Mailman 3 March 2012 - NumPy-Discussion

f2py function name issues
by Sameer Grover March 9, 2012

March 9, 2012

subroutine union () write(*,*)'Hello from Fortran90!!!' end subroutine union f2py is unable to wrap this function. Changing the name of the subroutine from 'union' to something else works. I understand that problems like these have been reported a long time ago (http://cens.ioc.ee/pipermail/f2py-users/2003-November/000605.html) with some other function names as well. This looks like a bug to me or is there something I'm missing? Regards, Sameer Grover

2 2

Memory leak in numpy
by FRENK Andreas March 9, 2012

March 9, 2012

Dear Community, I have an issue with numpy consuming more and more memory. According to ticket: http://projects.scipy.org/numpy/ticket/1427 This is a known issue. It should be fixed in 2.0.0.dev-9451260. What does this mean? It sound like a development release. Is there any chance to fix it in 1.6.1 also? Or, would it be possible to send me the fixes to include it in 1.6.1 (or 1.4.1) on my own?! Thanks, Andreas This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) you should not read, disclose, or copy it, (ii) please notify sender of your receipt by reply email and delete this email and all attachments, (iii) Dassault Systemes does not accept or assume any liability or responsibility for any use of or reliance on this email. For other languages, go to http://www.3ds.com/terms/email-disclaimer

2 1

Fromfile Issue
by Nicola Creati March 9, 2012

March 9, 2012

Hello, I'm writing a library able to read LAS lidar files. I generally use it under Linux without any problems. I'm now testing my library on a Windows 7 64 bit computer and I meet some problems reading the file. I generally use fromfile function to read the file. I noted that the fromfile returns an arry with some zeros at the end if I read the whole file or if i read only a finite number of data i get only a fraction of them. By the way I have created a sample script that reproduces the problem I noted: """ Sample code """ import numpy as np sz = 1000000 data = np.random.random(sz) output = open('test.bin', 'w') data.tofile(output) output.close() del output print 'Original data:', data fid = open('test.bin', 'r') new_data = np.fromfile(fid) fid.close() del fid print 'Data read:', new_data fid = open('test.bin', 'r') slice = np.fromfile(fid, count=100) fid.close() print '100 read data:', slice The "new_data" array has several zeros at the end. The "slice" array has not 100 items. At every code run the "slice" array size changes. I'm using numpy 1.6.1 64bit (taken from Christoph Gohlke website) , with python 2.7.2 64 bit. Under Linux Ubuntu 10.10 64bit and numpy 1.6.1 the code works as expected. Thanks. Nicola

2 2

memory leak in numpy.take
by Dmitrey March 9, 2012

March 9, 2012

memory leak was observed in numpy versions 1.5.1 and latest git trunc from numpy import * for i in range(100000): if i % 100 == 0: print(i) a = empty(10000,object) for j in range(10000): a[j] = array(1) a = take(a, range(9000),out=a[:9000])

1 0

solving linear equations
by salahudeen razac March 9, 2012

March 9, 2012

I wrote a script to solve the equation ‘*P =Kd .V2 + Kl.VA.BT + C’* . To solve the equation I have used the matrix method. Ie, K*X = P where *[P] = [ P1* * **P2 a column matrix with the total powers P1, P2,P3…….PN at (V1,T1),(V2,T2)……( VN.TN) respectively,\* * P3* * ..* * **PN ]* * * * [K] = [ V12 V1A.BT1 1* * V22 V2A.B T2 1* * V32 V3A.B T3 1* * ………………………..* * VN2 VNA.B TN 1 ]* * * * [X]= [ Kd A column matrix with the unknowns* * **Kl* * **C ]* Now in order to solve multiply both sides with KT, ie *KT.K.X = KTP *or *A.X = B* where *A*=* KT.K *and* B*=* KTP* * * Now we will get the matrix X by using *linalg.solve(A,B*) function which will eventually solve for a set of linear equations of the form Ax=B* * I was able to get the solution. But it is not acceptable since some of the values are negative. SO I want to know is there any way to give some constraints like the solution should contain only positive values and give any range for the solution? I also tried with linalg.lstsq and I am getting the same results * ----- Salahudeen razak* *| +917760902602* *o__* * _> /__ (_) \(_)*... *Burn fat not fuel * * *

2 1

More SPARC pain
by Matthew Brett March 8, 2012

March 8, 2012

Hi, I found this test caused a bus error on current trunk: <pre> import numpy as np from StringIO import StringIO as BytesIO from numpy.testing import assert_array_equal def test_2d_buf(): dtt = np.complex64 arr = np.arange(10, dtype=dtt) # 2D array arr2 = np.reshape(arr, (2, 5)) # Fortran write followed by (C or F) read caused bus error data_str = arr2.tostring('F') data_back = np.ndarray(arr2.shape, arr2.dtype, buffer=data_str, order='F') assert_array_equal(arr2, data_back) </pre> gdb run gives ... test_me3.test_2d_buf ... Program received signal SIGBUS, Bus error. 0xf78f5458 in _aligned_strided_to_contig_size8 ( dst=0xdc0e08 "\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\313\373\373\373\373", dst_stride=8, src=0xcdfc44 "", src_stride=16, N=5, __NPY_UNUSED_TAGGEDsrc_itemsize=8, __NPY_UNUSED_TAGGEDdata=0x0) at numpy/core/src/multiarray/lowlevel_strided_loops.c.src:137 137 (*((@type@ *)dst)) = @swap@@elsize@(*((@type@ *)src)); Debug log attached. Shall I make an issue? Best, Matthew

1 1

use for missing (ignored) data?
by Neal Becker March 8, 2012

March 8, 2012

I'm wondering what is the use for the ignored data feature? I can use: A[valid_A_indexes] = whatever to process only the 'non-ignored' portions of A. So at least some simple cases of ignored data are already supported without introducing a new type. OTOH: w = A[valid_A_indexes] will copy A's data, and subsequent use of w[:] = something will not update A. Is this the reason for wanting the ignored data feature?

4 5

Github key audit.
by Charles R Harris March 7, 2012

March 7, 2012

Hi All, Many here have probably received the message from github about push/pull access being blocked until you have auditied your ssh keys. To generate a key fingerprint on fedora, I did the following: $charris@f16 ~$ ssh-keygen -l -f .ssh/id_dsa.pub I don't how this looks for those of you using windows. The compromise looks to be a 'whitehat' attack telling the rails developers to "FIX THE G*DD*MNED PROBLEM". More here, Github compromized<http://lwn.net/Articles/485162/> . Chuck

2 1

checking for c compiler during build
by Skipper Seabold March 7, 2012

March 7, 2012

Is there a way to use numpy.distuils to programmatically check for a C compiler at build time in a platform independent way?

1 1

Fixing PyArray_Descr flags member size, ABI vs pickling issue
by David Cournapeau March 7, 2012

March 7, 2012

Hi, This is following the discussion on bug http://projects.scipy.org/numpy/ticket/2017 Essentially, there is a discrepency between the actual type of the flags member in the dtype C structure (char) and how it is declared in the descriptor table (T_INT). The problem is that we are damned if we fix it, damned if we are not: - fixing T_INT to T_BYTE. flag in python is now fixed, but it breaks pickled numpy arrays - not fixing it means that the value is broken at the python level. Changing the flag to be an actual int would break the ABI. I currently have this: https://github.com/numpy/numpy/pull/228 Which one is the more appropriate ? Maybe a deprecation warning for 1.7 and change it in 1.8 ? Note that we can fix the hash issue with either solution, David

3 6