Mailman 3 October 2010 - NumPy-Discussion

Re: [Numpy-discussion] ndarray of object dtype
by Ioan Ferencik Oct. 8, 2010

Oct. 8, 2010

Hello Robert, I dare to bother you again with some questions. this time I have a numpy array with fields ar = array([(1.0, 2.0, 3, 4), (2.0, 3.0, 4, 5)], dtype={'names': ['q','wl','cssid','br'], 'formats':['f4', 'f4', 'i4', 'i4'], 'offsets': [0, 4, 8, 12]}, order='F') on C API I want to match this struct typedef struct val1{ float q; float wl; int cssid; int br; }hm1dval1; to an element of this array I get the array object, i can see the fields. The type of the array elements is Pyarray_VOID however following code gives me a segfault hm1dval1 **s = PyArray_DATA(ao); fprintf(stdout, "q is %d\n", (**s).cssid); I also tried to use PyArray_BYTES but it failed too I was thinking to add 4 bytes to PyArray_DATA(ao) for each member of the struct and for each elem of the array and cast those pointers to the float, float respectively int, int values but that failed too. Can you see what am I doing wrong? Quoting Robert Kern <robert.kern(a)gmail.com>: > On Mon, Oct 4, 2010 at 00:41, Ioan Ferencik <ioan.ferencik(a)tkk.fi> wrote: >> Hello list, >> >> I am trying to pass elements of a custom defined with C API. >> I have successfully wrapped a type around a C struct. >> I intent to create a list with these objects and process it using >> numpy C API. >> So i create an array: >> >> array = (PyArrayObject *)PyArray_ContiguousFromObject(input, >> PyArray_OBJECT, 0, 0); >> >> to my understanding each el. in this array is a pointer to my type so >> a cast to this type >> should work. >> >> >> this is my custom type >> >> typedef struct val{ >> PyObject_HEAD >> float q; >> float wl; >> int cssid; >> int br; >> }hm1dval; >> >> I am passing only one element for testing purposes. >> >> in python >> a = [hm1d1.hm1dval() for i in range(0,1)] >> for c in a: >> c.set_values(q=3.0, wl=2.5, cssid=6, br=7) >> >> >> So following code should be valid in C: >> >> hm1dval s* = PyArray_DATA(array); >> >> but the members are 0 after casting in spite they were set previously. > > The elements of a dtype=object array are PyObject* pointers. In C, an > array of pointers would look like this: > > hm1dval **s = PyArray_DATA(array); > > -- > Robert Kern > > "I have come to believe that the whole world is an enigma, a harmless > enigma that is made terrible by our own mad attempt to interpret it as > though it had an underlying truth." > -- Umberto Eco > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > Ioan Ferencik PhD student Aalto University School of Science and Technology Faculty Of Civil and Env. Engineering Lahti Center Tel: +358505122707

2 1

unpack argument in loadtxt/genfromtxt does not work as documented
by Chris Fonnesbeck Oct. 7, 2010

Oct. 7, 2010

The documentation for loadtxt and genfromtxt state that the unpack argument functions as follows: If True, the returned array is transposed, so that arguments may be unpacked using x, y, z = loadtxt(...). In practice, this does not always occur. I have a csv file of mixed data types, and try importing it via: genfromtxt("progestogens.csv", delimiter=",", names=True, dtype=dtype([('id', int),('study', '|S25'),('year', int),('treat', int),('drug', '|S25'),('form', '|S10'),('ptb', int),('mgest', int),('lab', int),('n', int),('y', int),('var', '|S5'),('wt', int),('sdwt', int)]), unpack=True) With unpack=True, I would expect the data to be presented by columns, however the resulting array is by rows: array([(1, 'Meis', 2003, 1, '17P', 'IM', 1, 0, 0, 306, 111, 'ptb'), (1, 'Meis', 2003, 0, '17P', 'IM', 1, 0, 0, 153, 84, 'ptb'), (2, 'Rai', 2009, 1, 'Progesterone', 'Oral', 1, 0, 0, 74, 29, 'ptb'), (2, 'Rai', 2009, 0, 'Progesterone', 'Oral', 1, 0, 0, 74, 44, 'ptb'), ... The same behaviour occurs using loadtxt. Moreover, this array is untransposeable, so I am stuck with having to iterate over all the rows, making genfromtxt no better than csv.reader.

3 7

numpy mac binary for Python 2.7: which version is it for?
by Russell E. Owen Oct. 7, 2010

Oct. 7, 2010

There are two Python 2.7 installers available at python.org a 32 bit version for MacOS X 10.3.9 and later and a 64 bit version for Mac OS X 10.5 and later. There is one numpy 1.5.0 binary installer for Mac Python 2.7. Which Mac python was it built for? (Or if it is compatible with both, how did you manage that?). -- Russell

2 1

point line distance
by Renato Fabbri Oct. 7, 2010

Oct. 7, 2010

supose you have a line defined by two points and a point. you want the distance what are easiest possibilities? i am doing it, but its nasty'n ugly -- GNU/Linux User #479299 skype: fabbri.renato

4 3

puzzle with boolean dtype
by Alan G Isaac Oct. 6, 2010

Oct. 6, 2010

Integer exponentiation fails (i.e., changes type) with boolean dtype. See below. Expected? Alan Isaac >>> a = np.array([[0,1,0],[0,0,1],[1,0,0]], dtype=np.bool_) >>> a2 = a*a >>> a3 = a2*a >>> print(a3) [[False True False] [False False True] [ True False False]] >>> print(a**3) [[0 1 0] [0 0 1] [1 0 0]]

2 3

numpy on 64 bit x86_64
by P Sanjey Oct. 6, 2010

Oct. 6, 2010

Hi I have a x86_64 Fedora core 3 machine where I want to install numpy but python2.4 has been installed on this machine using Intel compilers instead of gcc Can someone tell me how I can install numpy on this architecture? Thanks

1 0

bug in ceil()
by Christian Fischer Oct. 6, 2010

Oct. 6, 2010

Hi All, I use numpy 1.4.1 on Debian squeeze amd64. I noticed that ceil() is not working properly. If the input to ceil() is a float I expect a float to be returned but for inputs in (-1.0, 0.0) the result is of type integer. In [65]: np.__version__ Out[65]: '1.4.1' In [66]: np.ceil(-1.1) Out[66]: -1.0 In [67]: np.ceil(-0.734) Out[67]: -0 In [68]: np.ceil(-0.256) Out[68]: -0 In [69]: np.ceil(-0.0) Out[69]: -0 In [70]: np.ceil(0.2) Out[70]: 1.0 Best wishes Christian -- Dipl.-Ing. Christian Fischer Institute of Engineering and Computational Mechanics (name in German: Institut für Technische und Numerische Mechanik) University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany mailto:cfischer@itm.uni-stuttgart.de, tel 0711-685-66565, fax -66400 http://www.itm.uni-stuttgart.de/staff/Fischer

4 3

index of a value in an array
by Chris Withers Oct. 6, 2010

Oct. 6, 2010

Hi All, Given an array such as: array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]) How can I find the index of a particular number in the array? (ie: if it was a list, I'd do [1,2,3,4].index(3)) cheers, Chris

5 5

alter_code1.py doesn't convert (any more)?
by Frank Thommen Oct. 6, 2010

Oct. 6, 2010

Hi, I'm trying to help a user to migrate from Numeric - which he used up to now - to numpy. I found reference to alter_code1.py on http://numpy.scipy.org/old_array_packages.html. First I tried the conversion script: # python2.6 /path/to/alter_code1.py test.py and alternatively # python2.6 /path/to/alter_code1.py ./ This didn't modify test.py at all. Then I tried to convert from within Python: # python2.6 Python 2.6.2 (r262:71600, Aug 5 2010, 14:21:11) [GCC 4.4.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy.numarray.alter_code1 as noa >>> noa.convertfile("test.py") >>> ^D # This modified test.py, but only partially. E.g. the import line was still untouched, meaning that it still imported Numeric instead of numpy: # diff ../test-original.py test.py 0a1,2 > ## Automatically adapted for numpy.numarray Oct 06, 2010 by > 49c51 < pyfid.byteswap() --- > pyfid.byteswap(True) 74c76 < databin.byteswap() --- > databin.byteswap(True) # After I've changed 'import os, string, array, Numeric' to 'import os, string, array, numpy' I realized, that the conversion had introduced errors: # python2.6 ./test.py <command line parameters> Traceback (most recent call last): File "./test.py", line 115, in <module> combineser3D(td3,td2,td1,ser,ser1,fidnum) File "./test.py", line 21, in combineser3D allser1=readBrukerSer(tdall,td3,ser) File "./test.py", line 51, in readBrukerSer pyfid.byteswap(True) TypeError: byteswap() takes no arguments (1 given) # So either this method doesn't work (any more) or I am doing something wrong. The numpy version we are using is 1.4.1 with Python 2.6.2 from python.org. Any help regarding this is highly appreciated. Thanks in advance frank

1 0

Please help on compilation fortran module using f2py
by Jing Oct. 6, 2010

Oct. 6, 2010

Hi, everyone: I am new to the python numpy and f2py. I really need help on compiling FORTRAN module using f2py. I have been searched internet without any success. Here is my setup: I have a Ubuntu 10.04 LTS with python 2.6, numpy 1.3.0 and f2py 2 (installed from ubuntu) and gfortran compiler 4.4. I have a simple Fortran subroutine (in CSM_CH01_P1_1a_F.f95 file) as shown below: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ! subroutine sim_model_1(ts, n, a) ! !f2py integer, intent(in) :: ts, n !f2py real,dimension(n), intent(inout) :: a implicit none integer :: t, m, i real :: ep, dm ! m=n/2; call init_random_seed() do if(t > ts) exit call randperm(n,a) call random_number(ep) do i=1,n,2 dm=a(i)+a(i+1) a(i)=ep*dm a(i+1)=(1-ep)*dm end do t = t + 1 end do return end subroutine sim_model_1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I use f2py -m sim_model_1 -h sim_model_1.pyf CSM_CH01_P1_1a_F.f95 to generate signature file which is OK as shown below: =================================================== ! -*- f90 -*- ! Note: the context of this file is case sensitive. python module sim_model_1 ! in interface ! in :sim_model_1 subroutine sim_model_1(ts,n,a) ! in :sim_model_1:CSM_CH01_P1_1a_F.f95 integer intent(in) :: ts integer optional,intent(in),check(len(a)>=n),depend(a) :: n=len(a) real dimension(n),intent(inout) :: a end subroutine sim_model_1 end interface end python module sim_model_1 ! This file was auto-generated with f2py (version:2). ! See http://cens.ioc.ee/projects/f2py2e =================================================== However, when I try to make the module, the compilation failed as if f2py does not pass the signature file to the compiler. The screen printout during compilation as shown below: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ f2py -c --fcompiler=gnu95 sim_model_1.pyf CSM_CH <> f2py -c --fcompiler=gnu95 sim_model_1.pyf CSM_CH0 1_P1_1a_F.f95 running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building extension "sim_model_1" sources creating /tmp/tmp6MXJY3 creating /tmp/tmp6MXJY3/src.linux-x86_64-2.6 f2py options: [] f2py: sim_model_1.pyf Reading fortran codes... Reading file 'sim_model_1.pyf' (format:free) Post-processing... Block: sim_model_1 Block: sim_model_1 Post-processing (stage 2)... Building modules... Building module "sim_model_1"... Constructing wrapper function "sim_model_1"... sim_model_1(ts,a,[n]) Wrote C/API module "sim_model_1" to file "/tmp/tmp6MXJY3/src.linux-x86_64-2.6/sim_model_1module.c" adding '/tmp/tmp6MXJY3/src.linux-x86_64-2.6/fortranobject.c' to sources. adding '/tmp/tmp6MXJY3/src.linux-x86_64-2.6' to include_dirs. copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmp6MXJY3/src.linux-x86_64-2.6 copying /usr/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmp6MXJY3/src.linux-x86_64-2.6 running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler using build_ext building 'sim_model_1' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC creating /tmp/tmp6MXJY3/tmp creating /tmp/tmp6MXJY3/tmp/tmp6MXJY3 creating /tmp/tmp6MXJY3/tmp/tmp6MXJY3/src.linux-x86_64-2.6 compile options: '-I/tmp/tmp6MXJY3/src.linux-x86_64-2.6 -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c' gcc: /tmp/tmp6MXJY3/src.linux-x86_64-2.6/fortranobject.c gcc: /tmp/tmp6MXJY3/src.linux-x86_64-2.6/sim_model_1module.c compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-I/tmp/tmp6MXJY3/src.linux-x86_64-2.6 -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c' gfortran:f90: CSM_CH01_P1_1a_F.f95 CSM_CH01_P1_1a_F.f95:29.7: a(i)=ep*dm 1 Error: 'a' at (1) is not a variable CSM_CH01_P1_1a_F.f95:30.7: a(i+1)=(1-ep)*dm 1 Error: 'a' at (1) is not a variable CSM_CH01_P1_1a_F.f95:9.25: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'ts' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:9.28: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'n' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:9.31: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'a' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:28.15: dm=a(i)+a(i+1) 1 Error: Function 'a' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:29.7: a(i)=ep*dm 1 Error: 'a' at (1) is not a variable CSM_CH01_P1_1a_F.f95:30.7: a(i+1)=(1-ep)*dm 1 Error: 'a' at (1) is not a variable CSM_CH01_P1_1a_F.f95:9.25: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'ts' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:9.28: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'n' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:9.31: subroutine sim_model_1(ts, n, a) 1 Error: Symbol 'a' at (1) has no IMPLICIT type CSM_CH01_P1_1a_F.f95:28.15: dm=a(i)+a(i+1) 1 Error: Function 'a' at (1) has no IMPLICIT type error: Command "/usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops -I/tmp/tmp6MXJY3/src.linux-x86_64-2.6 -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c -c CSM_CH01_P1_1a_F.f95 -o /tmp/tmp6MXJY3/CSM_CH01_P1_1a_F.o" failed with exit status 1 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ It looks like the two f2py directive declaration cause the problem. Any suggestion?

2 1