Mailman 3 November 2009 - SciPy-Dev

SLSQP Constrained Optimizer Status
by Rob Falck 24 Nov '13

24 Nov '13

I'm currently implementing the Sequential Least Squares Quadratic Programming (SLSQP) optimizer, by Dieter Kraft, for use in Scipy. The Fortran code being wrapped with F2PY is here: http://www.netlib.org/toms/733 (its use within Scipy has been cleared) SLSQP provides for bounds on the independent variables, as well as equality and inequality constraint functions, which is a capability that doesn't exist in scipy.optimize. Currently the code works, although the constraint normals are being generated by approximation. I'm working on a way to pass these in. I think the most elegant way will be a single function that returns the matrix of constraint normals. For a demonstration of what the code can do, here is an optimization of f(x,y) = 2xy + 2x - x**2 - 2y**2 Example 14.2 in Chapra & Canale gives the maximum as x=2.0, y=1.0. The unbounded optimization tests find this solution. As expected, its faster when derivatives are provided rather than approximated. Unbounded optimization. Derivatives approximated. Elapsed time: 1.45792961121 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] Unbounded optimization. Derivatives provided. Elapsed time: 1.03211402893 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] The following example uses an equality constraint to find the optimal when x=y. Bound optimization. Derivatives approximated. Elapsed time: 1.384973526 ms Results [[0.99999996845920858, 0.99999996845920858], -0.99999999999999889, 4, 0, 'Optimization terminated successfully.'] I've tried to conform to the syntax used by the other optimizers in scipy.optimize. The function definition and doc string are below. If anyone is interested in testing it out, let me know. def fmin_slsqp( func, x0 , eqcons=[], f_eqcons=None, ieqcons=[], f_ieqcons=None, bounds = [], fprime = None, fprime_cons=None,args = (), iter = 100, acc = 1.0E-6, iprint = 1, full_output = 0, epsilon = _epsilon ): """ Minimize a function using Sequential Least SQuares Programming Description: Python interface function for the SLSQP Optimization subroutine originally implemented by Dieter Kraft. Inputs: func - Objective function (in the form func(x, *args)) x0 - Initial guess for the independent variable(s). eqcons - A list of functions of length n such that eqcons[j](x0,*args) == 0.0 in a successfully optimized problem f_eqcons - A function of the form f_eqcons(x, *args) that returns an array in which each element must equal 0.0 in a successfully optimized problem. If f_eqcons is specified, eqcons is ignored. ieqcons - A list of functions of length n such that ieqcons[j](x0,*args) >= 0.0 in a successfully optimized problem f_ieqcons - A function of the form f_ieqcons(x0, *args) that returns an array in which each element must be greater or equal to 0.0 in a successfully optimized problem. If f_ieqcons is specified, ieqcons is ignored. bounds - A list of tuples specifying the lower and upper bound for each independent variable [ (xl0, xu0), (xl1, xu1), ...] fprime - A function that evaluates the partial derivatives of func fprime_cons - A function of the form f(x, *args) that returns the m by n array of constraint normals. If not provided, the normals will be approximated. Equality constraint normals precede inequality constraint normals. args - A sequence of additional arguments passed to func and fprime iter - The maximum number of iterations (int) acc - Requested accuracy (float) iprint - The verbosity of fmin_slsqp. iprint <= 0 : Silent operation iprint == 1 : Print summary upon completion (default) iprint >= 2 : Print status of each iterate and summary full_output - If 0, return only the minimizer of func (default). Otherwise, output final objective function and summary information. epsilon - The step size for finite-difference derivative estimates. Outputs: ( x, { fx, gnorm, its, imode, smode }) x - The final minimizer of func. fx - The final value of the objective function. its - The number of iterations. imode - The exit mode from the optimizer, as an integer. smode - A string describing the exit mode from the optimizer. Exit modes are defined as follows: -1 : Gradient evaluation required (g & a) 0 : Optimization terminated successfully. 1 : Function evaluation required (f & c) 2 : Number of equality constraints larger than number of independent variables 3 : More than 3*n iterations in LSQ subproblem 4 : Inequality constraints incompatible 5 : Singular matrix E in LSQ subproblem 6 : Singular matrix C in LSQ subproblem 7 : Rank-deficient equality constraint subproblem HFTI 8 : Positive directional derivative for linesearch 9 : Iteration limit exceeded -- - Rob Falck

4 16

np.savetxt: apply patch in enhancement ticket 1079 to add headers?
by Skipper Seabold 08 Jun '10

08 Jun '10

Hi all, I am assuming that this is ok to request via the list... Could we discuss or could someone apply the patch in enhancement ticket 1079? http://projects.scipy.org/numpy/ticket/1079 I needed this functionality recently, and this is a quick and easy fix that may have been overlooked. There is also another enhancement request about this here: http://projects.scipy.org/numpy/ticket/1236 The only thing that I can think of that might need to be added is a test to see that the header length is the same as the number of columns, but really that might just be up to the user to supply the right headers. It might also be nice to have a header = True, that uses the field names for a structured array, but I can live without that. Cheers, Skipper

3 11

Possible fix for scipy.sparse.lil_matrix column-slicing problem
by Tim Victor 21 Dec '09

21 Dec '09

Hi folks. My first attempt at contributing code to a Python project... Report of the problem prior to my finding it: http://mail.scipy.org/pipermail/scipy-user/2009-April/020688.html Ticket for the problem: http://projects.scipy.org/scipy/ticket/917 Related code change between SciPy 0.7.0 and 0.7.1: http://projects.scipy.org/scipy/changeset/5630 Diff of the changes is at the end of this message. I'm running: Ubuntu 9.04, Athlon64 X2 Python version 2.6.2 NumPy version 1.2.1 SciPy version 0.7.0 # under SciPy 0.7.0, I got: >>> m = sp.sparse.lil_matrix((20,20)) >>> m[:,0] = sp.ones((20,1),'d') >>> m[0,0] <1x1 sparse matrix of type '<type 'numpy.float64'>' with 1 stored elements in LInked List format> >>> m[0,0].todense() matrix([[ 1.]]) >>> m[0,0][0,0] 1.0 # using scipy.sparse.lil.py from SciPy 0.7.1, I get: >>> m = sp.sparse.lil_matrix((20,20)) >>> m[:,0] = sp.ones((20,1),'d') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.6/dist-packages/scipy/sparse/lil.py", line 329, in __setitem__ self._insertat3(row, data, j, xx) File "/usr/lib/python2.6/dist-packages/scipy/sparse/lil.py", line 285, in _insertat3 self._insertat2(row, data, j, x) File "/usr/lib/python2.6/dist-packages/scipy/sparse/lil.py", line 246, in _insertat2 raise ValueError('setting an array element with a sequence') ValueError: setting an array element with a sequence # My version does this: >>> m = sp.sparse.lil_matrix((20,20)) >>> m[:,0] = sp.ones((20,1),'d') >>> m[0,0] 1.0 >>> type(m[0,0]) <type 'numpy.float64'> # This matches the semantics for NumPy dense matrices: >>> m = sp.matrix(sp.zeros((20,20), 'd')) >>> m[:,0] = sp.ones((20,1),'d') >>> m[0,0] 1.0 >>> type(m[0,0]) <type 'numpy.float64'> Comments: * The modified lil.py file is about the same size, actually four lines longer I think. * I've timed a selection of operations and all were as fast or faster using my modified lil.py. Some are significantly faster now, such as when assigning to a tall, narrow range of cells. * It passes all unit tests in scipy.sparse.test(), but a special case in the code is needed to pass the "test_lil_sequence_assignement" test in scipy/sparse/tests/test_base.py. What I did might be excessively permissive. I couldn't figure out what the semantics should be to allow the assignment of a column vector to a row vector. # Trying the same "test_lil_sequence_assignement" operations on a dense matrix: >>> AA = sp.matrix(sp.zeros((4,3))) >>> BB = sp.matrix(sp.eye(3,4)) >>> i0 = [0,1,2] >>> i1 = (0,1,2) >>> i2 = sp.array( i0 ) >>> AA[0,i0] = BB[i0,0] Traceback (most recent call last): File "<stdin>", line 1, in <module> ValueError: array is not broadcastable to correct shape >>> AA[1,i1] = BB[i1,1] Traceback (most recent call last): File "<stdin>", line 1, in <module> ValueError: array is not broadcastable to correct shape >>> AA[2,i2] = BB[i2,2] Traceback (most recent call last): File "<stdin>", line 1, in <module> ValueError: array is not broadcastable to correct shape Best regards, Tim Victor ------------------------------- # apply with "patch lil.py <lil.py.diff" 226,233d225 < < def _insertat(self, i, j, x): < """ helper for __setitem__: insert a value at (i,j) where i, j and x < are all scalars """ < row = self.rows[i] < data = self.data[i] < self._insertat2(row, data, j, x) < 244d235 < 268,270c259 < < def _insertat3(self, row, data, j, x): < """ helper for __setitem__ """ --- > def _setitem_setrow(self, row, data, j, xrow, xdata, xcols): 274,277c263,274 < if isinstance(x, spmatrix): < x = x.todense() < x = np.asarray(x).squeeze() < if np.isscalar(x) or x.size == 1: --- > if xcols == len(j): > for jj, xi in zip(j, xrange(xcols)): > pos = bisect_left(xrow, xi) > if pos != len(xdata) and xrow[pos] == xi: > self._insertat2(row, data, jj, xdata[pos]) > else: > self._insertat2(row, data, jj, 0) > elif xcols == 1: # OK, broadcast across row > if len(xdata) > 0 and xrow[0] == 0: > val = xdata[0] > else: > val = 0 279c276 < self._insertat2(row, data, jj, x) --- > self._insertat2(row, data, jj,val) 281,283c278 < # x must be one D. maybe check these things out < for jj, xx in zip(j, x): < self._insertat2(row, data, jj, xx) --- > raise IndexError('invalid index') 285c280,285 < self._insertat2(row, data, j, x) --- > if not xcols == 1: > raise ValueError('array dimensions are not compatible for copy') > if len(xdata) > 0 and xrow[0] == 0: > self._insertat2(row, data, j, xdata[0]) > else: > self._insertat2(row, data, j, 0) 289d288 < 291,295d289 < if np.isscalar(x): < x = self.dtype.type(x) < elif not isinstance(x, spmatrix): < x = lil_matrix(x) < 300a295,300 > # shortcut for common case of single entry assign: > if np.isscalar(x) and np.isscalar(i) and np.isscalar(j): > self._insertat2(self.rows[i], self.data[i], j, x) > return > > # shortcut for common case of full matrix assign: 302,308c302,310 < if (isinstance(i, slice) and (i == slice(None))) and \ < (isinstance(j, slice) and (j == slice(None))): < # self[:,:] = other_sparse < x = lil_matrix(x) < self.rows = x.rows < self.data = x.data < return --- > if isinstance(i, slice) and i == slice(None) and \ > isinstance(j, slice) and j == slice(None): > x = lil_matrix(x) > self.rows = x.rows > self.data = x.data > return > > if isinstance(i, tuple): # can't index lists with tuple > i = list(i) 311,321c313,315 < row = self.rows[i] < data = self.data[i] < self._insertat3(row, data, j, x) < elif issequence(i) and issequence(j): < if np.isscalar(x): < for ii, jj in zip(i, j): < self._insertat(ii, jj, x) < else: < for ii, jj, xx in zip(i, j, x): < self._insertat(ii, jj, xx) < elif isinstance(i, slice) or issequence(i): --- > rows = [self.rows[i]] > datas = [self.data[i]] > else: 324,329c318,333 < if np.isscalar(x): < for row, data in zip(rows, datas): < self._insertat3(row, data, j, x) < else: < for row, data, xx in zip(rows, datas, x): < self._insertat3(row, data, j, xx) --- > > x = lil_matrix(x, copy=False) > xrows, xcols = x.shape > if xrows == len(rows): # normal rectangular copy > for row, data, xrow, xdata in zip(rows, datas, x.rows, x.data): > self._setitem_setrow(row, data, j, xrow, xdata, xcols) > elif xrows == 1: # OK, broadcast down column > for row, data in zip(rows, datas): > self._setitem_setrow(row, data, j, x.rows[0], x.data[0], xcols) > > # needed to pass 'test_lil_sequence_assignement' unit test: > # -- set row from column of entries -- > elif xcols == len(rows): > x = x.T > for row, data, xrow, xdata in zip(rows, datas, x.rows, x.data): > self._setitem_setrow(row, data, j, xrow, xdata, xrows) 331c335 < raise ValueError('invalid index value: %s' % str((i, j))) --- > raise IndexError('invalid index')

4 14

Ball Tree class
by Jake VanderPlas 03 Dec '09

03 Dec '09

Hello, I've been using scipy.spatial.KDTree for my research, and found it very useful. Recently, though, my datasets have been getting larger - upwards of 10,000 points in 1000-2000 dimensions. The KDTree starts getting slow with such a large dimensionality. I've addressed this by writing a C++ Ball Tree code, and wrapping it using swig and numpy.i. I've been wanting to begin contributing to the scipy project, and I think this would be a great place to start. I'd like to begin the process of adding this to the scipy.spatial package. A few questions: Is it preferable to have an implementation in C rather than C++? Cython, swig, or hand-wrapped code? cKDTree is written in Cython, with C. Should I stick to that convention to maintain uniformity in the scipy.spatial package? Please let me know what you think -Jake

4 3

slow setitem
by Benny Malengier 02 Dec '09

02 Dec '09

A question about the sparse matrix and suggestion for speed improvement. I have a code of 1000*1000 sparse matrix of 11 full diagonals. Using csr. Assigning the matrix via setdiags takes 14 seconds, of which 13 seconds is in the check_format function of sparse/base.py. This is due to setdiag doing: self[i, i + k] = v while setitem in compressed.py always does a self.check_format(full_check=True) Removing the check_format reduces assignment of the matrix to 1 second. Is it really needed that the assignmentof setdiag is again checked via check_format? Allowing for a setitem that does not call check_format would be usefull. One could set a dirty flag on a setitem call, and do a check_format only when a computation is performed and the flag is dirty. On the other hand, I'm not making errors, and to have a flag like NOCHECKS=TRUE would be handy as it would speed up the code a lot. I could create a solution that is acceptable for scipy, but then I'd need to know how such a solution should look like. Note that there are quite some zeroes in my diagonals now too, that are now set to 0., if setitem would be fast, I could drop setdiag call, and do a fast setitem call. Or are sparse matrixes supposed to be used differently? Benny

3 4

trouble building from svn
by Darren Dale 02 Dec '09

02 Dec '09

I am attempting to build scipy from svn sources on OS X 10.6. I get the following error, could anyone please advise? C compiler: gcc-4.2 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -arch x86_64 -pipe compile options: '-Iscipy/fftpack/src -Ibuild/src.macosx-10.6-universal-2.6 -I/Users/darren/.local/lib/python2.6/site-packages/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c' /usr/local/bin/gfortran -Wall -arch x86_64 build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/src/dct.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -Lbuild/temp.macosx-10.6-universal-2.6 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-universal-2.6/scipy/fftpack/_fftpack.so Undefined symbols: "_Py_BuildValue", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o "_PyExc_RuntimeError", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_call in fortranobject.o "_PyExc_ImportError", referenced from: _init_fftpack in _fftpackmodule.o "_PyCObject_Type", referenced from: _init_fftpack in _fftpackmodule.o "_PyString_ConcatAndDel", referenced from: _fortran_getattr in fortranobject.o "_MAIN__", referenced from: _main in libgfortranbegin.a(fmain.o) "_PyImport_ImportModule", referenced from: _init_fftpack in _fftpackmodule.o "_PyArg_ParseTupleAndKeywords", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o "_PyType_Type", referenced from: _init_fftpack in _fftpackmodule.o "_PySequence_GetItem", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyMem_Free", referenced from: _fortran_dealloc in fortranobject.o "_PyErr_NewException", referenced from: _init_fftpack in _fftpackmodule.o "_PyObject_Type", referenced from: _array_from_pyobj in fortranobject.o "_PyErr_Clear", referenced from: _int_from_pyobj in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o "_PyExc_AttributeError", referenced from: _fortran_setattr in fortranobject.o "_PyDict_SetItemString", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_getattr in fortranobject.o _fortran_getattr in fortranobject.o _PyFortranObject_New in fortranobject.o _F2PyDict_SetItemString in fortranobject.o _fortran_setattr in fortranobject.o "_PyCObject_AsVoidPtr", referenced from: _init_fftpack in _fftpackmodule.o "_PyErr_Format", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_call in fortranobject.o "_PyString_FromString", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_getattr in fortranobject.o _fortran_getattr in fortranobject.o "_PyObject_Str", referenced from: _array_from_pyobj in fortranobject.o "_PySequence_Check", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyObject_GetAttrString", referenced from: _int_from_pyobj in _fftpackmodule.o _init_fftpack in _fftpackmodule.o "_PyExc_TypeError", referenced from: _fortran_call in fortranobject.o _array_from_pyobj in fortranobject.o "_PyDict_DelItemString", referenced from: _fortran_setattr in fortranobject.o "_PyString_AsString", referenced from: _array_from_pyobj in fortranobject.o "_PyDict_New", referenced from: _PyFortranObject_NewAsAttr in fortranobject.o _PyFortranObject_New in fortranobject.o _fortran_setattr in fortranobject.o "_PyErr_Occurred", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _int_from_pyobj in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o "_PyType_IsSubtype", referenced from: _int_from_pyobj in _fftpackmodule.o _array_from_pyobj in fortranobject.o "_PyDict_GetItemString", referenced from: _fortran_getattr in fortranobject.o "__PyObject_New", referenced from: _PyFortranObject_NewAsAttr in fortranobject.o _PyFortranObject_New in fortranobject.o "_Py_InitModule4_64", referenced from: _init_fftpack in _fftpackmodule.o "_PyCObject_FromVoidPtr", referenced from: _fortran_getattr in fortranobject.o "_PyErr_SetString", referenced from: _int_from_pyobj in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _array_from_pyobj in fortranobject.o _fortran_setattr in fortranobject.o "_Py_FindMethod", referenced from: _fortran_getattr in fortranobject.o "_PyNumber_Int", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyComplex_Type", referenced from: _int_from_pyobj in _fftpackmodule.o "__Py_NoneStruct", referenced from: _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _fortran_getattr in fortranobject.o _array_from_pyobj in fortranobject.o _array_from_pyobj in fortranobject.o _fortran_setattr in fortranobject.o "_PyExc_ValueError", referenced from: _array_from_pyobj in fortranobject.o "_PyModule_GetDict", referenced from: _init_fftpack in _fftpackmodule.o "_PyErr_Print", referenced from: _init_fftpack in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o ld: symbol(s) not found collect2: ld returned 1 exit status Undefined symbols: "_Py_BuildValue", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o "_PyExc_RuntimeError", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_call in fortranobject.o "_PyExc_ImportError", referenced from: _init_fftpack in _fftpackmodule.o "_PyCObject_Type", referenced from: _init_fftpack in _fftpackmodule.o "_PyString_ConcatAndDel", referenced from: _fortran_getattr in fortranobject.o "_MAIN__", referenced from: _main in libgfortranbegin.a(fmain.o) "_PyImport_ImportModule", referenced from: _init_fftpack in _fftpackmodule.o "_PyArg_ParseTupleAndKeywords", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o "_PyType_Type", referenced from: _init_fftpack in _fftpackmodule.o "_PySequence_GetItem", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyMem_Free", referenced from: _fortran_dealloc in fortranobject.o "_PyErr_NewException", referenced from: _init_fftpack in _fftpackmodule.o "_PyObject_Type", referenced from: _array_from_pyobj in fortranobject.o "_PyErr_Clear", referenced from: _int_from_pyobj in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o "_PyExc_AttributeError", referenced from: _fortran_setattr in fortranobject.o "_PyDict_SetItemString", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_getattr in fortranobject.o _fortran_getattr in fortranobject.o _PyFortranObject_New in fortranobject.o _F2PyDict_SetItemString in fortranobject.o _fortran_setattr in fortranobject.o "_PyCObject_AsVoidPtr", referenced from: _init_fftpack in _fftpackmodule.o "_PyErr_Format", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_call in fortranobject.o "_PyString_FromString", referenced from: _init_fftpack in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_getattr in fortranobject.o _fortran_getattr in fortranobject.o "_PyObject_Str", referenced from: _array_from_pyobj in fortranobject.o "_PySequence_Check", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyObject_GetAttrString", referenced from: _int_from_pyobj in _fftpackmodule.o _init_fftpack in _fftpackmodule.o "_PyExc_TypeError", referenced from: _fortran_call in fortranobject.o _array_from_pyobj in fortranobject.o "_PyDict_DelItemString", referenced from: _fortran_setattr in fortranobject.o "_PyString_AsString", referenced from: _array_from_pyobj in fortranobject.o "_PyDict_New", referenced from: _PyFortranObject_NewAsAttr in fortranobject.o _PyFortranObject_New in fortranobject.o _fortran_setattr in fortranobject.o "_PyErr_Occurred", referenced from: _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_rfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_cfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o _int_from_pyobj in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o "_PyType_IsSubtype", referenced from: _int_from_pyobj in _fftpackmodule.o _array_from_pyobj in fortranobject.o "_PyDict_GetItemString", referenced from: _fortran_getattr in fortranobject.o "__PyObject_New", referenced from: _PyFortranObject_NewAsAttr in fortranobject.o _PyFortranObject_New in fortranobject.o "_Py_InitModule4_64", referenced from: _init_fftpack in _fftpackmodule.o "_PyCObject_FromVoidPtr", referenced from: _fortran_getattr in fortranobject.o "_PyErr_SetString", referenced from: _int_from_pyobj in _fftpackmodule.o _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _array_from_pyobj in fortranobject.o _fortran_setattr in fortranobject.o "_Py_FindMethod", referenced from: _fortran_getattr in fortranobject.o "_PyNumber_Int", referenced from: _int_from_pyobj in _fftpackmodule.o "_PyComplex_Type", referenced from: _int_from_pyobj in _fftpackmodule.o "__Py_NoneStruct", referenced from: _f2py_rout__fftpack_dct3 in _fftpackmodule.o _f2py_rout__fftpack_dct2 in _fftpackmodule.o _f2py_rout__fftpack_dct1 in _fftpackmodule.o _f2py_rout__fftpack_ddct3 in _fftpackmodule.o _f2py_rout__fftpack_ddct2 in _fftpackmodule.o _f2py_rout__fftpack_ddct1 in _fftpackmodule.o _f2py_rout__fftpack_crfft in _fftpackmodule.o _f2py_rout__fftpack_rfft in _fftpackmodule.o _f2py_rout__fftpack_cfft in _fftpackmodule.o _f2py_rout__fftpack_zrfft in _fftpackmodule.o _f2py_rout__fftpack_drfft in _fftpackmodule.o _f2py_rout__fftpack_zfft in _fftpackmodule.o _f2py_rout__fftpack_cfftnd in _fftpackmodule.o _f2py_rout__fftpack_zfftnd in _fftpackmodule.o _fortran_getattr in fortranobject.o _array_from_pyobj in fortranobject.o _array_from_pyobj in fortranobject.o _fortran_setattr in fortranobject.o "_PyExc_ValueError", referenced from: _array_from_pyobj in fortranobject.o "_PyModule_GetDict", referenced from: _init_fftpack in _fftpackmodule.o "_PyErr_Print", referenced from: _init_fftpack in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o ld: symbol(s) not found collect2: ld returned 1 exit status error: Command "/usr/local/bin/gfortran -Wall -arch x86_64 build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/src/dct.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -Lbuild/temp.macosx-10.6-universal-2.6 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-universal-2.6/scipy/fftpack/_fftpack.so" failed with exit status 1

3 5

Scipy on facebook ?
by Arkapravo Bhaumik 30 Nov '09

30 Nov '09

Hello everyone Thank you for replies to my previous postings. I recently came across this facebook group , http://www.facebook.com/group.php?gid=40809502527&ref=search&sid=1043259783… Is this the official group ? or there is some other ? Regards Arkapravo

3 2

Constants in Scipy
by Arkapravo Bhaumik 28 Nov '09

28 Nov '09

Hi everyone I had a question, how many built-in constants are there in Scipy ?, I am familiar with pi and e , how many more are there ? I had been trying to evaluate euler-gamma in Scipy, which is easy http://3chevrons.blogspot.com/2009/10/eulers-gamma.html . However, MATLAB in comparison has euler-gamma built-into it and intelligently recognises the expression as it is typed in, Scipy is not yet able to do so. If the desire is indeed to make Scipy into a dynamic and robust software then various constants must be built-into the software and Scipy made to identify such expressions. Many thanks David ( David Cournapeau) for replying to my previous posting and confirming my observations about sici. Regards Arkapravo

6 5

Issues in sici
by Arkapravo Bhaumik 27 Nov '09

27 Nov '09

Hi everyone I have come across a minor issue with the sici module which evaluates the sine integral. Evaluation is excellent and gives precise values, however for inputs of infinity the results are nan which is very annoying. I have compared MATLAB and Scipy in these regards, please have a look http://3chevrons.blogspot.com/2009/11/sine-integral-in-scipy.html . I would guess that there should be special provisions for infinity in sici module and an exception must be coded in. I have also been playing around with such integrals, http://3chevrons.blogspot.com/2009/10/exotic-integrals-in-scipy.html . Please feel free to reply. Regards Arkapravo

2 1

is this a bug (take with indices in a matrix)
by Thouis (Ray) Jones 27 Nov '09

27 Nov '09

>>> from numpy import * >>> q = matrix(arange(9).reshape((3,3))) >>> take(q, matrix([[0]]), axis=0) matrix([[0, 1, 2]]) >>> take(q, matrix([[0]]), axis=1) matrix([[0, 3, 6]]) Expected behavior for the last expression: >>> take(q, [0], axis=1) matrix([[0], [3], [6]])

2 1