NumPy-Discussion August 2006

numpy-discussion@python.org

136 participants
217 discussions

A minor annoyance with MA
by PGM 30 Aug '06

30 Aug '06

Folks, I keep running into the following problem since some recent update (I'm currently running 1.0b3, but the problem occurred roughly around 0.9.8): >>> import numpy.core.ma as MA >>> x=MA.array([[1],[2]],mask=False) >>> x.sum(None) /usr/lib64/python2.4/site-packages/numpy/core/ma.py in reduce(self, target, axis, dtype) 393 m.shape = (1,) 394 if m is nomask: --> 395 return masked_array (self.f.reduce (t, axis)) 396 else: 397 t = masked_array (t, m) TypeError: an integer is required #................................ Note that x.sum(0) and x.sum(1) work fine. I know some consensus seems to be lacking with MA, but still, I can't see why axis=None is not recognized. Corollary: with masked array, the default axis for sum is 0, when it's None for regular arrays. Is there a reason for this inconsistency ? Thanks a lot

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Py2exe / numpy troubles
by kortmann＠ideaworks.com 30 Aug '06

30 Aug '06

My 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 ---- 1) Be very careful on how you generate the file "...\dist\library.zip".I don't know why, but the zip file generated by hand doesn't work. Check its size! Specific zip format? Specific options to generate it? I didn't check source files to know how library.zip is generated.My method is the following one: - Extract the ...\test\dist\library.zip file in ...\test\dist\library - Add the file ...\Python24\Lib\site-packages\numpy\core\_internal.pyc in ...\test\dist\library\numpy\core. - Use Winzip to Add the ...\test\dist\library\numpy directory to the ...\dist\library.zip file I know, it is not really beautiful but it seems to work. It is a temporary solution for debug. I am new in Python so my style is not really "academic" ---- 2) If you use my setup.py file, one more time, be careful cause of the wx specific dll: wxmsw26uh_vc.dllI don't know why, but Py2Exe doesn't find it. I remove that dll from the compilation phase and I copy it by hand in ...\test\dist directory.An idea may be the modification of setup.py file to indicate the path of that dll or something like that.DOES ANYONE HAVE THE SOLUTION? ---- 3)I am still blocked on my second issue > >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? Regards,Tristan could you post your setup file please? i can look at it i may not be much help but some is better than none

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Py2exe / numpy troubles
by tristan CORCELLE 29 Aug '06

29 Aug '06

> >1) First Problem: numpy\core\_internal.pyc not included in Library.zip > >C:\Lameness\dist>templatewindow.exe > Traceback (most recent call last): > File "templatewindow.py", line 7, in ? > File "wxmpl.pyc", line 25, in ? > File "matplotlib\numerix\__init__.pyc", line 60, in ? > File "Numeric.pyc", line 91, in ? > File "numpy\__init__.pyc", line 35, 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? > > although mine was in \python23 respectively :) > > thanks for this fix > now i have this problem > > C:\Lameness\dist>templatewindow.exe > Traceback (most recent call last): > File "c:\python23\lib\site-packages\py2exe\boot_common.py", line 92, in ? > import linecache > ImportError: No module named linecache > Traceback (most recent call last): > File "templatewindow.py", line 1, in ? > ImportError: No module named wx > > C:\Lameness\dist> > > > current setup.py = > > ######################################################## > 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=['templatewindow.py'], > options = opts, > data_files = matplotlibdata_files > ) > ########################################################## > > anyone seen this problem before? > > first line of template window = import wx > My 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 ---- 1) Be very careful on how you generate the file "...\dist\library.zip".I don't know why, but the zip file generated by hand doesn't work. Check its size! Specific zip format? Specific options to generate it? I didn't check source files to know how library.zip is generated.My method is the following one: - Extract the ...\test\dist\library.zip file in ...\test\dist\library - Add the file ...\Python24\Lib\site-packages\numpy\core\_internal.pyc in ...\test\dist\library\numpy\core. - Use Winzip to Add the ...\test\dist\library\numpy directory to the ...\dist\library.zip fileI know, it is not really beautiful but it seems to work. It is a temporary solution for debug. I am new in Python so my style is not really "academic" ---- 2) If you use my setup.py file, one more time, be careful cause of the wx specific dll: wxmsw26uh_vc.dllI don't know why, but Py2Exe doesn't find it. I remove that dll from the compilation phase and I copy it by hand in ...\test\dist directory.An idea may be the modification of setup.py file to indicate the path of that dll or something like that.DOES ANYONE HAVE THE SOLUTION? ---- 3)I am still blocked on my second issue > >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? Regards,Tristan

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Re: [Numpy-discussion] Release of 1.0b5 this weekend
by kortmann＠ideaworks.com 29 Aug '06

29 Aug '06

>I find it much cleaner to write >x = foo.bar().baz(param).frob() >than >foo.bar() >foo.baz(param) >x = foo.frob() >but perhaps others disagree. Both of these look "clean" but i do not think that moving 3 lines to one line makes code "cleaner" They both do the same thing and if someone that does not know what .bar() .baz(param) and .frob() are IMO the second version that takes place on three lines would be easier to understand. >I'm generally +0 on this idea (it seems like the clarity in writing >comes largely for interactive users), and don't see much difficulty in >separating the constructs. On the other hand, I don't see much problem >in returning a reference to self either. >I guess you are worried about the situation where you write >b = a.sort() >and think you have a new array, but in fact have a new reference to the >already-altered 'a'? >Hmm.. So, how is this different from the fact that >b = a[1:10:3] already returns a reference to 'a' >(I suppose in the fact that it actually returns a new object just one >that happens to share the same data with a). >However, I suppose that other methods don't return a reference to an >already-altered object, do they. >Tim's argument has moved me from +0 to -0 >-Travis I couldn't agree more with you and Tim on this. I would rather have code that works all the time and will not possibly confuse people later, like the example of >b = a.sort() >and think you have a new array, but in fact have a new reference to the >already-altered 'a'? alot of people have problems grasping this "memory management" type of programming...or at least in my C class half of the kids dropped out because the couldnt keep track of b = a.sort() meaning that b was actually just referencing a and if you changed b then a was changed also. But then again who on this list has problems remembering things like that anyways right?... ~Kenny

2 1

Documentation
by Charles R Harris 29 Aug '06

29 Aug '06

Hi All, I've finished moving all the docstrings in arraymethods to add_newdocs. Much of the documentation is still incomplete and needs nicer formatting, so if you are so inclined, or even annoyed with some of the help messages, feel free to fix things up. Chuck

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py2exe error
by kortmann＠ideaworks.com 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 I am cross referencing this from the py2exe mailing list. There seems to have been a fix for this problem #---------------------------begining of setup.py--------------------# 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 ) #--------------------------End of setup.py--------------# >>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? the setup.py was from the person who wrote the instructions for this fix. also here is my setup.py just for reference although mine is probably incorrect due to me being new with py2exe #------------------------setup.py------------------------# 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])) setup( console=['templatewindow.py'], options={ "py2exe": { "compressed": 1, "optimize": 2, "packages": ["encodings", "kinterbasdb", "pytz.zoneinfo.UTC", "matplotlib.numerix", ], "dll_excludes": ["tcl84.dll", "tk84.dll"] } mpldata = glob.glob(r'C:\Python24\share\matplotlib\*') mpldata.append(r'C:\Python24\share\matplotlib\.matplotlibrc') data_files = [("prog\\locale\\fr\\LC_MESSAGES", mylocaleFR), ("prog\\locale\\de\\LC_MESSAGES", mylocaleDE), ("prog\\locale\\en\\LC_MESSAGES", mylocaleEN), ... ("matplotlibdata", mpldata), ("prog\\amaradata", amaradata), ("prog\\amaradata\\Schemata", amaraschemata), ] ) #-----------------------EOF-----------------# I was receiving this same "AttributeError: 'module' object has no attribute '_ARRAY_API'" error, and i did the same thing this person did, unzipped the folder, put the _internal.pyc file in the numpy/core folder and then rezipped the folder and I am receiving a wx error, but the numpy array_api error is gone. You may want to check this out and let us know if it works for you also. -Kenny p.s. i tried sending this 4 times prior but believe it did not send because it was alot longer so i shortened it, sorry if it posted 4 times

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Is numpy supposed to support the buffer protocol?
by Christopher Barker 29 Aug '06

29 Aug '06

HI all, Robin Dunn has been working on adding better support for dumping data directly to wxPython from the num* packages. I've been talking to him about the new array interface, and he might well support it (particularly if one of us contributes code), but in the meantime, he's got a number of things working with python buffers. For instance: wx.Image.SetDataBuffer(dataBuffer) That sets the data for a wxImage to the buffer handed in. This isn't as nice as the array protocol, as it has no way of checking anything other than if the length of the buffer is correct, but it is a good way to maximize performance for this sort of thing. he's now working on adding methods for creating wx.Bitmaps directly from buffers. In the process if testing some of this, I discovered that numarray (which Robin is testing with) works fine, but numpy does not. I get: File "/usr/lib/python2.4/site-packages/wx-2.6-gtk2-unicode/wx/_core.py", line 2814, in SetDataBuffer return _core_.Image_SetDataBuffer(*args, **kwargs) TypeError: non-character array cannot be interpreted as character buffer If I try to pass in a numpy array, while it works great with a numarray array. While I'm a great advocate of the new array protocol, it seems supporting the buffer protocol also would be a good idea. I've enclosed some simple test code. It works with numarray, but not numpy 1.0b4 Tested with Python 2.4.3, wxPython 2.6.3.0, Linux fedora core4 -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/OR&R/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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Problem with randn
by Keith Goodman 29 Aug '06

29 Aug '06

randn incorrectly returns random numbers only between 0 and 1 in numpy 1.0b1. random.randn works. >> from numpy.matlib import * >> randn(3,4) matrix([[ 0.60856413, 0.35500732, 0.48089868, 0.7044022 ], [ 0.71098538, 0.8506885 , 0.56154652, 0.4243273 ], [ 0.89655777, 0.92339559, 0.62247685, 0.70340003]]) >> randn(3,4) matrix([[ 0.84349201, 0.55638171, 0.19052097, 0.0927636 ], [ 0.60144183, 0.3788309 , 0.41451568, 0.61766302], [ 0.98992704, 0.94276652, 0.18569066, 0.69976656]]) >> randn(3,4) matrix([[ 0.69003273, 0.07171546, 0.34549767, 0.20901683], [ 0.1333439 , 0.4086678 , 0.80960253, 0.86864547], [ 0.75329427, 0.6760677 , 0.32496542, 0.99402779]]) >> random.randn(3,4) array([[ 1.00107604, 0.41418557, -0.07923699, 0.19203247], [-0.29386593, 0.02343702, -0.42366834, -1.27978993], [ 0.25722357, -0.53765827, 0.50569238, -2.44592854]])

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error in ctypes example from the numpy book?
by W. Bryan Smith 29 Aug '06

29 Aug '06

hi, i posted this to the forum, but it looks like the email list gets much more traffic, so here goes. i am attempting to reproduce a portion of the example on using ctypes from the current version of the numpy book (the example can be found on pps 313-16). here is what i am trying to do: import numpy import interface x = numpy.array(range(1,1)) y = numpy.ones_like(x) z = interface.add(a,b) prints the following error: BEGIN ERROR>> 26 b = N.require(b, dtype, requires) 27 c = N.empty_like(a) ---> 28 func(a,b,c,a.size) 29 return c 30 ArgumentError: argument 1: exceptions.TypeError: Don't know how to convert parameter 1 <<END ERROR In case it matters, here are the relevant bits of code I am using (since I have not just copied the entire text from the example): BEGIN testAddInt.c >> /* Add arrays of contiguous data */ typedef struct {double real;} cdouble; typedef struct {float real;} cfloat; void dadd(double *a, double *b, double *c, long n) { while (n--) { *c++ = *a++ + *b++; } } void sadd(float *a, float *b, float *c, long n) { while (n--) { *c++ = *a++ + *b++; } } <<END testAddInt.c and the interface code: BEGIN interface.py>> __all__ = ['add'] import numpy as N from ctypes import * import os _path = os.path.dirname('__file__') lib = N.ctypeslib.ctypes_load_library('testAddInt', _path) for name in ['sadd','dadd']: getattr(lib,name).restype=None def select(dtype): if dtype.char in['?bBhHf']: return lib.sadd, single else: return lib.dadd, float return func, ntype def add(a,b): requires = ['CONTIGUOUS','ALIGNED'] a = N.asanyarray(a) func, dtype = select(a.dtype) a = N.require(a, dtype, requires) b = N.require(b, dtype, requires) c = N.empty_like(a) func(a,b,c,a.size) return c <<END interface.py any hints/clues/suggestions as to what i am doing wrong here? since i am so new at this, i am assuming there is a simple mistake in what i am doing, but i cannot find it! thanks so much, bryan

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Re: [Numpy-discussion] possible bug with numpy.object_
by Matt Knox 29 Aug '06

29 Aug '06

# is the following behaviour expected? or is this a bug with numpy.object_ ? I'm using numpy 1.0b1# # >>> print numpy.array([],numpy.float64).size# 0## >>> print numpy.array([],numpy.object_).size# 1## Should the size of an array initialized from an empty list not always be 1 ? or am I just crazy?## Thanks,# # - Matt Knox Correction... I mean shouldn't it always be 0, not 1 _________________________________________________________________ Be one of the first to try Windows Live Mail. http://ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-49…

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NumPy-Discussion August 2006