Re: [Numpy-discussion] ragged array implimentation
Francesc Alted wrote: Just a C pointer to a malloc'ed area (it cannot be an ndarray, as the data area might be compressed). got it. Ok. Thanks. The code is really simple, and that's great. However, carray is quite more sophisticated, as it supports not only enlarging arrays, but also shrinking, that's handy. and since 0.4 on, it also supports n- dimensional arrays (although you can only resize along the first dimension). I've been meaning to add that, too - not much to it really, but haven't had a need yet, so haven't gotten around to it. I hope it was a bit helpful, and I'm looking forward to seeing what's next for carray! -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/ORR(206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception chris.bar...@noaa.gov ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] [OT] any image io module that works with python3?
Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT] any image io module that works with python3?
On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. On Windows, PIL (private port at http://www.lfd.uci.edu/~gohlke/pythonlibs/#pil), PythonMagick http://www.imagemagick.org/download/python/, and pygame 1.9.2pre http://www.pygame.org are working reasonably well for image IO. Also the FreeImage library http://freeimage.sourceforge.net/ is easy to use with ctypes http://docs.python.org/py3k/library/ctypes.html. Christoph ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] how to compile Fortran using setup.py
On Fri, Mar 11, 2011 at 3:58 AM, Ondrej Certik ond...@certik.cz wrote:
Hi,
I spent about an hour googling and didn't figure this out. Here is my
setup.py:
setup(
name = libqsnake,
cmdclass = {'build_ext': build_ext},
version = 0.1,
packages = [
'qsnake',
'qsnake.calculators',
'qsnake.calculators.tests',
'qsnake.data',
'qsnake.mesh2d',
'qsnake.tests',
],
package_data = {
'qsnake.tests': ['phaml_data/domain.*'],
},
include_dirs=[numpy.get_include()],
ext_modules = [Extension(qsnake.cmesh, [
qsnake/cmesh.pyx,
qsnake/fmesh.f90,
])],
description = Qsnake standard library,
license = BSD,
)
You can specify Fortran code, that you don't want to process with f2py, in
the libraries list
and then use the corresponding library in the extension, for example:
setup(...
libraries = [('foo', dict(sources=['qsnake/fmesh.f90']))],
ext_modules = [Extension(qsnake.cmesh,
sources =
[qsnake/cmesh.pyx],
libraries = ['foo']
)],
...
)
See also scipy/integrate/setup.py that resolves the same issue but just
using the configuration function approach.
HTH,
Pearu
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Re: [Numpy-discussion] how to compile Fortran using setup.py
On Fri, Mar 11, 2011 at 1:57 AM, Ondrej Certik ond...@certik.cz wrote:
On Thu, Mar 10, 2011 at 8:25 PM, Robert Kern robert.k...@gmail.com wrote:
On Thu, Mar 10, 2011 at 19:58, Ondrej Certik ond...@certik.cz wrote:
Hi,
I spent about an hour googling and didn't figure this out. Here is my
setup.py:
setup(
name = libqsnake,
cmdclass = {'build_ext': build_ext},
version = 0.1,
packages = [
'qsnake',
'qsnake.calculators',
'qsnake.calculators.tests',
'qsnake.data',
'qsnake.mesh2d',
'qsnake.tests',
],
package_data = {
'qsnake.tests': ['phaml_data/domain.*'],
},
include_dirs=[numpy.get_include()],
ext_modules = [Extension(qsnake.cmesh, [
qsnake/cmesh.pyx,
qsnake/fmesh.f90,
])],
description = Qsnake standard library,
license = BSD,
)
The qsnake.cmesh extension needs to compile .pyx into .c and later to
.o, it needs to use gfortran to compile fmesh.f90 to fmesh.o, and then
link both things. That's it. In other words, this is what I want
distutils to do:
$ cython cmesh.pyx
$ gcc -fPIC -o cmesh.o -c cmesh.c -I$SPKG_LOCAL/include/python2.6
-I$SPKG_LOCAL/lib/python2.6/site-packages/numpy/core/include
$ gfortran -fPIC -o fmesh.o -c fmesh.f90
$ gcc -shared -o cmesh.so cmesh.o fmesh.o
Difficult if sticking with distutils of any flavor. You would have
probably to replace the build_ext command to handle both the Fortran
and the Cython. You may want to give David Cournapeau's Bento a try:
http://pypi.python.org/pypi/bento/
Thanks Robert. I burned most of my today's evening on this, trying to
replace the command, but so far I didn't figure it out. It is indeed
difficult, but I wasn't sure, whether it is because I am not so
familiar with distutils.
I looked at bento, but I'll simply stick to cmake. I thought that for
a Python package (that uses cython + C or fortran, which I thought is
a pretty standard configuration for scientific computing), I would use
distutils, just like other Python packages.
The initial reason why I started bento is because this is practically
impossible: distutils is very adverse to changes, and you cannot
easily change this (I know because that's exactly what numscons was).
For example, if you generate a cmake file from distutils, you will
quickly realize that getting the necessary data is not easy - if you
create a build_cmake, you still need install options, but those are
not fully available before install is run (you can do some very
horrible hacks to get most of them by copying running commands).
Instead bento is based around the usual configure/build/install ala
autoconf, where all the options are resolved after configure.
I am not pretending that bento can solve all your issues, but you can
*today* build non trivial python packages with it, including metadata,
eggs and windows installers. And there is already a proof of concept
to use either distutils compiler classes, waf and a custom build tool
without the need to customize anything outside the build phase (i.e.
install is exactly the same and does not even need to know about
build).
As for supporting setup.py, I have started something in that direction:
http://cournape.wordpress.com/2011/03/06/adding-a-distutils-compatibility-layer-to-bento/
cheers,
David
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Re: [Numpy-discussion] assert_almost_equal bug?
On Sat, Mar 12, 2011 at 12:10 AM, Keith Goodman kwgood...@gmail.com wrote: assert_almost_equal() and assert_array_almost_equal() raise a ValueError instead of an AssertionError when the array contains np.inf: That's a bug, is fixed in 45269ee1. assert_array_compare was checking for nans but not for infs. Cheers, Ralf a = np.array([[1., 2.], [3., 4.]]) b = a.copy() np.testing.assert_almost_equal(a, b) b[0,0] = np.inf np.testing.assert_almost_equal(a, b) snip ValueError: Arrays are not almost equal x: array([[ 1., 2.], [ 3., 4.]]) y: array([[ inf, 2.], [ 3., 4.]]) np.testing.assert_array_almost_equal(a, b) snip ValueError: Arrays are not almost equal x: array([[ 1., 2.], [ 3., 4.]]) y: array([[ inf, 2.], [ 3., 4.]]) ticket: http://projects.scipy.org/numpy/ticket/1769 ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Structured array copying by field name (was: Numpy 1.6 schedule)
On Sat, Mar 12, 2011 at 6:51 AM, Benjamin Root ben.r...@ou.edu wrote:
On Fri, Mar 11, 2011 at 2:20 PM, Mark Wiebe mwwi...@gmail.com wrote:
On Fri, Mar 11, 2011 at 1:07 AM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote:
Structured array copying copies by field name.
Commit 22d96096bf7d5fb199ca80f2fcd04e8d27815476
Before:
x = np.array([(0, 1)], dtype=[('a', int), ('b', int)])
y = np.array([(2, 3)], dtype=[('a', int), ('b', int)])
y = np.array([(2, 3)], dtype=[('b', int), ('a', int)])
x[:] = y
x
array([(2, 3)],
dtype=[('a', 'i4'), ('b', 'i4')])
After:
x = np.array([(0, 1)], dtype=[('a', int), ('b', int)])
y = np.array([(2, 3)], dtype=[('b', int), ('a', int)])
x[:] = y
x
array([(3, 2)],
dtype=[('a', 'i4'), ('b', 'i4')])
This seems like a pretty hazardous change. Granted, it's in
a bit of a grey area, but people may rely on this.
This is still backwards incompatible in current master. Should it be
changed back for 1.6?
I strongly dislike the behavior in 1.5 and earlier, for reasons such as
the example given here:
http://mail.scipy.org/pipermail/numpy-discussion/2011-March/055214.html
No problems so far have been traced back to this change, indicating that
this type of assignment was previously utilized very little, so I'm strongly
in favor of keeping it in. Based on my knowledge of the code, I'm pretty
sure it's a significant performance improvement as well.
-Mark
Ditto on this.
If no problems turn up and no one objects, I am also okay with keeping
it in. Either way, I don't think this needs to be resolved before the
release of the first beta.
Cheers,
Ralf
However, it isn't like this is fully featured anyway.
Consider the following:
x = np.array([(0, 1.1)], dtype=[('a', int), ('b', float)])
y = np.array([(2.1, 4)], dtype=[('b', float), ('a', int)])
print x + y
Traceback (most recent call last):
File stdin, line 1, in module
TypeError: unsupported operand type(s) for +: 'numpy.ndarray' and
'numpy.ndarray'
So, how much has people been relying on either behaviors, given that basic
math operations weren't permissible in a similar manner? I doubt either
approaches would be that noticeable.
Note, I would love to be able to do the above eventually. I see a lot of
uses for labeled arrays, especially for in the matplotlib library. I
personally use the larry package from time to time.
Just my two cents.
Ben Root
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Re: [Numpy-discussion] [OT] any image io module that works with python3?
Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. On Windows, PIL (private port at http://www.lfd.uci.edu/~gohlke/pythonlibs/#pil), PythonMagick http://www.imagemagick.org/download/python/, and pygame 1.9.2pre http://www.pygame.org are working reasonably well for image IO. Also the FreeImage library http://freeimage.sourceforge.net/ is easy to use with ctypes http://docs.python.org/py3k/library/ctypes.html. Christoph ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Using ndpointer with ctypes argtypes
I found a solution that works. What I did was I wrote a custom class to define the argtypes. The from_param(obj) method calls ndpointer when it is a numpy array or if obj is none it returns a null pointer. On Fri, Mar 11, 2011 at 1:25 PM, Josh Mayer joshuaama...@gmail.com wrote: I am trying to call a C function that takes a double array as one of its parameters. I am using ndpointer to define the argtypes so that I can pass a numpy array directly. The issue I'm having is that this parameter need not always be set, and when it is not set, the C functions expects a null pointer to a double in it's place. Is there any way I can set up a numpy array such that when ndpointer calls from_param() it returns a null pointer? Or is there some other way to go about it? Thanks ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] assert_almost_equal bug?
On Sat, Mar 12, 2011 at 4:16 AM, Ralf Gommers ralf.gomm...@googlemail.com wrote: On Sat, Mar 12, 2011 at 12:10 AM, Keith Goodman kwgood...@gmail.com wrote: assert_almost_equal() and assert_array_almost_equal() raise a ValueError instead of an AssertionError when the array contains np.inf: That's a bug, is fixed in 45269ee1. assert_array_compare was checking for nans but not for infs. Thanks, Ralf! ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT] any image io module that works with python3?
I forgot to mention that I work on linux (gentoo x86-64).Here are my achievements till now: 1. PythonMagick: Needs boost which I do not have it avaiable on python3 2. Pygame: I have the stable version(1.9.1) should it work? 3. FreeImage: I installed FreeImagePy on python3, but it doesn't work yet. 4. PIL: I patched setup.py and map.c so python3 setup.py build is working, but: nadav@nadav_home /dev/shm/PIL-1.1.7-py3 $ sudo python3.1 setup.py install /usr/lib64/python3.1/distutils/dist.py:259: UserWarning: Unknown distribution option: 'ext_comp_args' warnings.warn(msg) running install running build running build_py running build_ext PIL 1.1.7 SETUP SUMMARY version 1.1.7 platform linux2 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] --- TKINTER support available --- JPEG support available --- ZLIB (PNG/ZIP) support available --- FREETYPE2 support available --- LITTLECMS support available . . . byte-compiling /usr/lib64/python3.1/site-packages/PIL/WalImageFile.py to WalImageFile.pyc Traceback (most recent call last): File setup.py, line 520, in module setup(*(), **configuration) # old school :-) File /usr/lib64/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /usr/lib64/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install.py, line 592, in run self.run_command(cmd_name) File /usr/lib64/python3.1/distutils/cmd.py, line 315, in run_command self.distribution.run_command(command) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install_lib.py, line 98, in run self.byte_compile(outfiles) File /usr/lib64/python3.1/distutils/command/install_lib.py, line 135, in byte_compile dry_run=self.dry_run) File /usr/lib64/python3.1/distutils/util.py, line 560, in byte_compile compile(file, cfile, dfile) File /usr/lib64/python3.1/py_compile.py, line 137, in compile codestring = f.read() File /usr/lib64/python3.1/codecs.py, line 300, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf8' codec can't decode byte 0xe4 in position 1909: invalid continuation byte Any idea on how to correct it? Any elegant way to avoid byte compiling? Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. On Windows, PIL (private port at http://www.lfd.uci.edu/~gohlke/pythonlibs/#pil), PythonMagick http://www.imagemagick.org/download/python/, and pygame 1.9.2pre http://www.pygame.org are working reasonably well for image IO. Also the FreeImage library http://freeimage.sourceforge.net/ is easy to use with ctypes http://docs.python.org/py3k/library/ctypes.html. Christoph ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Inplace remove some array rows
hi all, currently I use a = array(m,n) ... a = delete(a, indices, 0) # delete some rows Can I somehow perform the operation in-place, without creating auxiliary array? If I'll use numpy.compress(condition, a, axis=0, out=a), or numpy.take(a, indices, axis=0, out=a) will the operation be inplace? Thank you in advance, D. ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Inplace remove some array rows
On 2011-03-12, at 12:43 PM, Dmitrey wrote: hi all, currently I use a = array(m,n) ... a = delete(a, indices, 0) # delete some rows Can I somehow perform the operation in-place, without creating auxiliary array? If I'll use numpy.compress(condition, a, axis=0, out=a), or numpy.take(a, indices, axis=0, out=a) will the operation be inplace? a will be the wrong shape to hold the output of either of those operations. You could use a[:len(indices)], and that will be in-place, though it looks like numpy makes a temporary copy internally to avoid conflicts when the input array and output array share memory (at least in the case of take()). I was expecting In [15]: a = arange(50).reshape(10, 5) In [16]: numpy.take(a,[2,0,1],axis=0, out=a[:3]) to place 3 copies of original row 2 in rows 0, 1 and 2. The fact that it doesn't seems to suggest NumPy is being more clever (but also more memory-hungry). David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT] any image io module that works with python3?
On 3/12/2011 8:45 AM, Nadav Horesh wrote: I forgot to mention that I work on linux (gentoo x86-64).Here are my achievements till now: 1. PythonMagick: Needs boost which I do not have it avaiable on python3 Boost works on Python 3.1. You might need to compile it. 2. Pygame: I have the stable version(1.9.1) should it work? You need the developer version from svn. 3. FreeImage: I installed FreeImagePy on python3, but it doesn't work yet. FreeImagePy is unmaintained, does not work on Python 3, and has problems on 64 bit platforms. Just wrap the functions you need in ctypes. 4. PIL: I patched setup.py and map.c so python3 setup.py build is working, but: Try replace Hans Häggström with Hans Haggstrom in PIL/WalImageFile.py Christoph nadav@nadav_home /dev/shm/PIL-1.1.7-py3 $ sudo python3.1 setup.py install /usr/lib64/python3.1/distutils/dist.py:259: UserWarning: Unknown distribution option: 'ext_comp_args' warnings.warn(msg) running install running build running build_py running build_ext PIL 1.1.7 SETUP SUMMARY version 1.1.7 platform linux2 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] --- TKINTER support available --- JPEG support available --- ZLIB (PNG/ZIP) support available --- FREETYPE2 support available --- LITTLECMS support available . . . byte-compiling /usr/lib64/python3.1/site-packages/PIL/WalImageFile.py to WalImageFile.pyc Traceback (most recent call last): File setup.py, line 520, inmodule setup(*(), **configuration) # old school :-) File /usr/lib64/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /usr/lib64/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install.py, line 592, in run self.run_command(cmd_name) File /usr/lib64/python3.1/distutils/cmd.py, line 315, in run_command self.distribution.run_command(command) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install_lib.py, line 98, in run self.byte_compile(outfiles) File /usr/lib64/python3.1/distutils/command/install_lib.py, line 135, in byte_compile dry_run=self.dry_run) File /usr/lib64/python3.1/distutils/util.py, line 560, in byte_compile compile(file, cfile, dfile) File /usr/lib64/python3.1/py_compile.py, line 137, in compile codestring = f.read() File /usr/lib64/python3.1/codecs.py, line 300, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf8' codec can't decode byte 0xe4 in position 1909: invalid continuation byte Any idea on how to correct it? Any elegant way to avoid byte compiling? Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. On Windows, PIL (private port at http://www.lfd.uci.edu/~gohlke/pythonlibs/#pil), PythonMagick http://www.imagemagick.org/download/python/, and pygame 1.9.2pre http://www.pygame.org are working reasonably well for image IO. Also the FreeImage libraryhttp://freeimage.sourceforge.net/ is easy to use with ctypeshttp://docs.python.org/py3k/library/ctypes.html. Christoph ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org
Re: [Numpy-discussion] [OT] any image io module that works with python3?
It started to work after processing it with 2to3 and omitting the conversion of file names with the str function (I supply the file names as bytes). Issues: 1. It refuses to save in jpeg format 2. There is a worning of possible segfult on 64 bit machine (which is the target platform). I'll keep on test it. Thank you Nadav. From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how easyly construct my own module) are appreciated. Nadav. On Windows, PIL (private port at http://www.lfd.uci.edu/~gohlke/pythonlibs/#pil), PythonMagick http://www.imagemagick.org/download/python/, and pygame 1.9.2pre http://www.pygame.org are working reasonably well for image IO. Also the FreeImage library http://freeimage.sourceforge.net/ is easy to use with ctypes http://docs.python.org/py3k/library/ctypes.html. Christoph ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT] any image io module that works with python3?
After the replacement of ö with o, the installation went without errors, but: nadav@nadav_home ~ $ python3 Python 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] on linux2 Type help, copyright, credits or license for more information. import _imaging Traceback (most recent call last): File stdin, line 1, in module ImportError: /usr/lib64/python3.1/site-packages/PIL/_imaging.so: undefined symbol: Py_FindMethod Thank you, Nadav. From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Christoph Gohlke [cgoh...@uci.edu] Sent: 12 March 2011 21:49 To: numpy-discussion@scipy.org Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? On 3/12/2011 8:45 AM, Nadav Horesh wrote: I forgot to mention that I work on linux (gentoo x86-64).Here are my achievements till now: 1. PythonMagick: Needs boost which I do not have it avaiable on python3 Boost works on Python 3.1. You might need to compile it. 2. Pygame: I have the stable version(1.9.1) should it work? You need the developer version from svn. 3. FreeImage: I installed FreeImagePy on python3, but it doesn't work yet. FreeImagePy is unmaintained, does not work on Python 3, and has problems on 64 bit platforms. Just wrap the functions you need in ctypes. 4. PIL: I patched setup.py and map.c so python3 setup.py build is working, but: Try replace Hans Häggström with Hans Haggstrom in PIL/WalImageFile.py Christoph nadav@nadav_home /dev/shm/PIL-1.1.7-py3 $ sudo python3.1 setup.py install /usr/lib64/python3.1/distutils/dist.py:259: UserWarning: Unknown distribution option: 'ext_comp_args' warnings.warn(msg) running install running build running build_py running build_ext PIL 1.1.7 SETUP SUMMARY version 1.1.7 platform linux2 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] --- TKINTER support available --- JPEG support available --- ZLIB (PNG/ZIP) support available --- FREETYPE2 support available --- LITTLECMS support available . . . byte-compiling /usr/lib64/python3.1/site-packages/PIL/WalImageFile.py to WalImageFile.pyc Traceback (most recent call last): File setup.py, line 520, inmodule setup(*(), **configuration) # old school :-) File /usr/lib64/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /usr/lib64/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install.py, line 592, in run self.run_command(cmd_name) File /usr/lib64/python3.1/distutils/cmd.py, line 315, in run_command self.distribution.run_command(command) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install_lib.py, line 98, in run self.byte_compile(outfiles) File /usr/lib64/python3.1/distutils/command/install_lib.py, line 135, in byte_compile dry_run=self.dry_run) File /usr/lib64/python3.1/distutils/util.py, line 560, in byte_compile compile(file, cfile, dfile) File /usr/lib64/python3.1/py_compile.py, line 137, in compile codestring = f.read() File /usr/lib64/python3.1/codecs.py, line 300, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf8' codec can't decode byte 0xe4 in position 1909: invalid continuation byte Any idea on how to correct it? Any elegant way to avoid byte compiling? Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh wrote: Having numpy, scipy, and matplotlib working reasonably with python3, a major piece of code I miss for a major python3 migration is an image IO. I found that pylab's imread works fine for png image, but I need to read all the other image format as well as png and jpeg output. Any hints (including advices how
[Numpy-discussion] import error after compiling from HEAD
Sup y'all, I just installed numpy from github, but when I tried to import it I got some odd errors! What's going on, and how can it be fixed? josh@pidgey:~$ python -c 'import numpy; numpy.test()' Traceback (most recent call last): File string, line 1, in module File /usr/local/lib/python2.6/dist-packages/numpy/__init__.py, line 137, in module File /usr/local/lib/python2.6/dist-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/local/lib/python2.6/dist-packages/numpy/lib/__init__.py, line 4, in module # File /usr/local/lib/python2.6/dist-packages/numpy/lib/type_check.py, line 8, in module File /usr/local/lib/python2.6/dist-packages/numpy/core/__init__.py, line 10, in module # ImportError: No module named _sort Thanks, --Josh ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT] any image io module that works with python3?
On 3/12/2011 12:47 PM, Nadav Horesh wrote: After the replacement of ö with o, the installation went without errors, but: nadav@nadav_home ~ $ python3 Python 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] on linux2 Type help, copyright, credits or license for more information. import _imaging Traceback (most recent call last): File stdin, line 1, inmodule ImportError: /usr/lib64/python3.1/site-packages/PIL/_imaging.so: undefined symbol: Py_FindMethod Py_FindMethod should be excluded by `#ifndef PY3` or similar preprocessor statements. There is a typo in map.c line 65: change `#ifdef PY3` to `#ifndef PY3` and clean your build directory before rebuilding. Christoph Thank you, Nadav. From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Christoph Gohlke [cgoh...@uci.edu] Sent: 12 March 2011 21:49 To: numpy-discussion@scipy.org Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? On 3/12/2011 8:45 AM, Nadav Horesh wrote: I forgot to mention that I work on linux (gentoo x86-64).Here are my achievements till now: 1. PythonMagick: Needs boost which I do not have it avaiable on python3 Boost works on Python 3.1. You might need to compile it. 2. Pygame: I have the stable version(1.9.1) should it work? You need the developer version from svn. 3. FreeImage: I installed FreeImagePy on python3, but it doesn't work yet. FreeImagePy is unmaintained, does not work on Python 3, and has problems on 64 bit platforms. Just wrap the functions you need in ctypes. 4. PIL: I patched setup.py and map.c so python3 setup.py build is working, but: Try replace Hans Häggström with Hans Haggstrom in PIL/WalImageFile.py Christoph nadav@nadav_home /dev/shm/PIL-1.1.7-py3 $ sudo python3.1 setup.py install /usr/lib64/python3.1/distutils/dist.py:259: UserWarning: Unknown distribution option: 'ext_comp_args' warnings.warn(msg) running install running build running build_py running build_ext PIL 1.1.7 SETUP SUMMARY version 1.1.7 platform linux2 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] --- TKINTER support available --- JPEG support available --- ZLIB (PNG/ZIP) support available --- FREETYPE2 support available --- LITTLECMS support available . . . byte-compiling /usr/lib64/python3.1/site-packages/PIL/WalImageFile.py to WalImageFile.pyc Traceback (most recent call last): File setup.py, line 520, inmodule setup(*(), **configuration) # old school :-) File /usr/lib64/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /usr/lib64/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install.py, line 592, in run self.run_command(cmd_name) File /usr/lib64/python3.1/distutils/cmd.py, line 315, in run_command self.distribution.run_command(command) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install_lib.py, line 98, in run self.byte_compile(outfiles) File /usr/lib64/python3.1/distutils/command/install_lib.py, line 135, in byte_compile dry_run=self.dry_run) File /usr/lib64/python3.1/distutils/util.py, line 560, in byte_compile compile(file, cfile, dfile) File /usr/lib64/python3.1/py_compile.py, line 137, in compile codestring = f.read() File /usr/lib64/python3.1/codecs.py, line 300, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf8' codec can't decode byte 0xe4 in position 1909: invalid continuation byte Any idea on how to correct it? Any elegant way to avoid byte compiling? Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? Here's a ctypes interface to FreeImage that I wrote a while back and was since cleaned up (and maintained) by the scikits.image folk: https://github.com/stefanv/scikits.image/blob/master/scikits/image/io/_plugins/freeimage_plugin.py If it doesn't work out of the box on python 3, then it should be pretty simple to fix. Zach On Mar 12, 2011, at 4:40 AM, Christoph Gohlke wrote: On 3/12/2011 1:08 AM, Nadav Horesh
[Numpy-discussion] Not importing polynomial implementation functions by default
Hi All, I'd like to change the polynomial package to only import the Classes, leaving the large number of implementation functions to be imported directly from the different modules if needed. I always regarded those functions as implementation helpers and kept them separate from the class so that others could use them to build their own classes if they desired. For most purposes I think the classes are more useful. So I think it was a mistake to import the functions by; default and I'm looking for a graceful and acceptable way out. Any suggestions. Chuck ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Call for GSoC 2011 NumPy mentors
Hi, It is time to start preparing for the 2011 Google Summer of Code (SoC). As in the past, we will participate in SoC with the Python Software Foundation (PSF) as our mentoring organization. The PSF has requested that every project, which wishes to participate in the SoC, provide a list of at least *three* potential mentors. If you are interested and willing to potentially mentor someone this summer to work on NumPy, please send me the following information by Monday evening: Name, Email, Phone, and Link_ID. You can find additional information on the 2011 SoC homepage: http://socghop.appspot.com/ Here is the PSF SoC page: http://wiki.python.org/moin/SummerOfCode Please start thinking about potential projects and add them to the SoC ideas page: http://projects.scipy.org/scipy/wiki/SummerofCodeIdeas Thanks, Jarrod ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Not importing polynomial implementation functions by default
On 2011-03-12, at 9:32 PM, Charles R Harris wrote:
I'd like to change the polynomial package to only import the Classes, leaving
the large number of implementation functions to be imported directly from the
different modules if needed. I always regarded those functions as
implementation helpers and kept them separate from the class so that others
could use them to build their own classes if they desired. For most purposes
I think the classes are more useful. So I think it was a mistake to import
the functions by; default and I'm looking for a graceful and acceptable way
out. Any suggestions.
I hope this wouldn't include polyfit, polyval, roots and vander at least (I'd
also be -1 on removing poly{add,sub,mul,div,der,int}, but more weakly so).
Those 4 seem useful and basic enough to leave in the default namespace.
David
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Re: [Numpy-discussion] [OT] any image io module that works with python3?
This lead to another error probably due to line 68 in map.h. As much as I could trace it, ob_type is a member of PyObject, not of PyTypeObject. I have no clue how to resolve this. Nadav. From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Christoph Gohlke [cgoh...@uci.edu] Sent: 13 March 2011 00:37 To: numpy-discussion@scipy.org Subject: Re: [Numpy-discussion] [OT] any image io module thatworks withpython3? On 3/12/2011 12:47 PM, Nadav Horesh wrote: After the replacement of ö with o, the installation went without errors, but: nadav@nadav_home ~ $ python3 Python 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] on linux2 Type help, copyright, credits or license for more information. import _imaging Traceback (most recent call last): File stdin, line 1, inmodule ImportError: /usr/lib64/python3.1/site-packages/PIL/_imaging.so: undefined symbol: Py_FindMethod Py_FindMethod should be excluded by `#ifndef PY3` or similar preprocessor statements. There is a typo in map.c line 65: change `#ifdef PY3` to `#ifndef PY3` and clean your build directory before rebuilding. Christoph Thank you, Nadav. From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Christoph Gohlke [cgoh...@uci.edu] Sent: 12 March 2011 21:49 To: numpy-discussion@scipy.org Subject: Re: [Numpy-discussion] [OT] any image io module that works with python3? On 3/12/2011 8:45 AM, Nadav Horesh wrote: I forgot to mention that I work on linux (gentoo x86-64).Here are my achievements till now: 1. PythonMagick: Needs boost which I do not have it avaiable on python3 Boost works on Python 3.1. You might need to compile it. 2. Pygame: I have the stable version(1.9.1) should it work? You need the developer version from svn. 3. FreeImage: I installed FreeImagePy on python3, but it doesn't work yet. FreeImagePy is unmaintained, does not work on Python 3, and has problems on 64 bit platforms. Just wrap the functions you need in ctypes. 4. PIL: I patched setup.py and map.c so python3 setup.py build is working, but: Try replace Hans Häggström with Hans Haggstrom in PIL/WalImageFile.py Christoph nadav@nadav_home /dev/shm/PIL-1.1.7-py3 $ sudo python3.1 setup.py install /usr/lib64/python3.1/distutils/dist.py:259: UserWarning: Unknown distribution option: 'ext_comp_args' warnings.warn(msg) running install running build running build_py running build_ext PIL 1.1.7 SETUP SUMMARY version 1.1.7 platform linux2 3.1.3 (r313:86834, Feb 25 2011, 11:08:33) [GCC 4.4.4] --- TKINTER support available --- JPEG support available --- ZLIB (PNG/ZIP) support available --- FREETYPE2 support available --- LITTLECMS support available . . . byte-compiling /usr/lib64/python3.1/site-packages/PIL/WalImageFile.py to WalImageFile.pyc Traceback (most recent call last): File setup.py, line 520, inmodule setup(*(), **configuration) # old school :-) File /usr/lib64/python3.1/distutils/core.py, line 149, in setup dist.run_commands() File /usr/lib64/python3.1/distutils/dist.py, line 919, in run_commands self.run_command(cmd) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install.py, line 592, in run self.run_command(cmd_name) File /usr/lib64/python3.1/distutils/cmd.py, line 315, in run_command self.distribution.run_command(command) File /usr/lib64/python3.1/distutils/dist.py, line 938, in run_command cmd_obj.run() File /usr/lib64/python3.1/distutils/command/install_lib.py, line 98, in run self.byte_compile(outfiles) File /usr/lib64/python3.1/distutils/command/install_lib.py, line 135, in byte_compile dry_run=self.dry_run) File /usr/lib64/python3.1/distutils/util.py, line 560, in byte_compile compile(file, cfile, dfile) File /usr/lib64/python3.1/py_compile.py, line 137, in compile codestring = f.read() File /usr/lib64/python3.1/codecs.py, line 300, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf8' codec can't decode byte 0xe4 in position 1909: invalid continuation byte Any idea on how to correct it? Any elegant way to avoid byte compiling? Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of Zachary Pincus [zachary.pin...@yale.edu] Sent: 12 March 2011 14:35 To: Discussion of Numerical Python Subject:
