Mailman 3 September 2010 - NumPy-Discussion

mixed mode arithmetic
by Neal Becker July 11, 2023

July 11, 2023

I've been browsing the numpy source. I'm wondering about mixed-mode arithmetic on arrays. I believe the way numpy handles this is that it never does mixed arithmetic, but instead converts arrays to a common type. Arguably, that might be efficient for a mix of say, double and float. Maybe not. But for a mix of complex and a scalar type (say, CDouble * Double), it's clearly suboptimal in efficiency. So, do I understand this correctly? If so, is that something we should improve?

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Re: [Numpy-discussion] example reading binary Fortran file
by Neil Martinsen-Burrell July 22, 2021

July 22, 2021

David Froger <david.froger.info <at> gmail.com> writes: > Hy,My question is about reading Fortran binary file (oh no this question > again...) I've posted this before, but I finally got it cleaned up for the Cookbook. For this purpose I use a subclass of file that has methods for reading unformatted Fortran data. See http://www.scipy.org/Cookbook/FortranIO/FortranFile. I'd gladly see this in numpy or scipy somewhere, but I'm not sure where it belongs. > program makeArray > implicit none > integer,parameter:: nx=10,ny=20 > real(4),dimension(nx,ny):: ux,uy,p > integer :: i,j > open(11,file='uxuyp.bin',form='unformatted') > do i = 1,nx > do j = 1,ny > ux(i,j) = real(i*j) > uy(i,j) = real(i)/real(j) > p (i,j) = real(i) + real(j) > enddo > enddo > write(11) ux,uy > write(11) p > close(11) > end program makeArray When I run the above program compiled with gfortran on my Intel Mac, I can read it back with:: >>> import numpy as np >>> from fortranfile import FortranFile >>> f=FortranFile('uxuyp.bin', endian='<') >>> uxuy = f.readReals(prec='f') # 'f' for default reals >>> len(uxuy) 400 >>> ux = np.array(uxuy[:200]).reshape((20,10)).T >>> uy = np.array(uxuy[200:]).reshape((20,10)).T >>> p = f.readReals('f').reshape((20,10)).T >>> ux array([[ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20.], [ 2., 4., 6., 8., 10., 12., 14., 16., 18., 20., 22., 24., 26., 28., 30., 32., 34., 36., 38., 40.], [ 3., 6., 9., 12., 15., 18., 21., 24., 27., 30., 33., 36., 39., 42., 45., 48., 51., 54., 57., 60.], [ 4., 8., 12., 16., 20., 24., 28., 32., 36., 40., 44., 48., 52., 56., 60., 64., 68., 72., 76., 80.], [ 5., 10., 15., 20., 25., 30., 35., 40., 45., 50., 55., 60., 65., 70., 75., 80., 85., 90., 95., 100.], [ 6., 12., 18., 24., 30., 36., 42., 48., 54., 60., 66., 72., 78., 84., 90., 96., 102., 108., 114., 120.], [ 7.,Proxy-Connection: keep-alive Cache-Control: max-age=0 14., 21., 28., 35., 42., 49., 56., 63., 70., 77., 84., 91., 98., 105., 112., 119., 126., 133., 140.], [ 8., 16., 24., 32., 40., 48., 56., 64., 72., 80., 88., 96., 104., 112., 120., 128., 136., 144., 152., 160.], [ 9., 18., 27., 36., 45., 54., 63., 72., 81., 90., 99., 108., 117., 126., 135., 144., 153., 162., 171., 180.], [ 10., 20., 30., 40., 50., 60., 70., 80., 90., 100., 110., 120., 130., 140., 150., 160., 170., 180., 190., 200.]]) >>> uy array([[ 1. , 0.5 , 0.33333334, 0.25 , 0.2 , 0.16666667, 0.14285715, 0.125 , 0.11111111, 0.1 , 0.09090909, 0.08333334, 0.07692308, 0.07142857, 0.06666667, 0.0625 , 0.05882353, 0.05555556, 0.05263158, 0.05 ], [ 2. , 1. , 0.66666669, 0.5 , 0.40000001, 0.33333334, 0.2857143 , 0.25 , 0.22222222, 0.2 , 0.18181819, 0.16666667, 0.15384616, 0.14285715, 0.13333334, 0.125 , 0.11764706, 0.11111111, 0.10526316, 0.1 ], [ 3. , 1.5 , 1. , 0.75 , 0.60000002, 0.5 , 0.42857143, 0.375 , 0.33333334, 0.30000001, 0.27272728, 0.25 , 0.23076923, 0.21428572, 0.2 , 0.1875 , 0.17647059, 0.16666667, 0.15789473, 0.15000001], [ 4. , 2. , 1.33333337, 1. , 0.80000001, 0.66666669, 0.5714286 , 0.5 , 0.44444445, 0.40000001, 0.36363637, 0.33333334, 0.30769232, 0.2857143 , 0.26666668, 0.25 , 0.23529412, 0.22222222, 0.21052632, 0.2 ], [ 5. , 2.5 , 1.66666663, 1.25 , 1. , 0.83333331, 0.71428573, 0.625 , 0.55555558, 0.5 , 0.45454547, 0.41666666, 0.38461539, 0.35714287, 0.33333334, 0.3125 , 0.29411766, 0.27777779, 0.2631579 , 0.25 ], [ 6. , 3. , 2. , 1.5 , 1.20000005, 1. , 0.85714287, 0.75 , 0.66666669, 0.60000002, 0.54545456, 0.5 , 0.46153846, 0.42857143, 0.40000001, 0.375 , 0.35294119, 0.33333334, 0.31578946, 0.30000001], [ 7. , 3.5 , 2.33333325, 1.75 , 1.39999998, 1.16666663, 1. , 0.875 , 0.77777779, 0.69999999, 0.63636363, 0.58333331, 0.53846157, 0.5 , 0.46666667, 0.4375 , 0.41176471, 0.3888889 , 0.36842105, 0.34999999], [ 8. , 4. , 2.66666675, 2. , 1.60000002, 1.33333337, 1.14285719, 1. , 0.8888889 , 0.80000001, 0.72727275, 0.66666669, 0.61538464, 0.5714286 , 0.53333336, 0.5 , 0.47058824, 0.44444445, 0.42105263, 0.40000001], [ 9. , 4.5 , 3. , 2.25 , 1.79999995, 1.5 , 1.28571427, 1.125 , 1. , 0.89999998, 0.81818181, 0.75 , 0.69230771, 0.64285713, 0.60000002, 0.5625 , 0.52941179, 0.5 , 0.47368422, 0.44999999], [ 10. , 5. , 3.33333325, 2.5 , 2. , 1.66666663, 1.42857146, 1.25 , 1.11111116, 1. , 0.90909094, 0.83333331, 0.76923078, 0.71428573, 0.66666669, 0.625 , 0.58823532, 0.55555558, 0.52631581, 0.5 ]]) >>> p array([[ 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.], [ 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22.], [ 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23.], [ 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24.], [ 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25.], [ 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26.], [ 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27.], [ 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28.], [ 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29.], [ 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29., 30.]]) Note that you have to provide the shape information for ux and uy because fortran writes them together as a stream of 400 numbers. -Neil

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SVD errors
by mtrumpis＠berkeley.edu June 4, 2013

June 4, 2013

Hello list.. I've run into two SVD errors over the last few days. Both errors are identical in numpy/scipy. I've submitted a ticket for the 1st problem (numpy ticket #990). Summary is: some builds of the lapack_lite module linking against system LAPACK (not the bundled dlapack_lite.o, etc) give a "LinAlgError: SVD did not converge" exception on my matrix. This error does occur using Mac's Accelerate framework LAPACK, and a coworker's Ubuntu LAPACK version. It does not seem to happen using ATLAS LAPACK (nor using Octave/Matlab on said Ubuntu) Just today I've come across a negative singular value cropping up in an SVD of a different matrix. This error does occur on my ATLAS LAPACK based numpy, as well as on the Ubuntu setup. And once again, it does not happen in Octave/Matlab. I'm using numpy 1.3.0.dev6336 -- don't know what the Ubuntu box is running. Here are some npy files for the two different cases: https://cirl.berkeley.edu/twiki/pub/User/MikeTrumpis/noconverge_operator.npy https://cirl.berkeley.edu/twiki/pub/User/MikeTrumpis/negsval_operator.npy Mike

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example reading binary Fortran file
by David Froger Feb. 13, 2013

Feb. 13, 2013

Hy, My question is about reading Fortran binary file (oh no this question again...) Until now, I was using the unpack module like that : def lread(f,fourBeginning,fourEnd,*tuple): from struct import unpack """Reading a Fortran binary file in litte-endian""" if fourBeginning: f.seek(4,1) for array in tuple: for elt in xrange(array.size): transpose(array).flat[elt] = unpack(array.dtype.char,f.read(array.itemsize))[0] if fourEnd: f.seek(4,1) After googling, I read that fopen and npfille was deprecated, and we should use numpy.fromfile and ndarray.tofile, but despite of the documentaion, the cookbook, the mailling list and google, I don't succed in making a simple example. Considering the simple Fortran code below what is the Python script to read the four arrrays? What about if my pc is little endian and the file big endian? I think it will be a good idea to put the Fortran writting-arrays code and the Python reading-array script in the cookbook and maybe a page to help people comming from Fortran to start with Python ? Best, David Froger program makeArray implicit none integer,parameter:: nx=10,ny=20 real(4),dimension(nx,ny):: ux,uy,p integer :: i,j open(11,file='uxuyp.bin',form='unformatted') do i = 1,nx do j = 1,ny ux(i,j) = real(i*j) uy(i,j) = real(i)/real(j) p (i,j) = real(i) + real(j) enddo enddo write(11) ux,uy write(11) p close(11) end program makeArray

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dtype '|S0' not understood
by David Warde-Farley Oct. 7, 2012

Oct. 7, 2012

Howdy, It seems it's possible using e.g. In [25]: dtype([('foo', str)])Out[25]: dtype([('foo', '|S0')]) to get yourself a zero-length string. However dtype('|S0') results in a TypeError: data type not understood. I understand the stupidity of creating a 0-length string field but it's conceivable that it's accidental. For example, it could lead to a situation where you've created that field, are missing all the data you had meant to put in it, serialize with np.save, and upon np.load aren't able to get _any_ of your data back because the dtype descriptor is considered bogus (can you guess why I thought of this scenario?). It seems that either dtype(str) should do something more sensible than zero-length string, or it should be possible to create it with dtype('| S0'). Which should it be? David

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PyArray_ContiguousFromObject & PyDECREF
by Michiel Jan Laurens de Hoon May 17, 2011

May 17, 2011

Dear pythoneers, In Chapter 12 ("Writing a C extension") in the Numerical Python manual, in the first example PyArray_ContiguousFromObject is used together with PyDECREF, while in the last example PyArray_ContiguousFromObject is used but the arrays are not PyDECREF'ed before the function returns. From Chapter 13 ("C API Reference") it seems that a PyDECREF is needed in both cases. Or am I missing something here? Is PyDECREF not needed for some reason in the last example? Thanks in advance, Michiel de Hoon U Tokyo First example: ============== static PyObject * trace(PyObject *self, PyObject *args) { PyObject *input; PyArrayObject *array; double sum; int i, n; if (!PyArg_ParseTuple(args, "O", &input)) return NULL; array = (PyArrayObject *) PyArray_ContiguousFromObject(input, PyArray_DOUBLE, 2, 2); if (array == NULL) return NULL; n = array->dimensions[0]; if (n > array->dimensions[1]) n = array->dimensions[1]; sum = 0.; for (i = 0; i < n; i++) sum += *(double *)(array->data + i*array->strides[0] + i*array->strides[1]); Py_DECREF(array); return PyFloat_FromDouble(sum); } Last example: ============= static PyObject * matrix_vector(PyObject *self, PyObject *args) { PyObject *input1, *input2; PyArrayObject *matrix, *vector, *result; int dimensions[1]; double factor[1]; double real_zero[1] = {0.}; long int_one[1] = {1}; long dim0[1], dim1[1]; extern dgemv_(char *trans, long *m, long *n, double *alpha, double *a, long *lda, double *x, long *incx, double *beta, double *Y, long *incy); if (!PyArg_ParseTuple(args, "dOO", factor, &input1, &input2)) return NULL; matrix = (PyArrayObject *) PyArray_ContiguousFromObject(input1, PyArray_DOUBLE, 2, 2); if (matrix == NULL) return NULL; vector = (PyArrayObject *) PyArray_ContiguousFromObject(input2, PyArray_DOUBLE, 1, 1); if (vector == NULL) return NULL; if (matrix->dimensions[1] != vector->dimensions[0]) { PyErr_SetString(PyExc_ValueError, "array dimensions are not compatible"); return NULL; } dimensions[0] = matrix->dimensions[0]; result = (PyArrayObject *)PyArray_FromDims(1, dimensions, PyArray_DOUBLE); if (result == NULL) return NULL; dim0[0] = (long)matrix->dimensions[0]; dim1[0] = (long)matrix->dimensions[1]; dgemv_("T", dim1, dim0, factor, (double *)matrix->data, dim1, (double *)vector->data, int_one, real_zero, (double *)result->data, int_one); return PyArray_Return(result); } -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon

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Problems building NumPy with GotoBLAS
by ashford＠whisperpc.com March 28, 2011

March 28, 2011

I'm having problems getting the GotoBLAS library (Nehalem optimized BLAS - "http://www.tacc.utexas.edu/tacc-projects/gotoblas2/") working properly under the Python NumPy package ("http://numpy.scipy.org/") on a quad-core Nehalem under FC10. The command used to build the library is: make BINARY=64 USE_THREAD=1 MAX_CPU_NUMBER=4 I'm limiting this to four cores, as I believe HyperThreading will slow it down (I've seen this happen with other scientific code). I'll benchmark later to see whether or not HyperThreading helps. I built the library (it uses -fPIC), then installed it under /usr/local/lib64, and created the appropriate links: # cp libgoto2_nehalemp-r1.13.a /usr/local/lib64 # cp libgoto2_nehalemp-r1.13.so /usr/local/lib64 # cd /usr/local/lib64 # ln -s libgoto2_nehalemp-r1.13.a libgoto2.a # ln -s libgoto2_nehalemp-r1.13.so libgoto2.so # ln -s libgoto2_nehalemp-r1.13.a libblas.a # ln -s libgoto2_nehalemp-r1.13.so libblas.so Without the libblas links, the NumPy configuration used the system default BLAS library (single-threaded NetLib under FC10); it's set up for the NetLib and Atlas BLAS libraries. I used the latest release of NumPy, with no site.cfg file, and no NumPy directory ("rm -rf /usr/local/python2.6/lib/python2.6/site-packages/numpy"). The configuration step ("python setup.py config") appears to run OK, as do the build ("python setup.py build") and install ("python setup.py install") steps. The problem is that the benchmark takes 8.5 seconds, which is what it took before I changed the library. python -c "import numpy as N; a=N.random.randn(1000, 1000); N.dot(a, a)" I expect I'm missing something really simple here, but I've spent >10 hours on it, and I have no idea as to what it could be. I've tried various permutations on the site.cfg file, all to no avail. I've also tried different names on the library, and different locations. I've even tried a set of symbolic links in /usr/local/lib64 for liblapack that point to libgoto. Could someone offer some suggestions? Thank you for your time. Peter Ashford

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3d plane to point cloud fitting using SVD
by Peter Schmidtke Jan. 26, 2011

Jan. 26, 2011

Dear Numpy Users, I want to fit a 3d plane into a 3d point cloud and I saw that one could use svd for this purpose. So as I am very fond of numpy I saw that svd was implementented in the linalg module. Currently I have a numpy array called xyz with n lines (number of points) and 3 columns (x,y,z). I calculated the centroid as : xyz0=npy.mean(xyz, axis=0) #calculate the centroid Next I shift the centroid of the point cloud to the origin with. M=xyz-xyz0 next I saw by matlab analogy (http://www.mathworks.co.jp/matlabcentral/newsreader/view_thread/262996) that I can write this : u,s,vh=numpy.linalg.linalg.svd(M) Then in the matlab analog they use the last column of vh to get the a,b,c coefficients for the equation a,b,c=vh[:, -1] in numpy The problem is that the equation ax+by+cz=0 does not represent the plan through my point cloud at all. What am I doing wrong, how can I get the a,b and c coefficients? Thanks in advance. -- Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona

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Math Library
by Charles R Harris Jan. 17, 2011

Jan. 17, 2011

Hi All, David Cournapeau has mentioned that he would like to have a numpy math library that would supply missing functions and I'm wondering how we should organise the source code. Should we put a mathlib directory in numpy/core/src? Inside that directory would be functions for single/double/extended/quad precision. Should they be in separate directories? What about complex versions? I'm thinking that a good start would be to borrow the msun functions for doubles. We should also make a list of what functions would go into the library and what interface the complex functions present. Thoughts? Chuck

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A faster median (Wirth's method)
by Sturla Molden Dec. 1, 2010

Dec. 1, 2010

We recently has a discussion regarding an optimization of NumPy's median to average O(n) complexity. After some searching, I found out there is a selection algorithm competitive in speed with Hoare's quick select. It has the advantage of being a lot simpler to implement. In plain Python: import numpy as np def wirthselect(array, k): """ Niklaus Wirth's selection algortithm """ a = np.ascontiguousarray(array) if (a is array): a = a.copy() l = 0 m = a.shape[0] - 1 while l < m: x = a[k] i = l j = m while 1: while a[i] < x: i += 1 while x < a[j]: j -= 1 if i <= j: tmp = a[i] a[i] = a[j] a[j] = tmp i += 1 j -= 1 if i > j: break if j < k: l = i if k < i: m = j return a Now, the median can be obtained in average O(n) time as: def median(x): """ median in average O(n) time """ n = x.shape[0] k = n >> 1 s = wirthselect(x, k) if n & 1: return s[k] else: return 0.5*(s[k]+s[:k].max()) The beauty of this is that Wirth select is extremely easy to migrate to Cython: import numpy ctypedef numpy.double_t T # or whatever def wirthselect(numpy.ndarray[T, ndim=1] array, int k): cdef int i, j, l, m cdef T x, tmp cdef T *a _array = np.ascontiguousarray(array) if (_array is array): _array = _array.copy() a = <T *> _array.data l = 0 m = <int> a.shape[0] - 1 with nogil: while l < m: x = a[k] i = l j = m while 1: while a[i] < x: i += 1 while x < a[j]: j -= 1 if i <= j: tmp = a[i] a[i] = a[j] a[j] = tmp i += 1 j -= 1 if i > j: break if j < k: l = i if k < i: m = j return _array For example, we could have a small script that generates withselect for all NumPy dtypes (T as template), and use a dict as jump table. Chad, you can continue to write quick select using NumPy's C quick sort in numpy/core/src/_sortmodule.c.src. When you are done, it might be about 10% faster than this. :-) Reference: http://ndevilla.free.fr/median/median.pdf Best regards, Sturla Molden

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