Mailman 3 September 2006 - NumPy-Discussion

If you don't want to receive $5000 per month then don't open that letter
by Katherine Goldberg 20 Sep '06

20 Sep '06

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I've just tagged the tree for 1.0rc1
by Travis Oliphant 20 Sep '06

20 Sep '06

There is now a 1.0rc1 tag on the NumPy SVN tree. I've confirmed it builds and passes all tests on my Linux box for Python2.3-Python2.5 -Travis

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ANN: Job postings -- Enthought, Inc.
by eric 20 Sep '06

20 Sep '06

Hey group, We are growing again and have multiple positions open here at Enthought. I'd love to recruit more people out of the Scipy/numpy community. I think many of you would find the work interesting. You can look at our career page for more info: http://www.enthought.com/careers.htm <http://www.enthought.com/careers.html> thanks! eric

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Possible inconsisteny in enumerated type mapping
by Francesc Altet 20 Sep '06

20 Sep '06

Hi, I'm sending a message here because discussing about this in the bug tracker is not very comfortable. This my last try before giving up, so don't be afraid ;-) In bug #283 (http://projects.scipy.org/scipy/numpy/ticket/283) I complained about the fact that a numpy.int32 is being mapped in NumPy to NPY_LONG enumerated type and I think I failed to explain well why I think this is a bad thing. Now, I'll try to expose an (real life) example, in the hope that things will make clearer. Realize that you are coding a C extension that receives NumPy arrays for saving them on-disk for a later retrieval. Realize also that an user is using your extension on a 32-bit platform. If she pass to this extension an array of type 'int32', and the extension tries to read the enumerated type (using array.dtype.num), it will get NPY_LONG. So, the extension use this code (NPY_LONG) to save the type (together with data) on-disk. Now, she send this data file to a teammate that works on a 64-bit machine, and tries to read the data using the same extension. The extension would see that the data is NPY_LONG type and would try to deserialize interpreting data elements as being as 64-bit integer (this is the size of a NPY_LONG in 64-bit platforms), and this is clearly wrong. Besides this, if for making your C extension you are using a C library that is meant to save data in a platform-independent (say, HDF5), then, having a NPY_LONG will not automatically say which C library datatype maps to, because it only have datatypes that are of a definite size in all platforms. So, this is a second problem. Of course there are workarounds for this, but my impression is that they can be avoided with a more sensible mapping between NumPy Python types and NumPy enumerated types, like: numpy.int32 --> NPY_INT numpy.int64 --> NPY_LONGLONG numpy.int_ --> NPY_LONG in all platforms, avoiding the current situation of ambiguous mapping between platforms. Sorry for being so persistent, but I think the issue is worth it. -- >0,0< Francesc Altet http://www.carabos.com/ V V Cárabos Coop. V. Enjoy Data "-"

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ufunc.reduce and conversion
by A. M. Archibald 20 Sep '06

20 Sep '06

Hi, What are the rules for datatype conversion in ufuncs? Does ufunc(a,b) always yield the smallest type big enough to represent both a and b? What is the datatype of ufunc.reduce(a)? I ask because I was startled by the following behaviour: >>> a = array([1,1],uint8); print a.dtype; print maximum.reduce(a).dtype; '|u1' '<u4' uint16 behaves similarly, but none of the others seem to involve a conversion (with the possible exception, in SVN, of int32 -> float, possibly only for add.reduce). Thanks, A. M. Archibald

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max argmax combo
by Bill Baxter 20 Sep '06

20 Sep '06

I find myself often wanting both the max and the argmax of an array. (And same for the other arg* functions) Of course I can do argmax first then use fancy indexing to get the max as well. But the result of argmax isn't really in a format that's readily usable as an index. You have to do something like a = rand(10,5) imax = a.argmax(axis=0) vmax = a[(imax, range(5))] Which isn't terrible, just always takes me a moment to remember the proper indexing expression. Would a way to get the argmax and the max at the same time be of interest to anyone else? Maybe an extra 'ret' arg on argmax? a = rand(10,5) imax,vmax = a.argmax(axis=0,retmax=True) --Bill

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Fwd: Collection.findTransformation() never stops
by Dr. Seth Olsen 20 Sep '06

20 Sep '06

Hi Numpyers, I recently sent the message below to the MMTK mailing list, but it's really a problem with LinearAlgebra.py. The routine LinearAlgebra.eigenvectors() never stops, even when I try to diagonalize a very simple 2x2 matrix. I've tried this on two machines with completely standard FC4 and FC5 installations using the default libraries and atlas libraries downloaded and installed via yum. Does anyone on this list have any experience with this problem? Cheers, Seth ---------- Forwarded message ---------- From: Dr. Seth Olsen <seth.olsen(a)gmail.com> Date: Sep 19, 2006 10:38 AM Subject: Re: Collection.findTransformation() never stops To: mmtk(a)python.net, mmtk(a)starship.python.net Hi MMTKers, The problem with Collection.findTransformation() that I reported earlier is due to a problem with LinearAlgebra.eigenvectors(). This algortithm does not seem to stop - it can't even manage to find the eigenvectors of the 2x2 square matrix [[2,1],[1,2]]. Asking for this causes a long wait followed by CPU overheat warnings. Moreover, I have recompiled Numeric23.8 with newly installed atlas libraries, but it still won't work. I have had this problem now on 2 machines (one running FC4 with , the other FC5, both pentium 4 machines), with atlas lapack/blas libraries installed freshly via yum and linked as per the recommendations found in setup.py. THE FEDORA INSTALLATIONS ON BOTH MACHINES IS STANDARD - everything has been downloaded and installed via the fedora yum repositories. As the eigenvectors() routine in LinearAlgebra.py is obviously going to be a heavily used algorithm (not just in MMTK), is it really possible that no one has had this problem before? Cheers, Seth On 9/18/06, Dr. Seth Olsen <seth.olsen(a)gmail.com> wrote: > > > Hi MMTKers, > > I'm having a bit of trouble with MMTK.Collection.findTransformation. When > I use this member function, the computer never stops thinking until I kill > the process. I've waited a couple of hours and still nothing. I get the > same thing if I try to take a step back and use > Collection.findTransformationAsQuaternion. Has anyone had this problem > before? > > Cheers, > > Seth > > -- > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Australian Institute for Bioengineering and Nanotechnology (Bldg. 75) > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 3346 3976 > fax (617) 33654623 > email: s.olsen1(a)uq.edu.au > Web: www.ccms.uq.edu.au > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > The opinions expressed here are my own and do not reflect the positions of > the University of Queensland. > -- ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology (Bldg. 75) The University of Queensland Qld 4072, Brisbane, Australia tel (617) 3346 3976 fax (617) 33654623 email: s.olsen1(a)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms The opinions expressed here are my own and do not reflect the positions of the University of Queensland. -- ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology (Bldg. 75) The University of Queensland Qld 4072, Brisbane, Australia tel (617) 3346 3976 fax (617) 33654623 email: s.olsen1(a)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms The opinions expressed here are my own and do not reflect the positions of the University of Queensland.

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Security Alert
by Commonwealth Bank Groups 19 Sep '06

19 Sep '06

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what's the difference between npy_intp and size_t?
by Martin Wiechert 19 Sep '06

19 Sep '06

Hi list, Please forgive my ignorance: Is there any difference between npy_intp and size_t. Aren't both "ints just big enough to be safe with pointer arithmetics even on 64 bit architectures?". Thanks, Martin.

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Numpy fails to build with Python 2.5
by William Grant 19 Sep '06

19 Sep '06

Hi, I'm currently attempting to get scipy 0.5.1 into Ubuntu, however it currently cannot happen as numpy doesn't build with Python 2.5. I note that changeset 3109 (http://projects.scipy.org/scipy/numpy/changeset/3109#file1) is meant to give 2.5 compatibility, but it is those bits which seem to break it. The end of the build log with the errors can be found at http://people.ubuntu.com.au/~fujitsu/numpy_error.txt. Has anybody got any ideas on how to fix this? A number of Ubuntu users want scipy 0.5.1, but that can't happen while it won't build with Python 2.5. Thanks, William Grant.

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Resolution of tickets.
by Charles R Harris 19 Sep '06

19 Sep '06

Question, How does one mark a ticket as fixed? I don't see this field in the ticket views I get, is there a list of accepted fixers? Chuck

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1.0b5 Installation on OS X
by David Andrews 19 Sep '06

19 Sep '06

Hi, I'm unable to install the 1.0b5 release from the .mpkg on OS X - when it comes to the two checkboxes to select the platlib and the scripts, both are greyed out. The installer then claims 'Cannot continue: Nothing to install'. Any suggestions? Cheers, Dave

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feasability study to migrate from numarray to numpy
by mg 19 Sep '06

19 Sep '06

Hi all, I am doing a feseability study to migrate our Python based FEM applications from Numarray to Numpy. First, I tried to install Numpy from Python-2.4 on linux-x86, linux-86-64bit. So, all work fine. Great! Moreover, I change easily the BLAS linked libraries. I tried with ATLAS and GOTO. Great again! Second, I try to do the same think on windows-x86 without success. So my first question is: is Numpy-1.0b5 has been tested and is supported on Windows? Third, I tried to install Numpy from Python-2.5, which is our standard Python, on linux-x86... and the compilation stopped during the compilation of core/src/multiarraymodule.c. So my second question is: is there a workaround or is the porting to Python2.5 is yet schedule? My third question is: is the tool to migrate the numarray based Python scripts (numpy.numarray.alter_code1) work fine? (I suppose yes...) We have created a lot of bindings in order to pilote our generic-C++ framework with Python scripts. So, about the Numpy API, is it widely different than the Numarray API? (We will order the Numpy Guide too.) To not duplicate large numerical memory arrays, Numarray allows to aliasing the memory of some bindings with arrays from Numarray, and we have used this feature intensively. So, I wonder if it is currently supported (or even scheduled)? Thanks for your answer, Mathieu.

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unique1d: renaming retindx to return_index
by Stefan van der Walt 18 Sep '06

18 Sep '06

Hi, Would anyone object if I changed the signature of unique1d(ar1, retindx=False) to unique1d(ar1, return_index=False)? I find retindx both harder to read and to type than return_index. Thanks. Stéfan

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persecute ambidextrous
by Sam Estes 18 Sep '06

18 Sep '06

I will shed no blood, said Wi, not even that of those who hate me,for misery makes them mad. That stone was ill aimed, said Pag who stood by. I tried to stay them but theyfelled me with clubs, for they are fierce as wolves and more savage. Aye, let us go to the cave, for if we stay here upon the ice we shallperish, said Pag. He looked down upon the people and, by the shimmering moonlight,watched their faces. The people who called upon the Ice-dwellers, where arethey? If he is afraid todie, then let him give another to the gods. I am sure that it will be so, she replied simply. I tell you nothing, Wife, he answered sternly. Now let Wi the mightyman, our chief who rejects you, make answer to it if he is able. Wi, you have your answer, piped Ngae, as the shouting died. Was it not well that one should die for the sake ofmany? Shall we gather men and fall on them and kill them? I brought the trouble, Wi; surely I should have paid its price. I brought the trouble, Wi; surely I should have paid its price. They cowered before him and muttered together. All the white world was a desolation and a waste. Then he had come thither because theplace was holy to him. For he had sent command to Aaka that she must nomore sleep alone in her hut. They say that the Ice-gods demand ahuman sacrifice and that this sacrifice must be given to them. He, Wi himself,whom they dared not touch because he was chief and too strong forthem. They saw it creep into the sea and there break off in sharp-toppedhills of ice. Yes, a Voice has spoken tothem from the roof of their hut in the dead of night. Now let Wi the mightyman, our chief who rejects you, make answer to it if he is able. They are starvingbrutes, and such will fill themselves. Or, if you dare not, then send us oneof your household. Their prayers finished, they spoke together.

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record descriptors: trailing unused bytes
by Martin Wiechert 18 Sep '06

18 Sep '06

Hi list, does anybody know, if in C in the PyArray_Descr struct it is safe to manually change descr->elsize and descr->alignment as long as these are compatible and descr->elsize is large enough to hold all fields? Of course I mean before any array is constructed using descr. Thanks, Martin.

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visual programming
by Mathew Yeates 18 Sep '06

18 Sep '06

semi off topic. Does anyone know of any good visual programming tools? Forever ago, I used to use something called Khoros for image processing and I found it very useful. You connect boxes which represent different processing steps. At about the same time, there was something similar to Khoros from SGI. Explorer was its name, I think. Anybody out there use this sort of thing? Matlab doesn't offer it, right? Nor matplotlib? Mathew

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Segfault on byteswap() on recarrays
by Matthew Brett 18 Sep '06

18 Sep '06

Hi, I noticed this works: In [5]:a = array((1,), dtype=[('one', '<i4')]) In [6]:a.byteswap() Out[6]: array((16777216,), dtype=[('one', '<i4')]) But, extending the recarray leads to a segfault on byteswapping: In [8]:a = array((1, 2), dtype=[('one', '<i4'),('two', '<i4')]) In [9]:a.byteswap() Segmentation fault Thanks, Matthew

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Re: [Numpy-discussion] buggy buggy bugyy: format and casting ==> BUG in numpy.sum?
by Eric Emsellem 18 Sep '06

18 Sep '06

Hi again after some hours of debugging I finally (I think) found the problem: numpy.sum([[0,1,2],[2,3,4]]) 24 numpy.sum([[0,1,2],[2,3,4]],axis=0) array([2, 4, 6]) numpy.sum([[0,1,2],[2,3,4]],axis=1) array([3, 9]) Isn't the first line supposed to act as with "axis=0" by default (see help numpy.sum!)...??? Not setting axis=0 it sums everything! Is that the expected behaviour or is the doc not updated? (I realise it may be better to force axis=.. to indicate what you need but still.. the example in numpy.sum help gives: sum([[0, 1], [0, 5]]) array([0, 6]) which is not what it gives when you do it...) thanks Eric

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static build
by Mike Rovner 18 Sep '06

18 Sep '06

I need build core numpy (plus possible dft) static into python.a Can someone point me to the right direction. Currently I built some libs but blocked on _internal. From my Setup.local: NPSRC=/home/mrovner/src/numpy-0.9.8 NPBLD=$(NPSRC)/build/src.linux-i686-2.4 NPINC=-I$(NPSRC)/numpy/core/include -I$(NPBLD)/numpy/core -I$(NPSRC)/numpy/core/src multiarray $(NPSRC)/numpy/core/src/multiarraymodule.c $(NPINC) umath $(NPBLD)/numpy/core/src/umathmodule.c $(NPINC) scalarmath $(NPBLD)/numpy/core/src/scalarmathmodule.c $(NPINC) _sort $(NPBLD)/numpy/core/src/_sortmodule.c $(NPINC) _compiled_base $(NPSRC)/numpy/lib/src/_compiled_base.c $(NPINC) Thanks, Mike

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Changing byte ordering with astype fails with 0d arrays
by Matthew Brett 18 Sep '06

18 Sep '06

Hi, As expected: In [67]:a = array([1], dtype='<i4') In [68]:a.astype('>i4').dtype Out[68]:dtype('>i4') I was also expecting this to work for 0d arrays, but it doesn't: In [69]:a = array(1, dtype='<i4') In [70]:a.astype('>i4').dtype Out[70]:dtype('<i4') Is this as intended? Thanks a lot, Matthew

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recarray
by Lionel Roubeyrie 18 Sep '06

18 Sep '06

Hi all, I try to use recarray with rec.fromrecords on time-series, datas come from a file where they are stored in csv format, with after each data colum there is one column meanning the state of the data, and the first column is for dates. Then, is it possible to directly transform column of strings to a integer one (or datetime one), and to remove a not used column? thanks -- Lionel

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mournful
by Louisa Mata 17 Sep '06

17 Sep '06

This may have been regularan then again it may have been queer. Bilyen made a careful inspection of the spot, and then faced Brazos witha curious fire in his eyes. I raisedthe ante to two thousand dollars. Give me the lowdown on rustlin in eastern Colorado. Suddenly she sprang out from the wall, formidable as a tigress. Without any greeting, Brazos flung a query at the banker. Yu-all shorehave heahed of the Sewall McCoy combine with Russ Slaughter. Shes the most fascinating girl I ever met. But he could be made a target for speech thatwould sweep over town like fire in prairie grass. At the foot of the Odd Fellows stairway Brazos halted to load his gun. Father hasa deal on with Surface and Miller. I mixed with cowboys,cattlemen, gamblers, an town folks. Cross the street heah an walk up thetside an down on this side. Yu men held upNeece thet night an robbed him. Wal, this gang of three was after himfor reasons that bear strong in this deal. An lettin that gambler Howard runaround with her. Range talk blames me for alot thet Im innocent of. She met his piercing gaze with understanding, and avisible shudder. If they would be, yud never get a vote,onless from some of yore hired hands. No noticeable change showed in the ranchers pale face. Dealing Surface a powerful left-handed blow,Brazos knocked him flat. Lura designated her bag, which Brazostook up. Whats to keep mefrom shootin Raine Surfaces laig off?

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compile error with python2.5
by Achim Gaedke 17 Sep '06

17 Sep '06

Hi! I compiled numpy-1.0b5 with python2.5 on debian testing and raIn file included from numpy/core/src/multiarraymodule.c:65: numpy/core/src/arrayobject.c: In function 'PyArray_PyIntAsIntp': numpy/core/src/arrayobject.c:564: error: 'op' undeclared (first use in this function) numpy/core/src/arrayobject.c:564: error: (Each undeclared identifier is reported only once numpy/core/src/arrayobject.c:564: error: for each function it appears in.) numpy/core/src/arrayobject.c:565: warning: cast from pointer to integer of different size numpy/core/src/arrayobject.c: In function 'PyArray_PyIntAsInt': numpy/core/src/arrayobject.c:654: warning: cast from pointer to integer of different size numpy/core/src/arrayobject.c: In function 'array_subscript': numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union In file included from numpy/core/src/multiarraymodule.c:65: numpy/core/src/arrayobject.c: In function 'PyArray_PyIntAsIntp': numpy/core/src/arrayobject.c:564: error: 'op' undeclared (first use in this function) numpy/core/src/arrayobject.c:564: error: (Each undeclared identifier is reported only once numpy/core/src/arrayobject.c:564: error: for each function it appears in.) numpy/core/src/arrayobject.c:565: warning: cast from pointer to integer of different size numpy/core/src/arrayobject.c: In function 'PyArray_PyIntAsInt': numpy/core/src/arrayobject.c:654: warning: cast from pointer to integer of different size numpy/core/src/arrayobject.c: In function 'array_subscript': numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union numpy/core/src/arrayobject.c:2694: error: request for member 'ob_type' in something not a structure or union error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -Ibuild/src.linux-i686-2.5/numpy/core/src -Inumpy/core/include -Ibuild/src.linux-i686-2.5/numpy/core -Inumpy/core/src -Inumpy/core/include -I/home/achim/local/include/python2.5 -c numpy/core/src/multiarraymodule.c -o build/temp.linux-i686-2.5/numpy/core/src/multiarraymodule.o" failed with exit status 1 n into errors I fixed it by guessing the correct arguments. The patch is attached. I hope someone can revise this fix. Achim diff -ru numpy-1.0b5/numpy/core/src/arrayobject.c numpy-1.0b5_fixed/numpy/core/src/arrayobject.c --- numpy-1.0b5/numpy/core/src/arrayobject.c 2006-09-05 00:41:47.000000000 +0200 +++ numpy-1.0b5_fixed/numpy/core/src/arrayobject.c 2006-09-17 21:41:49.000000000 +0200 @@ -561,8 +561,8 @@ return ret; } #if (PY_VERSION_HEX >= 0x02050000) - if (PyIndex_Check(op)) { - long_value = (longlong) PyNumber_Index(op); + if (PyIndex_Check(o)) { + long_value = (longlong) PyNumber_Index(o); goto finish; } #endif @@ -2691,7 +2691,7 @@ } if (PyInt_Check(op) || PyArray_IsScalar(op, Integer) || - PyLong_Check(op) || PyIndex_Check(index)) { + PyLong_Check(op) || PyIndex_Check(op)) { intp value; value = PyArray_PyIntAsIntp(op); if (!PyErr_Occurred()) {

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PHAxqiRMA
by Aksel Booth 17 Sep '06

17 Sep '06

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NumPy-Discussion September 2006