 0x101598000 - 0x1015d4ff7 +umath.so ??? (???) <37e25b358bb7cd8d69d9492f59fd4bce> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/umath.so 0x1015f6000 - 0x1015fcff7 +lapack_lite.so ??? (???) <089b9ac702288962a3b8cbfdc69c55ee> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so 0x101700000 - 0x101714fff +_sort.so ??? (???) <8fdbc5c1ee32400a47a01c60ce06c8bb> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_sort.so 0x10175b000 - 0x10177cfff +scalarmath.so ??? (???) <37c8df02ca4c1e32de1eb658573a9083> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so 0x101829000 - 0x101830fff +fftpack_lite.so ??? (???) <ca862390c4bc798f51033d1097ee225d> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so 0x101834000 - 0x101868fff +mtrand.so ??? (???) <54df4764e45e853939907ba1864d4222> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/site-packages/numpy/random/mtrand.so 0x10190a000 - 0x101917ff7 +parser.so ??? (???) <9c53d967596af699135efde872ca8278> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/parser.so 0x101960000 - 0x101963ff7 +mmap.so ??? (???) <d5aaf66011ff93d2069ca217e6b452cd> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/mmap.so 0x101968000 - 0x10196afff +zlib.so ??? (???) <8eebc9c720a03f6bf1aabc79ad6e705e> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/zlib.so 0x101a7c000 - 0x101a7ffef +_hotshot.so ??? (???) <b41fdd1e7255a5c4c10e8a3d9b4c1057> /Library/Frameworks/Python64.framework/Versions/2.7/lib/python2.7/lib-dynload/_hotshot.so 0x7fff5fc00000 - 0x7fff5fc2e593 dyld 96.2 (???) <d9ab5c6362a1c7430d8f13b90977a7f4> /usr/lib/dyld 0x7fff80003000 - 0x7fff80014ffd libz.1.dylib ??? (???) <2022cc8950afdf485ba1df76364ba725> /usr/lib/libz.1.dylib 0x7fff816c6000 - 0x7fff8178afe2 com.apple.vImage 3.0 (3.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x7fff82091000 - 0x7fff82105fe7 libstdc++.6.dylib ??? (???) <379a6a2dc6e21ba77310b3d2d9ea30ac> /usr/lib/libstdc++.6.dylib 0x7fff821a7000 - 0x7fff822defff com.apple.CoreFoundation 6.5.4 (476.15) <4b970007410b71eca926819f3959548f> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x7fff8232e000 - 0x7fff8233aff1 libgcc_s.1.dylib ??? (???) <42e4fd8079ba44258ea9afc27d2f48f3> /usr/lib/libgcc_s.1.dylib 0x7fff82343000 - 0x7fff82343ffd com.apple.Accelerate 1.4.2 (Accelerate 1.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x7fff825c5000 - 0x7fff826a6fff libcrypto.0.9.7.dylib ??? (???) <66f1f8773bd9fdfdcfd09e2b4b010636> /usr/lib/libcrypto.0.9.7.dylib 0x7fff826b9000 - 0x7fff82e76fef libBLAS.dylib ??? (???) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x7fff82fec000 - 0x7fff830e0fff libobjc.A.dylib ??? (???) <118dc1ae05e685ad64290352fc94f1f0> /usr/lib/libobjc.A.dylib 0x7fff831ad000 - 0x7fff831dfff7 libauto.dylib ??? (???) <cc8eece8c0097b254c758bd4e8df9537> /usr/lib/libauto.dylib 0x7fff832fe000 - 0x7fff832feffd com.apple.Accelerate.vecLib 3.4.2 (vecLib 3.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib 0x7fff83308000 - 0x7fff8330cfff libmathCommon.A.dylib ??? (???) /usr/lib/system/libmathCommon.A.dylib 0x7fff83379000 - 0x7fff83379ffd com.apple.vecLib 3.4.2 (vecLib 3.4.2) /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib 0x7fff834f5000 - 0x7fff8350ffff libvDSP.dylib ??? (???) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib 0x7fff83757000 - 0x7fff838dbffb libSystem.B.dylib ??? (???) <61a1506a5f8d9ffa37298999e05f519c> /usr/lib/libSystem.B.dylib 0x7fff83907000 - 0x7fff8397dfef libvMisc.dylib ??? (???) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x7fff84035000 - 0x7fff841a3fff libicucore.A.dylib ??? (???) <25557e76cafa3f8a97ca7bffe42e2d97> /usr/lib/libicucore.A.dylib 0x7fff84315000 - 0x7fff846cdfff libLAPACK.dylib ??? (???) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x7fffffe00000 - 0x7fffffe01780 libSystem.B.dylib ??? (???) /usr/lib/libSystem.B.dylib 0xfffffffffffec000 - 0xfffffffffffeffff libobjc.A.dylib ??? (???) /usr/lib/libobjc.A.dylib

3 4

Exec format error
by Nils Wagner 24 Nov '08

24 Nov '08

Hi all, Sorry if my request is off-topic but what is the reason for the following message if I try to run python Exec format error. Binary file not executable. Nils

2 2

object-oriented help
by Benjamin J. Racine 21 Nov '08

21 Nov '08

Hello all, Please let me know if I should be posting just general OO stuff somewhere else, but I figure that this might be relevant to a lot of procedural programming types just jumping into python (and the example is straight out of FEA). Anyways, I have the following code below. The problem is, I need to be able to instantiate many nodes for a given element as well as many elements for a model. Tackling this with built-ins such as arrays, lists and dicts seems straightforward, but I can't wrap my head around it in OO for some reason. Do I just need to make my element and node inherit from a list and then use the ".append()" when I instantiate it? Any help greatly appreciated. Thanks, Ben Racine """ untitled.py Created by Ben Racine on 2008-11-21. Copyright (c) 2008 __MyCompanyName__. All rights reserved. """ import sys import os class model(object): """docstring for model""" def __init__(self): pass class element(object): """docstring for element""" def __init__(self): pass elementID = 'something' elementPressure = 'something else' nodeCount = 'something else altogether' class node(object): """docstring for node""" def __init__(self): pass nodeID = '1' x = 'xx' y = 'yy' z = 'zz' if __name__ == "__main__": test = model()

2 2

object-oriented help
by Benjamin J. Racine 21 Nov '08

21 Nov '08

Hello all, Please let me know if I should be posting just general OO stuff somewhere else, but I figure that this might be relevant to a lot of procedural programming types just jumping into python (and the example is straight out of FEA). Anyways, I have the following code below. The problem is, I need to be able to instantiate many nodes for a given element as well as many elements for a model. Tackling this with built-ins such as arrays, lists and dicts seems straightforward, but I can't wrap my head around it in OO for some reason. Do I just need to make my element and node inherit from a list and then use the ".append()" when I instantiate it? Any help greatly appreciated. Thanks, Ben Racine """ untitled.py Created by Ben Racine on 2008-11-21. Copyright (c) 2008 __MyCompanyName__. All rights reserved. """ import sys import os class model(object): """docstring for model""" def __init__(self): pass class element(object): """docstring for element""" def __init__(self): pass elementID = 'something' elementPressure = 'something else' nodeCount = 'something else altogether' class node(object): """docstring for node""" def __init__(self): pass nodeID = '1' x = 'xx' y = 'yy' z = 'zz' if __name__ == "__main__": test = model()

1 0

Question about scipy.optimize
by Gísli Óttarsson 21 Nov '08

21 Nov '08

Hello all. I am a relatively new user of python and scipy and I have been trying out scipy's optimization facilities. I am using scipy version 0.6.0, as distributed with Ubuntu 8.04. My exploration has centered around the minimization of x*x*y, subject to the equality constraint 2*x*x+y*y=3. In my experience, this problem is solved by introducing a Lagrange multiplier and minimizing the Lagrangian: L = x*x*y - lambda * ( 2*x*x+y*y-3 ) I have had no problem finding the desired solution via Newton-Raphson using the function and its first and second derivatives: import scipy.optimize as opt import numpy import numpy.linalg as l def f(r): x,y,lam=r return x*x*y -lam*(2*x*x+y*y-3) def g(r): x,y,lam=r return numpy.array([2*x*y-4*lam*x, x*x-2*lam*y, -(2*x*x+y*y-3)]) def h(r): x,y,lam=r return numpy.mat([[2.*y-4.*lam, 2.*x, -4.*x],[2.*x,-2.*lam,-2.*y],[-4.*x,-2.*y,0.]]) def NR(f, g, h, x0, tol=1e-5, maxit=100): "Find a local extremum of f (a root of g) using Newton-Raphson" x1 = numpy.asarray(x0) f1 = f(x1) for i in range(0,maxit): dx = l.solve(h(x1),g(x1)) ldx = numpy.sqrt(numpy.dot(dx,dx)) x2 = x1-dx f2 = f(x2) if(ldx < tol): # x is close enough df = numpy.abs(f1-f2) if(df < tol): # f is close enough return x2, f2, df, ldx, i x1=x2 f1=f2 return x2, f2, df, ldx, i print NR(f,g,h,[-2.,2.,3.],tol=1e-10) My Newton-Raphson iteration converges in 5 iterations, but I have had no success using any of the functions in scipy.optimize, for example: print opt.fmin_bfgs(f=f, x0=[-2.,2.,3.], fprime=g) print opt.fmin_ncg(f=f, x0=[-2.,2.,3.], fprime=g, fhess=h) neither of which converges. I am beginning to suspect some fundamental misunderstanding on my part. Could someone throw me a bone? Best regards Gísli

4 5

MATLAB ASCII format
by Gideon Simpson 21 Nov '08

21 Nov '08

Is there (or should there be) a routine for reading and writing numpy arrays and matrices in MATLAB ASCII m-file format? -gideon

1 0