Re: [Numpy-discussion] [ANN] Python for Scientific Computing conference in Boulder, CO; April'15
Le 28 oct. 2014 à 19:09, Fernando Perez fperez@gmail.com a écrit : a colleague from NCAR in Boulder just sent me this link about a conference they are organizing in the spring: Wrong year on the web page: April 13 - 17, 2014 Cheers, JB ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] EuroSciPy 2014 Call for Abstracts
Hi Ralf, EuroSciPy 2014, the Seventh Annual Conference on Python in Science, takes place in Cambridge, UK on 27 - 30 August 2013. The conference features two days of tutorials followed by two days of scientific talks. The day after the main conference, developer sprints will be organized on projects of interest to attendees. The topics presented at EuroSciPy are very diverse, with a focus on advanced software engineering and original uses of Python and its scientific libraries, either in theoretical or experimental research, from both academia and the industry. The program includes keynotes, contributed talks and posters. Submissions for talks and posters are welcome on our website (http://www.euroscipy.org/2014/). In your abstract, please provide details on what Python tools are being employed, and how. The deadline for submission is 14 April 2013. Some dates refer to 2013… Cheers, JB ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] EuroSciPy 2014 Call for Abstracts
Le 5 mars 2014 à 20:43, Ralf Gommers ralf.gomm...@gmail.com a écrit : Hmm, that's why one shouldn't send emails like these at the end of a long day. Dates are correct except for 2013--2014. « It's only those who do nothing that make no mistakes, I suppose. » Joseph Conrad (An Outcast of the Islands, 1896, pt. 3, chap. 2)___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Simple way to launch python processes?
You should consider the powerful multiprocessing package. Have a look on this
piece of code:
import glob
import os
import multiprocessing as multi
import subprocess as sub
import time
NPROC = 4
Python = '/Library/Frameworks/EPD64.framework/Versions/Current/bin/python'
Xterm = '/usr/X11/bin/xterm '
coord = []
Size = '100x10'
XPos = 810
YPos = 170
XOffset = 0
YOffset = 0
for i in range(NPROC):
if i % 2 == 0:
coord.append(Size + '+' + str(YPos) + '+' + str(YOffset))
else:
coord.append(Size + '+' + str(XPos) + '+' + str(YOffset))
YOffset = YOffset + YPos
def CompareColourRef(Champ):
BaseChamp = os.path.basename(Champ)
NameProc = int(multi.current_process().name[-1]) - 1
print 'Processing', BaseChamp, 'on processor', NameProc+1
os.putenv('ADAM_USER', DirWrk + 'adam_' + str(NameProc+1))
Command = Xterm + '-geometry ' + '' + coord[NameProc] + ' -T Proc' +
str(NameProc+1) + ' ' + BaseChamp + ' ' + ' -e ' + Python + ' ' + DirSrc + \
'CompareColourRef.py ' + BaseChamp + ' 21 | tee ' + DirLog +
BaseChamp + '.log'
Process = sub.Popen([Command], shell=True)
Process.wait()
print BaseChamp, 'processed on processor', NameProc+1
return
pool = multi.Pool(processes=NPROC)
Champs = glob.glob(DirImg + '*/*')
results = pool.map_async(CompareColourRef, Champs)
pool.close()
while results._number_left 0:
print Waiting for, results._number_left, 'tasks to complete'
time.sleep(15)
pool.join()
print 'Process completed'
exit(0)
Cheers
Jean-Baptiste
Le 7 déc. 2011 à 15:43, Olivier Delalleau a écrit :
Maybe try stackoverflow, since this isn't really a numpy question.
To run a command like python myscript.py arg1 arg2 in a separate process,
you can do:
p = subprocess.Popen(python myscript.py arg1 arg2.split())
You can launch many of these, and if you want to know if a process p is over,
you can call p.poll().
I'm sure there are other (and better) options though.
-=- Olivier
2011/12/7 Lou Pecora lou_boog2...@yahoo.com
I would like to launch python modules or functions (I don't know which is
easier to do, modules or functions) in separate Terminal windows so I can see
the output from each as they execute. I need to be able to pass each module
or function a set of parameters. I would like to do this from a python
script already running in a Terminal window. In other words, I'd start up a
master script and it would launch, say, three processes using another
module or a function with different parameter values for each launch and each
would run independently in its own Terminal window so stdout from each
process would go to it's own respective window. When the process terminated
the window would remain open.
I've begun to look at subprocess modules, etc., but that's pretty confusing.
I can do what I say above manually, but it's gotten clumsy as I want to run
eventually in 12 cores.
I have a Mac Pro running Mac OS X 10.6.
If there is a better forum to ask this question, please let me know.
Thanks for any advice.
-- Lou Pecora, my views are my own.
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Re: [Numpy-discussion] ANN: SciPy 0.10.0 released
Le 13 nov. 2011 à 20:19, Ralf Gommers a écrit : I am pleased to announce the availability of SciPy 0.10.0. Hi all, Thanks for this great job. I've run nosetests on my Mac (64-bit 10.7.2 build on EPD) which fails on the following test: test_definition (test_basic.TestDoubleIFFT) ... FAIL test_definition_real (test_basic.TestDoubleIFFT) ... ok test_djbfft (test_basic.TestDoubleIFFT) ... python(60968) malloc: *** error for object 0x105435b58: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6 Thanks for any hint, Cheers Jean-Baptiste___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] what to use in buildbot config for numpy testing
There is much more simple: the command nosetests numpy
Of course, nosetests needs to be installed...
Cheers
JB
Le 7 sept. 2011 à 23:44, Chris Kees a écrit :
Hi Derek,
Thanks! I forgot that python would exit with 0 even if numpy.test()
fails. That could have taken a while to realize.
Chris
On Wed, Sep 7, 2011 at 4:22 PM, Derek Homeier
de...@astro.physik.uni-goettingen.de wrote:
On 07.09.2011, at 10:52PM, Chris Kees wrote:
Is there a recommended way to run the numpy test suite as a buildbot
test? Just run ad python -c import numpy; numpy.test as ShellCommand
object?
It would be numpy.test() [or numpy.test('full')]; then it depends on what
you need
as the return value of your test. I am using for package verification
python -c 'import numpy, sys; ret=numpy.test(full);
sys.exit(2*len(ret.errors+ret.failures))'
so python will return with a value != 0 in case of an unsuccessful test
(which it
otherwise would not do). But this is just within a simple shell script.
Cheers,
Derek
--
Derek Homeier Centre de Recherche Astrophysique de Lyon
ENS Lyon 46, Allée d'Italie
69364 Lyon Cedex 07, France +33 1133 47272-8894
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Re: [Numpy-discussion] A question about dtype syntax
Hi Warren Pierre, Notice that your array is actually a 2D structured array with shape (n, 1). Try reshaping it to (n,) or apply np.squeeze before calling savetxt. Thanks to both of you, I made huge progress to understand how numpy arrays work. I use PyDev under Eclipse, and the debugger showed me that the vstack function generated a 2D array. So I used append instead, and my script now works! Cheers JB___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] A question about dtype syntax
Hi Pierre,
Thanks for the guess. Unfortunately, I got the same error:
[('bs3000k.cat', 280.60341, -7.09118, 9480, 0.2057, 0.14)]
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 40, in module
StatsAll = np.array(np.asarray(Stats), dtype=('a15, f8, f8, i4, f8, f8'))
ValueError: could not convert string to float: bs3000k.cat
The code is
Stats = [(CatBase, round(stats.mean(Data.Ra), 5), round(stats.mean(Data.Dec),
5), len(Sep), round(stats.mean(Sep),4), round(stats.stdev(Sep),4),)]
print Stats
if First:
StatsAll = np.array(np.asarray(Stats), dtype=('a15, f8, f8, i4, f8, f8'))
First = False
else:
StatsAll = np.vstack((StatsAll, np.asarray(Stats)))
print len(StatsAll)
I tried various syntaxes, without success.
Cheers
JB
On Aug 30, 2011, at 10:46 AM, Marquette Jean-Baptiste wrote:
Hi all,
I have this piece of code:
Stats = [CatBase, round(stats.mean(Data.Ra), 5), round(stats.mean(Data.Dec),
5), len(Sep), round(stats.mean(Sep),4), round(stats.stdev(Sep),4)]
print Stats
if First:
StatsAll = np.array(np.asarray(Stats), dtype=('a11, f8, f8, i4, f8,
f8'))
First = False
else:
StatsAll = np.vstack((StatsAll, np.asarray(Stats)))
print len(StatsAll)
This yields the error:
['bs3000k.cat', 280.60341, -7.09118, 9480, 0.2057, 0.14]
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 40, in
module
StatsAll = np.array(np.asarray(Stats), dtype=('a11, f8, f8, i4, f8, f8'))
ValueError: could not convert string to float: bs3000k.cat
What's wrong ?
My guess:
Stats is a list of 5 elements, but you want a list of 1 5-element tuple to
match the type.
Stats = [(CatBase, round(stats.mean(Data.Ra), 5),
round(stats.mean(Data.Dec), 5), len(Sep), round(stats.mean(Sep),4),
round(stats.stdev(Sep),4),)]
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Re: [Numpy-discussion] A question about dtype syntax
Hi Pierre,
Bingo ! That works. I finally coded like:
Stats = [(CatBase, round(stats.mean(Data.Ra), 5),
round(stats.mean(Data.Dec), 5), len(Sep), round(stats.mean(Sep),4),
round(stats.stdev(Sep),4),)]
StatArray = np.array(Stats, dtype=([('Catalog', 'a15'), ('RaMean',
'f8'), ('DecMean', 'f8'), ('NStars', 'i4'), ('RMS', 'f8'), ('StdDev', 'f8')]))
print StatArray
if First:
StatsAll = StatArray
First = False
else:
StatsAll = np.vstack((StatsAll, StatArray))
My next problem deals with the writing of data to a file. I use the command:
np.savetxt(Table, StatsAll, delimiter=' ', fmt=['%15s %.5f %.5f %5d %.4f %.4f'])
which yields:
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 44, in module
np.savetxt(Table, StatsAll, delimiter=' ', fmt=['%15s %.5f %.5f %5d %.4f
%.4f'])
File
/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/lib/npyio.py,
line 979, in savetxt
fh.write(asbytes(format % tuple(row) + newline))
TypeError: not enough arguments for format string
I struggled with various unsuccessful fmt syntaxes, and the numpy doc is very
discrete about that topic:
fmt : string or sequence of strings
A single format (%10.5f), a sequence of formats
But I don't find this valid sequence nor an example...
Cheers
JB
On Aug 31, 2011, at 12:20 PM, Jean-Baptiste Marquette wrote:
Hi Pierre,
Thanks for the guess. Unfortunately, I got the same error:
[('bs3000k.cat', 280.60341, -7.09118, 9480, 0.2057, 0.14)]
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 40, in
module
StatsAll = np.array(np.asarray(Stats), dtype=('a15, f8, f8, i4, f8, f8'))
ValueError: could not convert string to float: bs3000k.cat
Of course, silly me
Your line 40 is actually
StatsAll = np.array(np.asarray(Stats), dtype=('a15, f8, f8, i4, f8, f8'))
With np.asarray(Stats), you're trying to load Stats as an array using a dtype
of float by default. Of course, np.asarray is choking on the first element.
So, try to use instead
StatsAll = np.array(Stats, dtype=('a15, f8, f8, i4, f8, f8'))
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Re: [Numpy-discussion] A question about dtype syntax
Hi Pierre,
On Aug 31, 2011, at 3:40 PM, Jean-Baptiste Marquette wrote:
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 44, in
module
np.savetxt(Table, StatsAll, delimiter=' ', fmt=['%15s %.5f %.5f %5d %.4f
%.4f'])
File
/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/lib/npyio.py,
line 979, in savetxt
fh.write(asbytes(format % tuple(row) + newline))
TypeError: not enough arguments for format string
Without knowing StatsAll, it ain't easy… From the exception message, we could
expect that one of rows is empty or as less than the 6 elements required by
your format string.
If you're using IPython, switch to debugger mode (pdb), then inspect row and
format to find out the content of the offending line.
Here is a (short) sample of StatsAll:
[[('bs3000k.cat', 280.60341, -7.09118, 9480, 0.2057, 0.14)]
[('bs3000l.cat', 280.61389, -7.24097, 11490, 0.1923, 0.0747)]
[('bs3000m.cat', 280.77074, -7.08237, 13989, 0.2289, 0.1009)]
[('bs3000n.cat', 280.77228, -7.23563, 15811, 0.1767, 0.1327)]
[('bs3001k.cat', 280.95383, -7.10004, 7402, 0.2539, 0.0777)]
[('bs3001l.cat', 280.95495, -7.23409, 13840, 0.1463, 0.1008)]
[('bs3001m.cat', 281.1172, -7.08094, 9608, 0.2311, 0.1458)]
[('bs3001n.cat', 281.12447, -7.23398, 14030, 0.2538, 0.1022)]
[('bs3002k.cat', 280.62533, -7.47818, 593, 0.0291, 0.0237)]
[('bs3002l.cat', 280.61508, -7.60359, 9122, 0.0518, 0.0205)]
[('bs3002m.cat', 280.77209, -7.46262, 1510, 0.0415, 0.0302)]
[('bs3002n.cat', 280.77578, -7.60117, 14177, 0.0807, 0.0327)]
[('bs3003k.cat', 280.96463, -7.42967, 13506, 0.0305, 0.0225)]
[('bs3003l.cat', 280.95638, -7.58462, 17903, 0.0458, 0.0298)]
[('bs3003m.cat', 281.12729, -7.42516, 15676, 0.0879, 0.0446)]
[('bs3003n.cat', 281.1354, -7.58497, 16015, 0.0685, 0.0376)]
[('bs3004k.cat', 280.61148, -7.78976, 14794, 0.079, 0.0473)]
[('bs3004l.cat', 280.61791, -7.94186, 15455, 0.0818, 0.0727)]
[('bs3004m.cat', 280.78388, -7.78834, 14986, 0.0966, 0.0313)]
[('bs3004n.cat', 280.78261, -7.93932, 18713, 0.0925, 0.0472)]
[('bs3005k.cat', 280.9659, -7.78816, 14906, 0.0456, 0.022)]
[('bs3005l.cat', 280.96811, -7.93894, 19744, 0.021, 0.0218)]
[('bs3005m.cat', 281.1344, -7.78035, 15943, 0.0687, 0.0203)]
[('bs3005n.cat', 281.13915, -7.93027, 18183, 0.1173, 0.0695)]
[('bs3006k.cat', 280.61294, -8.14201, 13309, 0.143, 0.065)]
[('bs3006l.cat', 280.65109, -8.29416, 405, 0.258, 0.1147)]
[('bs3006m.cat', 280.78767, -8.13916, 14527, 0.1106, 0.0568)]
[('bs3006n.cat', 280.80935, -8.28823, 818, 0.2382, 0.0764)]
[('bs3007k.cat', 280.96614, -8.1401, 13251, 0.0946, 0.0415)]
[('bs3007l.cat', 280.97158, -8.23797, 5807, 0.1758, 0.0636)]
[('bs3007m.cat', 281.14129, -8.13799, 13886, 0.1524, 0.0517)]
[('bs3007n.cat', 281.15309, -8.2476, 214, 0.1584, 0.0648)]]
I struggled with various unsuccessful fmt syntaxes, and the numpy doc is
very discrete about that topic:
fmt : string or sequence of strings
A single format (%10.5f), a sequence of formats
Looks clear enough to me… But yes, a comment in the code shows that`fmt`
can be a string with multiple insertion points or a list of formats. E.g.
'%10.5f\t%10d' or ('%10.5f', '$10d') (so we should probably update the doc
to this regard)
The command with parentheses:
np.savetxt(Table, StatsAll, delimiter=' ', fmt=('%15s %.5f %.5f %5d
%.4f %.4f'))
fails as well, but with a different error:
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 44, in module
np.savetxt(Table, StatsAll, delimiter=' ', fmt=('%15s %.5f %.5f %5d %.4f
%.4f'))
File
/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/lib/npyio.py,
line 974, in savetxt
% fmt)
AttributeError: fmt has wrong number of % formats. %15s %.5f %.5f %5d %.4f %.4f
Plus, this one:
np.savetxt(Table, StatsAll, delimiter=' ', fmt=('%15s', '%.5f', '%.5f',
'%5d', '%.4f', '%.4f'))
yields:
Traceback (most recent call last):
File /Users/marquett/workspace/Distort/src/StatsSep.py, line 44, in module
np.savetxt(Table, StatsAll, delimiter=' ', fmt=('%15s', '%.5f', '%.5f',
'%5d', '%.4f', '%.4f'))
File
/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/lib/npyio.py,
line 966, in savetxt
raise AttributeError('fmt has wrong shape. %s' % str(fmt))
AttributeError: fmt has wrong shape. ('%15s', '%.5f', '%.5f', '%5d', '%.4f',
'%.4f')
Quite puzzling...
Should I switch to the I/O of asciitable package ?
Anyway, thanks again for your help.
JB
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