Mailman 3 August 2006 - NumPy-Discussion

Py2exe / numpy troubles
by tristan CORCELLE 29 Aug '06

29 Aug '06

Hello, I am having troubles with py2exe and numpy/matplotlib... Configuration : Windows XP pro ActivePython 2.4.2.10 Scipy 0.4.9 Numpy 0.9.8 MatplotLib 0.87.1 Py2exe 0.6.5 WxPython 2.6 I am using the following setup.py file: #--------------------------------------------------------- from distutils.core import setup import py2exe from distutils.filelist import findall import os import matplotlib matplotlibdatadir = matplotlib.get_data_path() matplotlibdata = findall(matplotlibdatadir) matplotlibdata_files = [] for f in matplotlibdata: dirname = os.path.join('matplotlibdata', f[len(matplotlibdatadir)+1:]) matplotlibdata_files.append((os.path.split(dirname)[0], [f])) packages = ['matplotlib', 'pytz'] includes = [] excludes = [] dll_excludes = ['libgdk_pixbuf-2.0-0.dll', 'libgobject-2.0-0.dll', 'libgdk-win32-2.0-0.dll', 'wxmsw26uh_vc.dll'] opts = { 'py2exe': { 'packages' : packages, 'includes' : includes, 'excludes' : excludes, 'dll_excludes' : dll_excludes } } setup ( console=['test.py'], options = opts, data_files = matplotlibdata_files ) #----------------------------- EOF --------------------------- I compile the application by running ">setup.py py2exe" At the end of compilation phase, it is written : The following modules appear to be missing ['AppKit', 'FFT', 'Foundation', 'Image', 'LinearAlgebra', 'MA', 'MLab', 'Matrix', 'Numeric', 'PyObjCTools', 'P yQt4', 'Pyrex', 'Pyrex.Compiler', 'RandomArray', '_curses', '_ssl', 'backends.draw_if_interactive', 'backends. new_figure_manager', 'backends.pylab_setup', 'backends.show', 'cairo', 'cairo.gtk', 'fcompiler.FCompiler', 'fc ompiler.show_fcompilers', 'fltk', 'gd', 'gobject', 'gtk', 'lib.add_newdoc', 'matplotlib.enthought.pyface.actio n', 'mlab.amax', 'mlab.amin', 'numarray', 'numarray.convolve', 'numarray.fft', 'numarray.ieeespecial', 'numarr ay.linear_algebra', 'numarray.linear_algebra.mlab', 'numarray.ma', 'numarray.numeric', 'numarray.random_array' , 'numerix.ArrayType', 'numerix.Complex', 'numerix.Complex32', 'numerix.Complex64', 'numerix.Float', 'numerix. Float32', 'numerix.Float64', 'numerix.Int', 'numerix.Int16', 'numerix.Int32', 'numerix.Int8', 'numerix.NewAxis ', 'numerix.UInt16', 'numerix.UInt32', 'numerix.UInt8', 'numerix.absolute', 'numerix.add', 'numerix.all', 'num erix.allclose', 'numerix.alltrue', 'numerix.arange', 'numerix.arccos', 'numerix.arccosh', 'numerix.arcsin', 'n umerix.arcsinh', 'numerix.arctan', 'numerix.arctan2', 'numerix.arctanh', 'numerix.argmax', 'numerix.argmin', ' numerix.argsort', 'numerix.around', 'numerix.array', 'numerix.arrayrange', 'numerix.asarray', 'numerix.asum', 'numerix.bitwise_and', 'numerix.bitwise_or', 'numerix.bitwise_xor', 'numerix.ceil', 'numerix.choose', 'numerix .clip', 'numerix.compress', 'numerix.concatenate', 'numerix.conjugate', 'numerix.convolve', 'numerix.cos', 'nu merix.cosh', 'numerix.cross_correlate', 'numerix.cumproduct', 'numerix.cumsum', 'numerix.diagonal', 'numerix.d ivide', 'numerix.dot', 'numerix.equal', 'numerix.exp', 'numerix.fabs', 'numerix.fft.fft', 'numerix.fft.inverse _fft', 'numerix.floor', 'numerix.fmod', 'numerix.fromfunction', 'numerix.fromstring', 'numerix.greater', 'nume rix.greater_equal', 'numerix.hypot', 'numerix.identity', 'numerix.indices', 'numerix.innerproduct', 'numerix.i scontiguous', 'numerix.less', 'numerix.less_equal', 'numerix.log', 'numerix.log10', 'numerix.logical_and', 'nu merix.logical_not', 'numerix.logical_or', 'numerix.logical_xor', 'numerix.matrixmultiply', 'numerix.maximum', 'numerix.minimum', 'numerix.mlab.amax', 'numerix.mlab.amin', 'numerix.mlab.cov', 'numerix.mlab.diff', 'numerix .mlab.hanning', 'numerix.mlab.rand', 'numerix.mlab.std', 'numerix.mlab.svd', 'numerix.multiply', 'numerix.nega tive', 'numerix.newaxis', 'numerix.nonzero', 'numerix.not_equal', 'numerix.nx', 'numerix.ones', 'numerix.outer product', 'numerix.pi', 'numerix.power', 'numerix.product', 'numerix.put', 'numerix.putmask', 'numerix.rank', 'numerix.ravel', 'numerix.repeat', 'numerix.reshape', 'numerix.resize', 'numerix.searchsorted', 'numerix.shape ', 'numerix.sin', 'numerix.sinh', 'numerix.size', 'numerix.sometrue', 'numerix.sort', 'numerix.sqrt', 'numerix .subtract', 'numerix.swapaxes', 'numerix.take', 'numerix.tan', 'numerix.tanh', 'numerix.trace', 'numerix.trans pose', 'numerix.typecode', 'numerix.typecodes', 'numerix.where', 'numerix.which', 'numerix.zeros', 'numpy.Comp lex', 'numpy.Complex32', 'numpy.Complex64', 'numpy.Float', 'numpy.Float32', 'numpy.Float64', 'numpy.Infinity', 'numpy.Int', 'numpy.Int16', 'numpy.Int32', 'numpy.Int8', 'numpy.UInt16', 'numpy.UInt32', 'numpy.UInt8', 'nump y.inf', 'numpy.infty', 'numpy.oldnumeric', 'objc', 'paint', 'pango', 'pre', 'pyemf', 'qt', 'setuptools', 'setu ptools.command', 'setuptools.command.egg_info', 'trait_sheet', 'matplotlib.numerix.Float', 'matplotlib.numerix .Float32', 'matplotlib.numerix.absolute', 'matplotlib.numerix.alltrue', 'matplotlib.numerix.asarray', 'matplot lib.numerix.ceil', 'matplotlib.numerix.equal', 'matplotlib.numerix.fromstring', 'matplotlib.numerix.indices', 'matplotlib.numerix.put', 'matplotlib.numerix.ravel', 'matplotlib.numerix.sqrt', 'matplotlib.numerix.take', 'm atplotlib.numerix.transpose', 'matplotlib.numerix.where', 'numpy.core.conjugate', 'numpy.core.equal', 'numpy.c ore.less', 'numpy.core.less_equal', 'numpy.dft.old', 'numpy.random.rand', 'numpy.random.randn'] 1) First Problem: numpy\core\_internal.pyc not included in Library.zip No scipy-style subpackage 'core' found in C:\WinCE\Traces\py2exe test\dist\library.zip\numpy. Ignoring: No module named _internal Traceback (most recent call last): File "profiler_ftt.py", line 15, in ? from matplotlib.backends.backend_wx import Toolbar, FigureCanvasWx,\ File "matplotlib\backends\backend_wx.pyc", line 152, in ? File "matplotlib\backend_bases.pyc", line 10, in ? File "matplotlib\colors.pyc", line 33, in ? File "matplotlib\numerix\__init__.pyc", line 67, in ? File "numpy\__init__.pyc", line 35, in ? File "numpy\_import_tools.pyc", line 173, in __call__ File "numpy\_import_tools.pyc", line 68, in _init_info_modules File "<string>", line 1, in ? File "numpy\lib\__init__.pyc", line 5, in ? File "numpy\lib\type_check.pyc", line 8, in ? File "numpy\core\__init__.pyc", line 6, in ? File "numpy\core\umath.pyc", line 12, in ? File "numpy\core\umath.pyc", line 10, in __load AttributeError: 'module' object has no attribute '_ARRAY_API' I resolved that issue by adding the file ...\Python24\Lib\site-packages\numpy\core\_internal.pyc in ...\test\dist\library.zip\numpy\core. Each time I compile that executable, I add the file by hand. Does anybody know how to automatically add that file? 2) Second problem: I don't know how to resolve that issue: Traceback (most recent call last): File "profiler_ftt.py", line 15, in ? from matplotlib.backends.backend_wx import Toolbar, FigureCanvasWx,\ File "matplotlib\backends\backend_wx.pyc", line 152, in ? File "matplotlib\backend_bases.pyc", line 10, in ? File "matplotlib\colors.pyc", line 33, in ? File "matplotlib\numerix\__init__.pyc", line 67, in ? File "numpy\__init__.pyc", line 35, in ? File "numpy\_import_tools.pyc", line 173, in __call__ File "numpy\_import_tools.pyc", line 68, in _init_info_modules File "<string>", line 1, in ? File "numpy\random\__init__.pyc", line 3, in ? File "numpy\random\mtrand.pyc", line 12, in ? File "numpy\random\mtrand.pyc", line 10, in __load File "numpy.pxi", line 32, in mtrand AttributeError: 'module' object has no attribute 'dtype' I don't find the file numpy.pxi in my file tree nor in \test\dist\library.zip. I browsed the web in the hope to find a solution but nothing. It seems that this issue is well known but no solution provided in mailing lists. What is that file "numpix.pxi"? Where to find it or how is it generated? How to resolve that execution issue? Thanks, Regards, Tristan

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ignorance gust
by Connor Pritchard 29 Aug '06

29 Aug '06

Cleohad become a sinister young huntress, a chipmunk-stalker and adabbler after fish. Ill just say I admire Jinny, and will he lay off, or else. I wish youd have a talk with your friend Jay. Or her laudable griefover the sickness of the second child of Cousin Mary, who lived inIndiana. Benjamin took to staying away from the business, to guard her. Only one of them had a bar, and this was the Laverick-Crileyestablishment. Wellgo up on the porch, like little mice, and not disturb the BigBoys. He saw Jinny snatch it away, but not tooswiftly, after what seemed to be a laughing debate. Whoever said there wasnt a lot of wanton in everygood woman? Jinny said reverently, Now is that a pretty trick! Werent they seen leaving you two fellows shack at dawn onWednesday? The cottage, of pine clapboards apparently once painted green, wasairy as a birdcage. The true American is active even in his inactivities. Im going to stay right with you all the time hes here! Benjamin was very sorry when she spoke thus. Her circle felt that that was too many Indiana relatives toounexpectedly. They couldscarce avoid meeting, with the swimming, tennis, canoeing. But I do wish she wouldnt so perpetuallyget herself ambushed by Nimbus and Jay. We have a very fine old house now, and to get a new onewould be spending our CAPITAL. For my own honor, if there is such a thing, but morefor HER honor and contentment. Howl would hate to havesomebody offer me a hundred-thousand-dollar bribe! I told him to go jump inthe lake, said Jinny, in a refined manner. On her way home, with bottle, a policeman stopped her. How can you insult her withsuch suspicions? They say that if I dont go in voluntarily, the Marines will forceme to. On her way home, with bottle, a policeman stopped her. Doyou mean to tell me Frank Brightwing gets three thousand dollars ofour money? Ive always loved Jinny like an uncle,and I want to protect her almost as much as you do.

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Re: [Numpy-discussion] [ANN] NumPy 1.0b4 now available
by Bruce Who 29 Aug '06

29 Aug '06

Hi, Travis I can pack my scripts into an executable with py2exe, but errors occur once it runs: No scipy-style subpackage 'random' found in D:\test\dist\numpy. Ignoring: No module named info import core -> failed: No module named _internal import lib -> failed: 'module' object has no attribute '_ARRAY_API' import linalg -> failed: 'module' object has no attribute '_ARRAY_API' import dft -> failed: 'module' object has no attribute '_ARRAY_API' Traceback (most recent call last): File "main.py", line 9, in ? File "numpy\__init__.pyc", line 49, in ? File "numpy\add_newdocs.pyc", line 2, in ? gkDc File "numpy\lib\__init__.pyc", line 5, in ? File "numpy\lib\type_check.pyc", line 8, in ? File "numpy\core\__init__.pyc", line 6, in ? File "numpy\core\umath.pyc", line 12, in ? File "numpy\core\umath.pyc", line 10, in __load AttributeError: 'module' object has no attribute '_ARRAY_API' This is the main.py file: #======================================= # filename:main.py import wx import numpy class myFrame(wx.Frame): def __init__(self, *args, **kwds): wx.Frame.__init__(self, *args, **kwds) ##------ your widgets ##------ put stuff into sizer self.sizer_ = wx.BoxSizer(wx.VERTICAL) ## self.sizer_.Add(your_ctrl, proportion = 1, flag = wx.EXPAND) ## apply sizer self.SetSizer(self.sizer_) self.SetAutoLayout(True) def main(): ## {{{ app = wx.PySimpleApp(0) frame = myFrame(None, -1, title = '') frame.Show(True) app.SetTopWindow(frame) app.MainLoop() ## }}} if __name__ == "__main__":main() #======================================= # filename:setup.py import glob import sys from distutils.core import setup import py2exe includes = ["encodings", "encodings.*", ] excludes = ["javax.comm"] options = { "py2exe": { #"compressed": 1, #"optimize": 0, #"bundle_files":2, "skip_archive":1, "includes": includes, 'excludes': excludes } } setup( version = "0.1", description = "", name = "test", options = options, windows = [ { "script":"main.py", } ], #zipfile = None, ) and I run this command to compile the scripts: python setup.py py2exe and all packages I use are: python2.4.3 numpy-0.98 py2exe-0.6.5 wxpython-2.6.3.2 I unistalled Numeric before I compiled scripts. If you google "numpy py2exe", you can find others guys stumbled by the same issue with ease: http://aspn.activestate.com/ASPN/Mail/Message/py2exe-users/3249182 http://www.nabble.com/matplotlib,-numpy-and-py2exe-t1901429.html I just hope this can be fixed in the next table release of numpy. On 8/29/06, Travis Oliphant <oliphant.travis(a)ieee.org> wrote: > bruce.who.hk wrote: > > Hi, Travis > > > > I just wonder if NumPy 1.0b4 can get along with py2exe? Just a few weeks ago I made a application in Python. At first I used Numpy, it works OK, but I cannot pack it into a workable executable with py2exe and the XXX.log saied that numpy cannot find some module. I found some hints in py2exe wiki, but it still doesn't work. At Last I tried Numeric instead and it got OK. I just hope that you donnot stop the maintenance of Numeric before you are sure that Numpy can work with py2exe. > > > We've already stopped maintenance of Numeric nearly 1 year ago. If > NumPy doesn't work with py2exe then we need help figuring out why. The > beta-release period is the perfect time to fix that. I've never used > py2exe myself, but I seem to recall that some have been able to make it > work. > > The problem may just be listing the right set of modules to carry along > because you may not be able to get that with just the Python-side > imports. Post any errors you receive to > numpy-discussion(a)lists.sourceforge.net > > Thanks, > > > -Travis > > Bruce Who

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tensor dot ?
by Simon Burton 28 Aug '06

28 Aug '06

>>> numpy.dot.__doc__ matrixproduct(a,b) Returns the dot product of a and b for arrays of floating point types. Like the generic numpy equivalent the product sum is over the last dimension of a and the second-to-last dimension of b. NB: The first argument is not conjugated. Does numpy support summing over arbitrary dimensions, as in tensor calculus ? I could cook up something that uses transpose and dot, but it's reasonably tricky i think :) Simon. -- Simon Burton, B.Sc. Licensed PO Box 8066 ANU Canberra 2601 Australia Ph. 61 02 6249 6940 http://arrowtheory.com

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std(axis=1) memory footprint issues + moving avg / stddev
by Torgil Svensson 28 Aug '06

28 Aug '06

Hi ndarray.std(axis=1) seems to have memory issues on large 2D-arrays. I first thought I had a performance issue but discovered that std() used lots of memory and therefore caused lots of swapping. I want to get an array where element i is the stadard deviation of row i in the 2D array. Using valgrind on the std() function... $ valgrind --tool=massif python -c "from numpy import *; a=reshape(arange(100000*100),(100000,100)).std(axis=1)" ... showed me a peak of 200Mb memory while iterating line by line... $ valgrind --tool=massif python -c "from numpy import *; a=array([x.std() for x in reshape(arange(100000*100),(100000,100))])" ... got a peak of 40Mb memory. This seems unnecessary since we know before calculations what the output shape will be and should therefore be able to preallocate memory. My original problem was to get an moving average and a moving standard deviation (120k rows and N=1000). For average I guess convolve should perform good, but is there anything smart for std()? For now I use ... >>> moving_std=array([a[i:i+n].std() for i in range(len(a)-n)]) which seems to perform quite well. BR, //Torgil

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nausea
by Lillian Slaughter 28 Aug '06

28 Aug '06

Kit took Pentreaths book away; it was Jukes Brownes Geology. During the winter he made a change in his own habit of life. My dear old chap, exams arent everything. His room hadtwo windows and a mahogany door, a bookcase, and two or three oddchairs. The barbarians were growing too strongfor him. The shop becamealive, with liquid capital circulating in its blood vessels. Maurice flinched; he flinched too easily. That she did appear inthat echoing room was another revealing of the world to Kit. On Saturdays he played soccer for the hospital. His impetus swung him along,and he cultivated this impetus. Also Kit met people in the Chelsea house, people who mattered, whohad done things. The barbarians were growing too strongfor him. Appreciation matters, and his fathers understanding keenness wasno small part of Kits inspiration. Kit confessed that he passed through the centre of the spiders webonce each day. Maurice was always looking fearfully at theclock. If anyone appreciated the pretty and nicely wingedjibes in Punch, Sorrell appreciated them. She put a live slow-worm in his bed, filled his tennisshoes with flour, and mocked him openly. Ada, the middle-aged maid who had been withMrs. Maurice was always looking fearfully at theclock. Youth explores, and Kits questing hada serious and high ardour. Gibbins provided him with breakfast and a hot meal atnight. She put out a hand and touched a rigid arm.

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1.0b4 problem continuted from 1.0b3
by kortmann＠ideaworks.com 28 Aug '06

28 Aug '06

On 8/25/06, Travis Oliphant <oliphant.travis(a)ieee.org> wrote: > kortmann(a)ideaworks.com wrote: > > Message: 4 > > Date: Thu, 24 Aug 2006 14:17:44 -0600 > > From: Travis Oliphant <oliphant(a)ee.byu.edu> > > Subject: Re: [Numpy-discussion] (no subject) > > To: Discussion of Numerical Python > > <numpy-discussion(a)lists.sourceforge.net> > > Message-ID: <44EE0968.1030904(a)ee.byu.edu> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > kortmann(a)ideaworks.com wrote: > > > > > > > > You have a module built against an older version of NumPy. What modules > > are being loaded? Perhaps it is matplotlib or SciPy > > > > You need to re-build matplotlib. They should be producing a binary that > is compatible with 1.0b2 (I'm being careful to make sure future releases > are binary compatible with 1.0b2). > > Also, make sure that you remove the build directory under numpy if you > have previously built a version of numpy prior to 1.0b2. > > -Travis > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Numpy-discussion mailing list > Numpy-discussion(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/numpy-discussion > Travis I have recompiled everything. I removed sci py numpy and matplotlib. I installed the numpy 1.0b4 win32exe, and then installed scipi 0.5 and then the latest matplotlib 0.87.4 I recieved this error at first, which is a matplot lib error, C:\Lameness>c:\python23\python templatewindow.py Traceback (most recent call last): File "templatewindow.py", line 7, in ? import wxmpl File "c:\python23\lib\site-packages\wxmpl.py", line 25, in ? import matplotlib.numerix as Numeric File "C:\PYTHON23\Lib\site-packages\matplotlib\numerix\__init__.py", line 74, in ? Matrix = matrix NameError: name 'matrix' is not defined , and then switched matplotlib to use numeric, and i recieve this error once again Overwriting info=<function info at 0x02097C30> from scipy.misc.helpmod (was <fun ction info at 0x020777F0> from numpy.lib.utils) Overwriting who=<function who at 0x020971B0> from scipy.misc.common (was <functi on who at 0x020776F0> from numpy.lib.utils) Overwriting source=<function source at 0x02097EB0> from scipy.misc.helpmod (was <function source at 0x02077830> from numpy.lib.utils) RuntimeError: module compiled against version 1000000 of C-API but this version of numpy is 1000002 Fatal Python error: numpy.core.multiarray failed to import... exiting. abnormal program termination i googled the error and also found this thread but have not found a solution http://www.mail-archive.com/numpy-discussion@lists.sourceforge.net/msg01700… any help? thanks -Kenny

3 2

request for new array method: arr.abs()
by Sebastian Haase 28 Aug '06

28 Aug '06

Hi! numpy renamed the *function* abs to absolute. Most functions like mean, min, max, average, ... have an equivalent array *method*. Why is absolute left out ? I think it should be added . Furthermore, looking at some line of code that have multiple calls to absolute [ like f(absolute(a), absolute(b), absolute(c)) ] I think "some people" might prefer less typing and less reading, like f( a.abs(), b.abs(), c.abs() ). One could even consider not requiring the "function call" parenthesis '()' at all - but I don't know about further implications that might have. Thanks, Sebastian Haase PS: is there any performace hit in using the built-in abs function ?

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weave using numeric or numpy?
by Carlos Pita 28 Aug '06

28 Aug '06

Hi all! I'm rewriting some swig-based extensions that implement intensive inner loops dealing with numeric/numpy arrays. The intention is to build these extensions by means of weave inline, ext_module, ext_function, etc. I'm not sure about how to point weave to my numpy instalation. By default it tries to include "Numeric/arrayobject.h" and fails if you hack things to get that resolved to numpy arrayobject.h (for example, it complaints that PyArray_SBYTE is undefined). Anyway, even if I managed myself to force weave to compile against numpy/arrayobject.h, I'd still not be sure about the "runtime" that will be chosen. I'm very confused at this point, no library flags are provided at compile/link time, so how is the runtime selected between numpy, Numeric (or even numarray)? Thank you in advance. Best regards, Carlos --------------------------------- Preguntá. Respondé. Descubrí. Todo lo que querías saber, y lo que ni imaginabas, está en Yahoo! Respuestas (Beta). Probalo ya!

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Numeric/numpy incompatibility
by Andrew Straw 28 Aug '06

28 Aug '06

The following code indicates there is a problem adding a numpy scalar type to a Numeric array. Is this expected behavior or is there a bug somewhere? This bit me in the context of updating some of my code to numpy, while part of it still uses Numeric. import Numeric import numpy print 'Numeric.__version__',Numeric.__version__ print 'numpy.__version__',numpy.__version__ a = Numeric.zeros( (10,2), Numeric.Float ) b = numpy.float64(23.39) a[0,1] = a[0,1] + b assert a[0,1]==b

2 1